Unnamed: 0
int64 0
10k
| repository_name
stringlengths 7
54
| func_path_in_repository
stringlengths 5
223
| func_name
stringlengths 1
134
| whole_func_string
stringlengths 100
30.3k
| language
stringclasses 1
value | func_code_string
stringlengths 100
30.3k
| func_code_tokens
stringlengths 138
33.2k
| func_documentation_string
stringlengths 1
15k
| func_documentation_tokens
stringlengths 5
5.14k
| split_name
stringclasses 1
value | func_code_url
stringlengths 91
315
|
|---|---|---|---|---|---|---|---|---|---|---|---|
1,300 | hectane/python-hectane | pyhectane/connection.py | Connection.send | def send(self, from_, to, subject, text='', html='', cc=[], bcc=[],
headers={}, attachments=[]):
"""
Send an email.
"""
if isinstance(to, string_types):
raise TypeError('"to" parameter must be enumerable')
if text == '' and html == '':
raise ValueError('"text" and "html" must not both be empty')
return self._session.post('{}/send'.format(self._url), json={
'from': from_,
'to': to,
'cc': cc,
'bcc': bcc,
'subject': subject,
'headers': headers,
'text': text,
'html': html,
'attachments': list(self._process_attachments(attachments)),
}).json() | python | def send(self, from_, to, subject, text='', html='', cc=[], bcc=[],
headers={}, attachments=[]):
"""
Send an email.
"""
if isinstance(to, string_types):
raise TypeError('"to" parameter must be enumerable')
if text == '' and html == '':
raise ValueError('"text" and "html" must not both be empty')
return self._session.post('{}/send'.format(self._url), json={
'from': from_,
'to': to,
'cc': cc,
'bcc': bcc,
'subject': subject,
'headers': headers,
'text': text,
'html': html,
'attachments': list(self._process_attachments(attachments)),
}).json() | ['def', 'send', '(', 'self', ',', 'from_', ',', 'to', ',', 'subject', ',', 'text', '=', "''", ',', 'html', '=', "''", ',', 'cc', '=', '[', ']', ',', 'bcc', '=', '[', ']', ',', 'headers', '=', '{', '}', ',', 'attachments', '=', '[', ']', ')', ':', 'if', 'isinstance', '(', 'to', ',', 'string_types', ')', ':', 'raise', 'TypeError', '(', '\'"to" parameter must be enumerable\'', ')', 'if', 'text', '==', "''", 'and', 'html', '==', "''", ':', 'raise', 'ValueError', '(', '\'"text" and "html" must not both be empty\'', ')', 'return', 'self', '.', '_session', '.', 'post', '(', "'{}/send'", '.', 'format', '(', 'self', '.', '_url', ')', ',', 'json', '=', '{', "'from'", ':', 'from_', ',', "'to'", ':', 'to', ',', "'cc'", ':', 'cc', ',', "'bcc'", ':', 'bcc', ',', "'subject'", ':', 'subject', ',', "'headers'", ':', 'headers', ',', "'text'", ':', 'text', ',', "'html'", ':', 'html', ',', "'attachments'", ':', 'list', '(', 'self', '.', '_process_attachments', '(', 'attachments', ')', ')', ',', '}', ')', '.', 'json', '(', ')'] | Send an email. | ['Send', 'an', 'email', '.'] | train | https://github.com/hectane/python-hectane/blob/e0fe1df576f776566e813f71782f8adf60146383/pyhectane/connection.py#L64-L83 |
1,301 | raphaelvallat/pingouin | pingouin/plotting.py | plot_paired | def plot_paired(data=None, dv=None, within=None, subject=None, order=None,
boxplot=True, figsize=(4, 4), dpi=100, ax=None,
colors=['green', 'grey', 'indianred'],
pointplot_kwargs={'scale': .6, 'markers': '.'},
boxplot_kwargs={'color': 'lightslategrey', 'width': .2}):
"""
Paired plot.
Parameters
----------
data : pandas DataFrame
Long-format dataFrame.
dv : string
Name of column containing the dependant variable.
within : string
Name of column containing the within-subject factor. Note that
``within`` must have exactly two within-subject levels
(= two unique values).
subject : string
Name of column containing the subject identifier.
order : list of str
List of values in ``within`` that define the order of elements on the
x-axis of the plot. If None, uses alphabetical order.
boxplot : boolean
If True, add a boxplot to the paired lines using the
:py:func:`seaborn.boxplot` function.
figsize : tuple
Figsize in inches
dpi : int
Resolution of the figure in dots per inches.
ax : matplotlib axes
Axis on which to draw the plot.
colors : list of str
Line colors names. Default is green when value increases from A to B,
indianred when value decreases from A to B and grey when the value is
the same in both measurements.
pointplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.pointplot` function.
boxplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.boxplot` function.
Returns
-------
ax : Matplotlib Axes instance
Returns the Axes object with the plot for further tweaking.
Notes
-----
Data must be a long-format pandas DataFrame.
Examples
--------
Default paired plot:
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova')
>>> df = df.query("Group == 'Meditation' and Subject > 40")
>>> df = df.query("Time == 'August' or Time == 'June'")
>>> import pingouin as pg
>>> ax = pg.plot_paired(data=df, dv='Scores', within='Time',
... subject='Subject', dpi=150)
Paired plot on an existing axis (no boxplot and uniform color):
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova').query("Time != 'January'")
>>> import pingouin as pg
>>> import matplotlib.pyplot as plt
>>> fig, ax1 = plt.subplots(1, 1, figsize=(5, 4))
>>> pg.plot_paired(data=df[df['Group'] == 'Meditation'],
... dv='Scores', within='Time', subject='Subject',
... ax=ax1, boxplot=False,
... colors=['grey', 'grey', 'grey']) # doctest: +SKIP
"""
from pingouin.utils import _check_dataframe, remove_rm_na
# Validate args
_check_dataframe(data=data, dv=dv, within=within, subject=subject,
effects='within')
# Remove NaN values
data = remove_rm_na(dv=dv, within=within, subject=subject, data=data)
# Extract subjects
subj = data[subject].unique()
# Extract within-subject level (alphabetical order)
x_cat = np.unique(data[within])
assert len(x_cat) == 2, 'Within must have exactly two unique levels.'
if order is None:
order = x_cat
else:
assert len(order) == 2, 'Order must have exactly two elements.'
# Start the plot
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=figsize, dpi=dpi)
for idx, s in enumerate(subj):
tmp = data.loc[data[subject] == s, [dv, within, subject]]
x_val = tmp[tmp[within] == order[0]][dv].values[0]
y_val = tmp[tmp[within] == order[1]][dv].values[0]
if x_val < y_val:
color = colors[0]
elif x_val > y_val:
color = colors[2]
elif x_val == y_val:
color = colors[1]
# Plot individual lines using Seaborn
sns.pointplot(data=tmp, x=within, y=dv, order=order, color=color,
ax=ax, **pointplot_kwargs)
if boxplot:
sns.boxplot(data=data, x=within, y=dv, order=order, ax=ax,
**boxplot_kwargs)
# Despine and trim
sns.despine(trim=True, ax=ax)
return ax | python | def plot_paired(data=None, dv=None, within=None, subject=None, order=None,
boxplot=True, figsize=(4, 4), dpi=100, ax=None,
colors=['green', 'grey', 'indianred'],
pointplot_kwargs={'scale': .6, 'markers': '.'},
boxplot_kwargs={'color': 'lightslategrey', 'width': .2}):
"""
Paired plot.
Parameters
----------
data : pandas DataFrame
Long-format dataFrame.
dv : string
Name of column containing the dependant variable.
within : string
Name of column containing the within-subject factor. Note that
``within`` must have exactly two within-subject levels
(= two unique values).
subject : string
Name of column containing the subject identifier.
order : list of str
List of values in ``within`` that define the order of elements on the
x-axis of the plot. If None, uses alphabetical order.
boxplot : boolean
If True, add a boxplot to the paired lines using the
:py:func:`seaborn.boxplot` function.
figsize : tuple
Figsize in inches
dpi : int
Resolution of the figure in dots per inches.
ax : matplotlib axes
Axis on which to draw the plot.
colors : list of str
Line colors names. Default is green when value increases from A to B,
indianred when value decreases from A to B and grey when the value is
the same in both measurements.
pointplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.pointplot` function.
boxplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.boxplot` function.
Returns
-------
ax : Matplotlib Axes instance
Returns the Axes object with the plot for further tweaking.
Notes
-----
Data must be a long-format pandas DataFrame.
Examples
--------
Default paired plot:
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova')
>>> df = df.query("Group == 'Meditation' and Subject > 40")
>>> df = df.query("Time == 'August' or Time == 'June'")
>>> import pingouin as pg
>>> ax = pg.plot_paired(data=df, dv='Scores', within='Time',
... subject='Subject', dpi=150)
Paired plot on an existing axis (no boxplot and uniform color):
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova').query("Time != 'January'")
>>> import pingouin as pg
>>> import matplotlib.pyplot as plt
>>> fig, ax1 = plt.subplots(1, 1, figsize=(5, 4))
>>> pg.plot_paired(data=df[df['Group'] == 'Meditation'],
... dv='Scores', within='Time', subject='Subject',
... ax=ax1, boxplot=False,
... colors=['grey', 'grey', 'grey']) # doctest: +SKIP
"""
from pingouin.utils import _check_dataframe, remove_rm_na
# Validate args
_check_dataframe(data=data, dv=dv, within=within, subject=subject,
effects='within')
# Remove NaN values
data = remove_rm_na(dv=dv, within=within, subject=subject, data=data)
# Extract subjects
subj = data[subject].unique()
# Extract within-subject level (alphabetical order)
x_cat = np.unique(data[within])
assert len(x_cat) == 2, 'Within must have exactly two unique levels.'
if order is None:
order = x_cat
else:
assert len(order) == 2, 'Order must have exactly two elements.'
# Start the plot
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=figsize, dpi=dpi)
for idx, s in enumerate(subj):
tmp = data.loc[data[subject] == s, [dv, within, subject]]
x_val = tmp[tmp[within] == order[0]][dv].values[0]
y_val = tmp[tmp[within] == order[1]][dv].values[0]
if x_val < y_val:
color = colors[0]
elif x_val > y_val:
color = colors[2]
elif x_val == y_val:
color = colors[1]
# Plot individual lines using Seaborn
sns.pointplot(data=tmp, x=within, y=dv, order=order, color=color,
ax=ax, **pointplot_kwargs)
if boxplot:
sns.boxplot(data=data, x=within, y=dv, order=order, ax=ax,
**boxplot_kwargs)
# Despine and trim
sns.despine(trim=True, ax=ax)
return ax | ['def', 'plot_paired', '(', 'data', '=', 'None', ',', 'dv', '=', 'None', ',', 'within', '=', 'None', ',', 'subject', '=', 'None', ',', 'order', '=', 'None', ',', 'boxplot', '=', 'True', ',', 'figsize', '=', '(', '4', ',', '4', ')', ',', 'dpi', '=', '100', ',', 'ax', '=', 'None', ',', 'colors', '=', '[', "'green'", ',', "'grey'", ',', "'indianred'", ']', ',', 'pointplot_kwargs', '=', '{', "'scale'", ':', '.6', ',', "'markers'", ':', "'.'", '}', ',', 'boxplot_kwargs', '=', '{', "'color'", ':', "'lightslategrey'", ',', "'width'", ':', '.2', '}', ')', ':', 'from', 'pingouin', '.', 'utils', 'import', '_check_dataframe', ',', 'remove_rm_na', '# Validate args', '_check_dataframe', '(', 'data', '=', 'data', ',', 'dv', '=', 'dv', ',', 'within', '=', 'within', ',', 'subject', '=', 'subject', ',', 'effects', '=', "'within'", ')', '# Remove NaN values', 'data', '=', 'remove_rm_na', '(', 'dv', '=', 'dv', ',', 'within', '=', 'within', ',', 'subject', '=', 'subject', ',', 'data', '=', 'data', ')', '# Extract subjects', 'subj', '=', 'data', '[', 'subject', ']', '.', 'unique', '(', ')', '# Extract within-subject level (alphabetical order)', 'x_cat', '=', 'np', '.', 'unique', '(', 'data', '[', 'within', ']', ')', 'assert', 'len', '(', 'x_cat', ')', '==', '2', ',', "'Within must have exactly two unique levels.'", 'if', 'order', 'is', 'None', ':', 'order', '=', 'x_cat', 'else', ':', 'assert', 'len', '(', 'order', ')', '==', '2', ',', "'Order must have exactly two elements.'", '# Start the plot', 'if', 'ax', 'is', 'None', ':', 'fig', ',', 'ax', '=', 'plt', '.', 'subplots', '(', '1', ',', '1', ',', 'figsize', '=', 'figsize', ',', 'dpi', '=', 'dpi', ')', 'for', 'idx', ',', 's', 'in', 'enumerate', '(', 'subj', ')', ':', 'tmp', '=', 'data', '.', 'loc', '[', 'data', '[', 'subject', ']', '==', 's', ',', '[', 'dv', ',', 'within', ',', 'subject', ']', ']', 'x_val', '=', 'tmp', '[', 'tmp', '[', 'within', ']', '==', 'order', '[', '0', ']', ']', '[', 'dv', ']', '.', 'values', '[', '0', ']', 'y_val', '=', 'tmp', '[', 'tmp', '[', 'within', ']', '==', 'order', '[', '1', ']', ']', '[', 'dv', ']', '.', 'values', '[', '0', ']', 'if', 'x_val', '<', 'y_val', ':', 'color', '=', 'colors', '[', '0', ']', 'elif', 'x_val', '>', 'y_val', ':', 'color', '=', 'colors', '[', '2', ']', 'elif', 'x_val', '==', 'y_val', ':', 'color', '=', 'colors', '[', '1', ']', '# Plot individual lines using Seaborn', 'sns', '.', 'pointplot', '(', 'data', '=', 'tmp', ',', 'x', '=', 'within', ',', 'y', '=', 'dv', ',', 'order', '=', 'order', ',', 'color', '=', 'color', ',', 'ax', '=', 'ax', ',', '*', '*', 'pointplot_kwargs', ')', 'if', 'boxplot', ':', 'sns', '.', 'boxplot', '(', 'data', '=', 'data', ',', 'x', '=', 'within', ',', 'y', '=', 'dv', ',', 'order', '=', 'order', ',', 'ax', '=', 'ax', ',', '*', '*', 'boxplot_kwargs', ')', '# Despine and trim', 'sns', '.', 'despine', '(', 'trim', '=', 'True', ',', 'ax', '=', 'ax', ')', 'return', 'ax'] | Paired plot.
Parameters
----------
data : pandas DataFrame
Long-format dataFrame.
dv : string
Name of column containing the dependant variable.
within : string
Name of column containing the within-subject factor. Note that
``within`` must have exactly two within-subject levels
(= two unique values).
subject : string
Name of column containing the subject identifier.
order : list of str
List of values in ``within`` that define the order of elements on the
x-axis of the plot. If None, uses alphabetical order.
boxplot : boolean
If True, add a boxplot to the paired lines using the
:py:func:`seaborn.boxplot` function.
figsize : tuple
Figsize in inches
dpi : int
Resolution of the figure in dots per inches.
ax : matplotlib axes
Axis on which to draw the plot.
colors : list of str
Line colors names. Default is green when value increases from A to B,
indianred when value decreases from A to B and grey when the value is
the same in both measurements.
pointplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.pointplot` function.
boxplot_kwargs : dict
Dictionnary of optional arguments that are passed to the
:py:func:`seaborn.boxplot` function.
Returns
-------
ax : Matplotlib Axes instance
Returns the Axes object with the plot for further tweaking.
Notes
-----
Data must be a long-format pandas DataFrame.
Examples
--------
Default paired plot:
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova')
>>> df = df.query("Group == 'Meditation' and Subject > 40")
>>> df = df.query("Time == 'August' or Time == 'June'")
>>> import pingouin as pg
>>> ax = pg.plot_paired(data=df, dv='Scores', within='Time',
... subject='Subject', dpi=150)
Paired plot on an existing axis (no boxplot and uniform color):
.. plot::
>>> from pingouin import read_dataset
>>> df = read_dataset('mixed_anova').query("Time != 'January'")
>>> import pingouin as pg
>>> import matplotlib.pyplot as plt
>>> fig, ax1 = plt.subplots(1, 1, figsize=(5, 4))
>>> pg.plot_paired(data=df[df['Group'] == 'Meditation'],
... dv='Scores', within='Time', subject='Subject',
... ax=ax1, boxplot=False,
... colors=['grey', 'grey', 'grey']) # doctest: +SKIP | ['Paired', 'plot', '.'] | train | https://github.com/raphaelvallat/pingouin/blob/58b19fa4fffbfe09d58b456e3926a148249e4d9b/pingouin/plotting.py#L489-L617 |
1,302 | buguroo/pyknow | pyknow/matchers/rete/abstract.py | TwoInputNode.activate_right | def activate_right(self, token):
"""Make a copy of the received token and call `_activate_right`."""
watchers.MATCHER.debug(
"Node <%s> activated right with token %r", self, token)
return self._activate_right(token.copy()) | python | def activate_right(self, token):
"""Make a copy of the received token and call `_activate_right`."""
watchers.MATCHER.debug(
"Node <%s> activated right with token %r", self, token)
return self._activate_right(token.copy()) | ['def', 'activate_right', '(', 'self', ',', 'token', ')', ':', 'watchers', '.', 'MATCHER', '.', 'debug', '(', '"Node <%s> activated right with token %r"', ',', 'self', ',', 'token', ')', 'return', 'self', '.', '_activate_right', '(', 'token', '.', 'copy', '(', ')', ')'] | Make a copy of the received token and call `_activate_right`. | ['Make', 'a', 'copy', 'of', 'the', 'received', 'token', 'and', 'call', '_activate_right', '.'] | train | https://github.com/buguroo/pyknow/blob/48818336f2e9a126f1964f2d8dc22d37ff800fe8/pyknow/matchers/rete/abstract.py#L68-L72 |
1,303 | AndrewAnnex/SpiceyPy | spiceypy/spiceypy.py | dskstl | def dskstl(keywrd, dpval):
"""
Set the value of a specified DSK tolerance or margin parameter.
https://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/dskstl_c.html
:param keywrd: Code specifying parameter to set.
:type keywrd: int
:param dpval: Value of parameter.
:type dpval: float
:return:
"""
keywrd = ctypes.c_int(keywrd)
dpval = ctypes.c_double(dpval)
libspice.dskstl_c(keywrd, dpval) | python | def dskstl(keywrd, dpval):
"""
Set the value of a specified DSK tolerance or margin parameter.
https://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/dskstl_c.html
:param keywrd: Code specifying parameter to set.
:type keywrd: int
:param dpval: Value of parameter.
:type dpval: float
:return:
"""
keywrd = ctypes.c_int(keywrd)
dpval = ctypes.c_double(dpval)
libspice.dskstl_c(keywrd, dpval) | ['def', 'dskstl', '(', 'keywrd', ',', 'dpval', ')', ':', 'keywrd', '=', 'ctypes', '.', 'c_int', '(', 'keywrd', ')', 'dpval', '=', 'ctypes', '.', 'c_double', '(', 'dpval', ')', 'libspice', '.', 'dskstl_c', '(', 'keywrd', ',', 'dpval', ')'] | Set the value of a specified DSK tolerance or margin parameter.
https://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/dskstl_c.html
:param keywrd: Code specifying parameter to set.
:type keywrd: int
:param dpval: Value of parameter.
:type dpval: float
:return: | ['Set', 'the', 'value', 'of', 'a', 'specified', 'DSK', 'tolerance', 'or', 'margin', 'parameter', '.', 'https', ':', '//', 'naif', '.', 'jpl', '.', 'nasa', '.', 'gov', '/', 'pub', '/', 'naif', '/', 'toolkit_docs', '/', 'C', '/', 'cspice', '/', 'dskstl_c', '.', 'html', ':', 'param', 'keywrd', ':', 'Code', 'specifying', 'parameter', 'to', 'set', '.', ':', 'type', 'keywrd', ':', 'int', ':', 'param', 'dpval', ':', 'Value', 'of', 'parameter', '.', ':', 'type', 'dpval', ':', 'float', ':', 'return', ':'] | train | https://github.com/AndrewAnnex/SpiceyPy/blob/fc20a9b9de68b58eed5b332f0c051fb343a6e335/spiceypy/spiceypy.py#L3164-L3178 |
1,304 | ssato/python-anyconfig | src/anyconfig/backend/xml.py | container_to_etree | def container_to_etree(obj, parent=None, to_str=None, **options):
"""
Convert a dict-like object to XML ElementTree.
:param obj: Container instance to convert to
:param parent: XML ElementTree parent node object or None
:param to_str: Callable to convert value to string or None
:param options: Keyword options,
- tags: Dict of tags for special nodes to keep XML info, attributes,
text and children nodes, e.g. {"attrs": "@attrs", "text": "#text"}
"""
if to_str is None:
to_str = _to_str_fn(**options)
if not anyconfig.utils.is_dict_like(obj):
if parent is not None and obj:
parent.text = to_str(obj) # Parent is a leaf text node.
return parent # All attributes and text should be set already.
options = _complement_tag_options(options)
(attrs, text, children) = operator.itemgetter(*_ATC)(options)
for key, val in anyconfig.compat.iteritems(obj):
if key == attrs:
_elem_set_attrs(val, parent, to_str)
elif key == text:
parent.text = to_str(val)
elif key == children:
for celem in _elem_from_descendants(val, **options):
parent.append(celem)
else:
parent = _get_or_update_parent(key, val, to_str, parent=parent,
**options)
return ET.ElementTree(parent) | python | def container_to_etree(obj, parent=None, to_str=None, **options):
"""
Convert a dict-like object to XML ElementTree.
:param obj: Container instance to convert to
:param parent: XML ElementTree parent node object or None
:param to_str: Callable to convert value to string or None
:param options: Keyword options,
- tags: Dict of tags for special nodes to keep XML info, attributes,
text and children nodes, e.g. {"attrs": "@attrs", "text": "#text"}
"""
if to_str is None:
to_str = _to_str_fn(**options)
if not anyconfig.utils.is_dict_like(obj):
if parent is not None and obj:
parent.text = to_str(obj) # Parent is a leaf text node.
return parent # All attributes and text should be set already.
options = _complement_tag_options(options)
(attrs, text, children) = operator.itemgetter(*_ATC)(options)
for key, val in anyconfig.compat.iteritems(obj):
if key == attrs:
_elem_set_attrs(val, parent, to_str)
elif key == text:
parent.text = to_str(val)
elif key == children:
for celem in _elem_from_descendants(val, **options):
parent.append(celem)
else:
parent = _get_or_update_parent(key, val, to_str, parent=parent,
**options)
return ET.ElementTree(parent) | ['def', 'container_to_etree', '(', 'obj', ',', 'parent', '=', 'None', ',', 'to_str', '=', 'None', ',', '*', '*', 'options', ')', ':', 'if', 'to_str', 'is', 'None', ':', 'to_str', '=', '_to_str_fn', '(', '*', '*', 'options', ')', 'if', 'not', 'anyconfig', '.', 'utils', '.', 'is_dict_like', '(', 'obj', ')', ':', 'if', 'parent', 'is', 'not', 'None', 'and', 'obj', ':', 'parent', '.', 'text', '=', 'to_str', '(', 'obj', ')', '# Parent is a leaf text node.', 'return', 'parent', '# All attributes and text should be set already.', 'options', '=', '_complement_tag_options', '(', 'options', ')', '(', 'attrs', ',', 'text', ',', 'children', ')', '=', 'operator', '.', 'itemgetter', '(', '*', '_ATC', ')', '(', 'options', ')', 'for', 'key', ',', 'val', 'in', 'anyconfig', '.', 'compat', '.', 'iteritems', '(', 'obj', ')', ':', 'if', 'key', '==', 'attrs', ':', '_elem_set_attrs', '(', 'val', ',', 'parent', ',', 'to_str', ')', 'elif', 'key', '==', 'text', ':', 'parent', '.', 'text', '=', 'to_str', '(', 'val', ')', 'elif', 'key', '==', 'children', ':', 'for', 'celem', 'in', '_elem_from_descendants', '(', 'val', ',', '*', '*', 'options', ')', ':', 'parent', '.', 'append', '(', 'celem', ')', 'else', ':', 'parent', '=', '_get_or_update_parent', '(', 'key', ',', 'val', ',', 'to_str', ',', 'parent', '=', 'parent', ',', '*', '*', 'options', ')', 'return', 'ET', '.', 'ElementTree', '(', 'parent', ')'] | Convert a dict-like object to XML ElementTree.
:param obj: Container instance to convert to
:param parent: XML ElementTree parent node object or None
:param to_str: Callable to convert value to string or None
:param options: Keyword options,
- tags: Dict of tags for special nodes to keep XML info, attributes,
text and children nodes, e.g. {"attrs": "@attrs", "text": "#text"} | ['Convert', 'a', 'dict', '-', 'like', 'object', 'to', 'XML', 'ElementTree', '.'] | train | https://github.com/ssato/python-anyconfig/blob/f2f4fb8d8e232aadea866c202e1dd7a5967e2877/src/anyconfig/backend/xml.py#L410-L445 |
1,305 | coin-or/GiMPy | src/gimpy/graph.py | Graph.set_node_attr | def set_node_attr(self, name, attr, value):
'''
API: set_node_attr(self, name, attr)
Description:
Sets attr attribute of node named name to value.
Input:
name: Name of node.
attr: Attribute of node to set.
Pre:
Graph should have this node.
Post:
Node attribute will be updated.
'''
self.get_node(name).set_attr(attr, value) | python | def set_node_attr(self, name, attr, value):
'''
API: set_node_attr(self, name, attr)
Description:
Sets attr attribute of node named name to value.
Input:
name: Name of node.
attr: Attribute of node to set.
Pre:
Graph should have this node.
Post:
Node attribute will be updated.
'''
self.get_node(name).set_attr(attr, value) | ['def', 'set_node_attr', '(', 'self', ',', 'name', ',', 'attr', ',', 'value', ')', ':', 'self', '.', 'get_node', '(', 'name', ')', '.', 'set_attr', '(', 'attr', ',', 'value', ')'] | API: set_node_attr(self, name, attr)
Description:
Sets attr attribute of node named name to value.
Input:
name: Name of node.
attr: Attribute of node to set.
Pre:
Graph should have this node.
Post:
Node attribute will be updated. | ['API', ':', 'set_node_attr', '(', 'self', 'name', 'attr', ')', 'Description', ':', 'Sets', 'attr', 'attribute', 'of', 'node', 'named', 'name', 'to', 'value', '.', 'Input', ':', 'name', ':', 'Name', 'of', 'node', '.', 'attr', ':', 'Attribute', 'of', 'node', 'to', 'set', '.', 'Pre', ':', 'Graph', 'should', 'have', 'this', 'node', '.', 'Post', ':', 'Node', 'attribute', 'will', 'be', 'updated', '.'] | train | https://github.com/coin-or/GiMPy/blob/51853122a50eb6019d06bbdedbfc396a833b5a22/src/gimpy/graph.py#L523-L536 |
1,306 | praekeltfoundation/molo | molo/core/api/importers.py | ContentImporter.recreate_article_body | def recreate_article_body(self):
'''
Handles case where article body contained page or image.
Assumes all articles and images have been created.
'''
for foreign_id, body in iteritems(self.record_keeper.article_bodies):
try:
local_page_id = self.record_keeper.get_local_page(foreign_id)
page = Page.objects.get(id=local_page_id).specific
# iterate through the body
new_body = []
for item in body:
if not item['value']:
continue
if item['type'] == 'page':
new_page_id = self.record_keeper.get_local_page(
item['value'])
item['value'] = new_page_id
elif item['type'] == 'image':
new_image_id = self.record_keeper.get_local_image(
item['value'])
item['value'] = new_image_id
new_body.append(item)
setattr(page, 'body', json.dumps(new_body))
page.save_revision().publish()
except Exception as e:
self.log(ERROR, "recreating article body",
{
"exception": e,
"foreign_id": foreign_id,
"body": body,
},
depth=1) | python | def recreate_article_body(self):
'''
Handles case where article body contained page or image.
Assumes all articles and images have been created.
'''
for foreign_id, body in iteritems(self.record_keeper.article_bodies):
try:
local_page_id = self.record_keeper.get_local_page(foreign_id)
page = Page.objects.get(id=local_page_id).specific
# iterate through the body
new_body = []
for item in body:
if not item['value']:
continue
if item['type'] == 'page':
new_page_id = self.record_keeper.get_local_page(
item['value'])
item['value'] = new_page_id
elif item['type'] == 'image':
new_image_id = self.record_keeper.get_local_image(
item['value'])
item['value'] = new_image_id
new_body.append(item)
setattr(page, 'body', json.dumps(new_body))
page.save_revision().publish()
except Exception as e:
self.log(ERROR, "recreating article body",
{
"exception": e,
"foreign_id": foreign_id,
"body": body,
},
depth=1) | ['def', 'recreate_article_body', '(', 'self', ')', ':', 'for', 'foreign_id', ',', 'body', 'in', 'iteritems', '(', 'self', '.', 'record_keeper', '.', 'article_bodies', ')', ':', 'try', ':', 'local_page_id', '=', 'self', '.', 'record_keeper', '.', 'get_local_page', '(', 'foreign_id', ')', 'page', '=', 'Page', '.', 'objects', '.', 'get', '(', 'id', '=', 'local_page_id', ')', '.', 'specific', '# iterate through the body', 'new_body', '=', '[', ']', 'for', 'item', 'in', 'body', ':', 'if', 'not', 'item', '[', "'value'", ']', ':', 'continue', 'if', 'item', '[', "'type'", ']', '==', "'page'", ':', 'new_page_id', '=', 'self', '.', 'record_keeper', '.', 'get_local_page', '(', 'item', '[', "'value'", ']', ')', 'item', '[', "'value'", ']', '=', 'new_page_id', 'elif', 'item', '[', "'type'", ']', '==', "'image'", ':', 'new_image_id', '=', 'self', '.', 'record_keeper', '.', 'get_local_image', '(', 'item', '[', "'value'", ']', ')', 'item', '[', "'value'", ']', '=', 'new_image_id', 'new_body', '.', 'append', '(', 'item', ')', 'setattr', '(', 'page', ',', "'body'", ',', 'json', '.', 'dumps', '(', 'new_body', ')', ')', 'page', '.', 'save_revision', '(', ')', '.', 'publish', '(', ')', 'except', 'Exception', 'as', 'e', ':', 'self', '.', 'log', '(', 'ERROR', ',', '"recreating article body"', ',', '{', '"exception"', ':', 'e', ',', '"foreign_id"', ':', 'foreign_id', ',', '"body"', ':', 'body', ',', '}', ',', 'depth', '=', '1', ')'] | Handles case where article body contained page or image.
Assumes all articles and images have been created. | ['Handles', 'case', 'where', 'article', 'body', 'contained', 'page', 'or', 'image', '.'] | train | https://github.com/praekeltfoundation/molo/blob/57702fda4fab261d67591415f7d46bc98fa38525/molo/core/api/importers.py#L718-L755 |
1,307 | jobovy/galpy | galpy/df/diskdf.py | surfacemass | def surfacemass(self,R,romberg=False,nsigma=None,relative=False):
"""
NAME:
surfacemass
PURPOSE:
calculate the surface-mass at R by marginalizing over velocity
INPUT:
R - radius at which to calculate the surfacemass density (can be Quantity)
OPTIONAL INPUT:
nsigma - number of sigma to integrate the velocities over
KEYWORDS:
romberg - if True, use a romberg integrator (default: False)
OUTPUT:
surface mass at R
HISTORY:
2010-03-XX - Written - Bovy (NYU)
"""
if nsigma == None:
nsigma= _NSIGMA
logSigmaR= self.targetSurfacemass(R,log=True,use_physical=False)
sigmaR2= self.targetSigma2(R,use_physical=False)
sigmaR1= sc.sqrt(sigmaR2)
logsigmaR2= sc.log(sigmaR2)
if relative:
norm= 1.
else:
norm= sc.exp(logSigmaR)
#Use the asymmetric drift equation to estimate va
va= sigmaR2/2./R**self._beta*(1./self._gamma**2.-1.
-R*self._surfaceSigmaProfile.surfacemassDerivative(R,log=True)
-R*self._surfaceSigmaProfile.sigma2Derivative(R,log=True))
if math.fabs(va) > sigmaR1: va = 0.#To avoid craziness near the center
if romberg:
return sc.real(bovy_dblquad(_surfaceIntegrand,
self._gamma*(R**self._beta-va)/sigmaR1-nsigma,
self._gamma*(R**self._beta-va)/sigmaR1+nsigma,
lambda x: 0., lambda x: nsigma,
[R,self,logSigmaR,logsigmaR2,sigmaR1,
self._gamma],
tol=10.**-8)/sc.pi*norm)
else:
return integrate.dblquad(_surfaceIntegrand,
self._gamma*(R**self._beta-va)/sigmaR1-nsigma,
self._gamma*(R**self._beta-va)/sigmaR1+nsigma,
lambda x: 0., lambda x: nsigma,
(R,self,logSigmaR,logsigmaR2,sigmaR1,
self._gamma),
epsrel=_EPSREL)[0]/sc.pi*norm | python | def surfacemass(self,R,romberg=False,nsigma=None,relative=False):
"""
NAME:
surfacemass
PURPOSE:
calculate the surface-mass at R by marginalizing over velocity
INPUT:
R - radius at which to calculate the surfacemass density (can be Quantity)
OPTIONAL INPUT:
nsigma - number of sigma to integrate the velocities over
KEYWORDS:
romberg - if True, use a romberg integrator (default: False)
OUTPUT:
surface mass at R
HISTORY:
2010-03-XX - Written - Bovy (NYU)
"""
if nsigma == None:
nsigma= _NSIGMA
logSigmaR= self.targetSurfacemass(R,log=True,use_physical=False)
sigmaR2= self.targetSigma2(R,use_physical=False)
sigmaR1= sc.sqrt(sigmaR2)
logsigmaR2= sc.log(sigmaR2)
if relative:
norm= 1.
else:
norm= sc.exp(logSigmaR)
#Use the asymmetric drift equation to estimate va
va= sigmaR2/2./R**self._beta*(1./self._gamma**2.-1.
-R*self._surfaceSigmaProfile.surfacemassDerivative(R,log=True)
-R*self._surfaceSigmaProfile.sigma2Derivative(R,log=True))
if math.fabs(va) > sigmaR1: va = 0.#To avoid craziness near the center
if romberg:
return sc.real(bovy_dblquad(_surfaceIntegrand,
self._gamma*(R**self._beta-va)/sigmaR1-nsigma,
self._gamma*(R**self._beta-va)/sigmaR1+nsigma,
lambda x: 0., lambda x: nsigma,
[R,self,logSigmaR,logsigmaR2,sigmaR1,
self._gamma],
tol=10.**-8)/sc.pi*norm)
else:
return integrate.dblquad(_surfaceIntegrand,
self._gamma*(R**self._beta-va)/sigmaR1-nsigma,
self._gamma*(R**self._beta-va)/sigmaR1+nsigma,
lambda x: 0., lambda x: nsigma,
(R,self,logSigmaR,logsigmaR2,sigmaR1,
self._gamma),
epsrel=_EPSREL)[0]/sc.pi*norm | ['def', 'surfacemass', '(', 'self', ',', 'R', ',', 'romberg', '=', 'False', ',', 'nsigma', '=', 'None', ',', 'relative', '=', 'False', ')', ':', 'if', 'nsigma', '==', 'None', ':', 'nsigma', '=', '_NSIGMA', 'logSigmaR', '=', 'self', '.', 'targetSurfacemass', '(', 'R', ',', 'log', '=', 'True', ',', 'use_physical', '=', 'False', ')', 'sigmaR2', '=', 'self', '.', 'targetSigma2', '(', 'R', ',', 'use_physical', '=', 'False', ')', 'sigmaR1', '=', 'sc', '.', 'sqrt', '(', 'sigmaR2', ')', 'logsigmaR2', '=', 'sc', '.', 'log', '(', 'sigmaR2', ')', 'if', 'relative', ':', 'norm', '=', '1.', 'else', ':', 'norm', '=', 'sc', '.', 'exp', '(', 'logSigmaR', ')', '#Use the asymmetric drift equation to estimate va', 'va', '=', 'sigmaR2', '/', '2.', '/', 'R', '**', 'self', '.', '_beta', '*', '(', '1.', '/', 'self', '.', '_gamma', '**', '2.', '-', '1.', '-', 'R', '*', 'self', '.', '_surfaceSigmaProfile', '.', 'surfacemassDerivative', '(', 'R', ',', 'log', '=', 'True', ')', '-', 'R', '*', 'self', '.', '_surfaceSigmaProfile', '.', 'sigma2Derivative', '(', 'R', ',', 'log', '=', 'True', ')', ')', 'if', 'math', '.', 'fabs', '(', 'va', ')', '>', 'sigmaR1', ':', 'va', '=', '0.', '#To avoid craziness near the center', 'if', 'romberg', ':', 'return', 'sc', '.', 'real', '(', 'bovy_dblquad', '(', '_surfaceIntegrand', ',', 'self', '.', '_gamma', '*', '(', 'R', '**', 'self', '.', '_beta', '-', 'va', ')', '/', 'sigmaR1', '-', 'nsigma', ',', 'self', '.', '_gamma', '*', '(', 'R', '**', 'self', '.', '_beta', '-', 'va', ')', '/', 'sigmaR1', '+', 'nsigma', ',', 'lambda', 'x', ':', '0.', ',', 'lambda', 'x', ':', 'nsigma', ',', '[', 'R', ',', 'self', ',', 'logSigmaR', ',', 'logsigmaR2', ',', 'sigmaR1', ',', 'self', '.', '_gamma', ']', ',', 'tol', '=', '10.', '**', '-', '8', ')', '/', 'sc', '.', 'pi', '*', 'norm', ')', 'else', ':', 'return', 'integrate', '.', 'dblquad', '(', '_surfaceIntegrand', ',', 'self', '.', '_gamma', '*', '(', 'R', '**', 'self', '.', '_beta', '-', 'va', ')', '/', 'sigmaR1', '-', 'nsigma', ',', 'self', '.', '_gamma', '*', '(', 'R', '**', 'self', '.', '_beta', '-', 'va', ')', '/', 'sigmaR1', '+', 'nsigma', ',', 'lambda', 'x', ':', '0.', ',', 'lambda', 'x', ':', 'nsigma', ',', '(', 'R', ',', 'self', ',', 'logSigmaR', ',', 'logsigmaR2', ',', 'sigmaR1', ',', 'self', '.', '_gamma', ')', ',', 'epsrel', '=', '_EPSREL', ')', '[', '0', ']', '/', 'sc', '.', 'pi', '*', 'norm'] | NAME:
surfacemass
PURPOSE:
calculate the surface-mass at R by marginalizing over velocity
INPUT:
R - radius at which to calculate the surfacemass density (can be Quantity)
OPTIONAL INPUT:
nsigma - number of sigma to integrate the velocities over
KEYWORDS:
romberg - if True, use a romberg integrator (default: False)
OUTPUT:
surface mass at R
HISTORY:
2010-03-XX - Written - Bovy (NYU) | ['NAME', ':'] | train | https://github.com/jobovy/galpy/blob/9c5b9fe65d58835624dffe432be282060918ee08/galpy/df/diskdf.py#L664-L725 |
1,308 | iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/msvs.py | msvs_parse_version | def msvs_parse_version(s):
"""
Split a Visual Studio version, which may in fact be something like
'7.0Exp', into is version number (returned as a float) and trailing
"suite" portion.
"""
num, suite = version_re.match(s).groups()
return float(num), suite | python | def msvs_parse_version(s):
"""
Split a Visual Studio version, which may in fact be something like
'7.0Exp', into is version number (returned as a float) and trailing
"suite" portion.
"""
num, suite = version_re.match(s).groups()
return float(num), suite | ['def', 'msvs_parse_version', '(', 's', ')', ':', 'num', ',', 'suite', '=', 'version_re', '.', 'match', '(', 's', ')', '.', 'groups', '(', ')', 'return', 'float', '(', 'num', ')', ',', 'suite'] | Split a Visual Studio version, which may in fact be something like
'7.0Exp', into is version number (returned as a float) and trailing
"suite" portion. | ['Split', 'a', 'Visual', 'Studio', 'version', 'which', 'may', 'in', 'fact', 'be', 'something', 'like', '7', '.', '0Exp', 'into', 'is', 'version', 'number', '(', 'returned', 'as', 'a', 'float', ')', 'and', 'trailing', 'suite', 'portion', '.'] | train | https://github.com/iotile/coretools/blob/2d794f5f1346b841b0dcd16c9d284e9bf2f3c6ec/iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/msvs.py#L97-L104 |
1,309 | linode/linode_api4-python | linode_api4/objects/tag.py | Tag._get_raw_objects | def _get_raw_objects(self):
"""
Helper function to populate the first page of raw objects for this tag.
This has the side effect of creating the ``_raw_objects`` attribute of
this object.
"""
if not hasattr(self, '_raw_objects'):
result = self._client.get(type(self).api_endpoint, model=self)
# I want to cache this to avoid making duplicate requests, but I don't
# want it in the __init__
self._raw_objects = result # pylint: disable=attribute-defined-outside-init
return self._raw_objects | python | def _get_raw_objects(self):
"""
Helper function to populate the first page of raw objects for this tag.
This has the side effect of creating the ``_raw_objects`` attribute of
this object.
"""
if not hasattr(self, '_raw_objects'):
result = self._client.get(type(self).api_endpoint, model=self)
# I want to cache this to avoid making duplicate requests, but I don't
# want it in the __init__
self._raw_objects = result # pylint: disable=attribute-defined-outside-init
return self._raw_objects | ['def', '_get_raw_objects', '(', 'self', ')', ':', 'if', 'not', 'hasattr', '(', 'self', ',', "'_raw_objects'", ')', ':', 'result', '=', 'self', '.', '_client', '.', 'get', '(', 'type', '(', 'self', ')', '.', 'api_endpoint', ',', 'model', '=', 'self', ')', "# I want to cache this to avoid making duplicate requests, but I don't", '# want it in the __init__', 'self', '.', '_raw_objects', '=', 'result', '# pylint: disable=attribute-defined-outside-init', 'return', 'self', '.', '_raw_objects'] | Helper function to populate the first page of raw objects for this tag.
This has the side effect of creating the ``_raw_objects`` attribute of
this object. | ['Helper', 'function', 'to', 'populate', 'the', 'first', 'page', 'of', 'raw', 'objects', 'for', 'this', 'tag', '.', 'This', 'has', 'the', 'side', 'effect', 'of', 'creating', 'the', '_raw_objects', 'attribute', 'of', 'this', 'object', '.'] | train | https://github.com/linode/linode_api4-python/blob/1dd7318d2aed014c746d48c7957464c57af883ca/linode_api4/objects/tag.py#L32-L45 |
1,310 | marazmiki/django-ulogin | django_ulogin/views.py | PostBackView.handle_authenticated_user | def handle_authenticated_user(self, response):
"""
Handles the ULogin response if user is already
authenticated
"""
current_user = get_user(self.request)
ulogin, registered = ULoginUser.objects.get_or_create(
uid=response['uid'],
network=response['network'],
defaults={'identity': response['identity'],
'user': current_user})
if not registered:
ulogin_user = ulogin.user
logger.debug('uLogin user already exists')
if current_user != ulogin_user:
logger.debug(
"Mismatch: %s is not a %s. Take over it!" % (current_user,
ulogin_user)
)
ulogin.user = current_user
ulogin.save()
return get_user(self.request), ulogin, registered | python | def handle_authenticated_user(self, response):
"""
Handles the ULogin response if user is already
authenticated
"""
current_user = get_user(self.request)
ulogin, registered = ULoginUser.objects.get_or_create(
uid=response['uid'],
network=response['network'],
defaults={'identity': response['identity'],
'user': current_user})
if not registered:
ulogin_user = ulogin.user
logger.debug('uLogin user already exists')
if current_user != ulogin_user:
logger.debug(
"Mismatch: %s is not a %s. Take over it!" % (current_user,
ulogin_user)
)
ulogin.user = current_user
ulogin.save()
return get_user(self.request), ulogin, registered | ['def', 'handle_authenticated_user', '(', 'self', ',', 'response', ')', ':', 'current_user', '=', 'get_user', '(', 'self', '.', 'request', ')', 'ulogin', ',', 'registered', '=', 'ULoginUser', '.', 'objects', '.', 'get_or_create', '(', 'uid', '=', 'response', '[', "'uid'", ']', ',', 'network', '=', 'response', '[', "'network'", ']', ',', 'defaults', '=', '{', "'identity'", ':', 'response', '[', "'identity'", ']', ',', "'user'", ':', 'current_user', '}', ')', 'if', 'not', 'registered', ':', 'ulogin_user', '=', 'ulogin', '.', 'user', 'logger', '.', 'debug', '(', "'uLogin user already exists'", ')', 'if', 'current_user', '!=', 'ulogin_user', ':', 'logger', '.', 'debug', '(', '"Mismatch: %s is not a %s. Take over it!"', '%', '(', 'current_user', ',', 'ulogin_user', ')', ')', 'ulogin', '.', 'user', '=', 'current_user', 'ulogin', '.', 'save', '(', ')', 'return', 'get_user', '(', 'self', '.', 'request', ')', ',', 'ulogin', ',', 'registered'] | Handles the ULogin response if user is already
authenticated | ['Handles', 'the', 'ULogin', 'response', 'if', 'user', 'is', 'already', 'authenticated'] | train | https://github.com/marazmiki/django-ulogin/blob/f41ad4b4ca130ad8af25be72ad882c8cf94a80dc/django_ulogin/views.py#L82-L107 |
1,311 | bfontaine/term2048 | term2048/ui.py | parse_cli_args | def parse_cli_args():
"""parse args from the CLI and return a dict"""
parser = argparse.ArgumentParser(description='2048 in your terminal')
parser.add_argument('--mode', dest='mode', type=str,
default=None, help='colors mode (dark or light)')
parser.add_argument('--az', dest='azmode', action='store_true',
help='Use the letters a-z instead of numbers')
parser.add_argument('--resume', dest='resume', action='store_true',
help='restart the game from where you left')
parser.add_argument('-v', '--version', action='store_true')
parser.add_argument('-r', '--rules', action='store_true')
return vars(parser.parse_args()) | python | def parse_cli_args():
"""parse args from the CLI and return a dict"""
parser = argparse.ArgumentParser(description='2048 in your terminal')
parser.add_argument('--mode', dest='mode', type=str,
default=None, help='colors mode (dark or light)')
parser.add_argument('--az', dest='azmode', action='store_true',
help='Use the letters a-z instead of numbers')
parser.add_argument('--resume', dest='resume', action='store_true',
help='restart the game from where you left')
parser.add_argument('-v', '--version', action='store_true')
parser.add_argument('-r', '--rules', action='store_true')
return vars(parser.parse_args()) | ['def', 'parse_cli_args', '(', ')', ':', 'parser', '=', 'argparse', '.', 'ArgumentParser', '(', 'description', '=', "'2048 in your terminal'", ')', 'parser', '.', 'add_argument', '(', "'--mode'", ',', 'dest', '=', "'mode'", ',', 'type', '=', 'str', ',', 'default', '=', 'None', ',', 'help', '=', "'colors mode (dark or light)'", ')', 'parser', '.', 'add_argument', '(', "'--az'", ',', 'dest', '=', "'azmode'", ',', 'action', '=', "'store_true'", ',', 'help', '=', "'Use the letters a-z instead of numbers'", ')', 'parser', '.', 'add_argument', '(', "'--resume'", ',', 'dest', '=', "'resume'", ',', 'action', '=', "'store_true'", ',', 'help', '=', "'restart the game from where you left'", ')', 'parser', '.', 'add_argument', '(', "'-v'", ',', "'--version'", ',', 'action', '=', "'store_true'", ')', 'parser', '.', 'add_argument', '(', "'-r'", ',', "'--rules'", ',', 'action', '=', "'store_true'", ')', 'return', 'vars', '(', 'parser', '.', 'parse_args', '(', ')', ')'] | parse args from the CLI and return a dict | ['parse', 'args', 'from', 'the', 'CLI', 'and', 'return', 'a', 'dict'] | train | https://github.com/bfontaine/term2048/blob/8b5ce8b65f44f20a7ad36022a34dce56184070af/term2048/ui.py#L30-L41 |
1,312 | pecan/pecan | pecan/commands/serve.py | ServeCommand.serve | def serve(self, app, conf):
"""
A very simple approach for a WSGI server.
"""
if self.args.reload:
try:
self.watch_and_spawn(conf)
except ImportError:
print('The `--reload` option requires `watchdog` to be '
'installed.')
print(' $ pip install watchdog')
else:
self._serve(app, conf) | python | def serve(self, app, conf):
"""
A very simple approach for a WSGI server.
"""
if self.args.reload:
try:
self.watch_and_spawn(conf)
except ImportError:
print('The `--reload` option requires `watchdog` to be '
'installed.')
print(' $ pip install watchdog')
else:
self._serve(app, conf) | ['def', 'serve', '(', 'self', ',', 'app', ',', 'conf', ')', ':', 'if', 'self', '.', 'args', '.', 'reload', ':', 'try', ':', 'self', '.', 'watch_and_spawn', '(', 'conf', ')', 'except', 'ImportError', ':', 'print', '(', "'The `--reload` option requires `watchdog` to be '", "'installed.'", ')', 'print', '(', "' $ pip install watchdog'", ')', 'else', ':', 'self', '.', '_serve', '(', 'app', ',', 'conf', ')'] | A very simple approach for a WSGI server. | ['A', 'very', 'simple', 'approach', 'for', 'a', 'WSGI', 'server', '.'] | train | https://github.com/pecan/pecan/blob/833d0653fa0e6bbfb52545b091c30182105f4a82/pecan/commands/serve.py#L139-L152 |
1,313 | clld/pycdstar | src/pycdstar/commands.py | c_metadata | def c_metadata(api, args, verbose=False):
"""
Set or get metadata associated with an object::
usage: cdstar metadata <URL> [<JSON>]
<JSON> Path to metadata in JSON, or JSON literal.
"""
obj = api.get_object(args['<URL>'].split('/')[-1])
if not set_metadata(args['<JSON>'], obj):
return json.dumps(obj.metadata.read(), indent=4) | python | def c_metadata(api, args, verbose=False):
"""
Set or get metadata associated with an object::
usage: cdstar metadata <URL> [<JSON>]
<JSON> Path to metadata in JSON, or JSON literal.
"""
obj = api.get_object(args['<URL>'].split('/')[-1])
if not set_metadata(args['<JSON>'], obj):
return json.dumps(obj.metadata.read(), indent=4) | ['def', 'c_metadata', '(', 'api', ',', 'args', ',', 'verbose', '=', 'False', ')', ':', 'obj', '=', 'api', '.', 'get_object', '(', 'args', '[', "'<URL>'", ']', '.', 'split', '(', "'/'", ')', '[', '-', '1', ']', ')', 'if', 'not', 'set_metadata', '(', 'args', '[', "'<JSON>'", ']', ',', 'obj', ')', ':', 'return', 'json', '.', 'dumps', '(', 'obj', '.', 'metadata', '.', 'read', '(', ')', ',', 'indent', '=', '4', ')'] | Set or get metadata associated with an object::
usage: cdstar metadata <URL> [<JSON>]
<JSON> Path to metadata in JSON, or JSON literal. | ['Set', 'or', 'get', 'metadata', 'associated', 'with', 'an', 'object', '::'] | train | https://github.com/clld/pycdstar/blob/1a225b472c4e6bf9b8078fa3198f939395c53d22/src/pycdstar/commands.py#L24-L34 |
1,314 | TissueMAPS/TmDeploy | tmdeploy/config.py | CloudSection.key_file_public | def key_file_public(self):
'''str: path to the public key that will be uploaded to the cloud
provider (by default looks for a ``.pub`` file with name
:attr:`key_name <tmdeploy.config.CloudSection.key_name>` in ``~/.ssh``
directory)
'''
if not hasattr(self, '_key_file_public'):
self.key_file_public = '~/.ssh/{key}.pub'.format(key=self.key_name)
return self._key_file_public | python | def key_file_public(self):
'''str: path to the public key that will be uploaded to the cloud
provider (by default looks for a ``.pub`` file with name
:attr:`key_name <tmdeploy.config.CloudSection.key_name>` in ``~/.ssh``
directory)
'''
if not hasattr(self, '_key_file_public'):
self.key_file_public = '~/.ssh/{key}.pub'.format(key=self.key_name)
return self._key_file_public | ['def', 'key_file_public', '(', 'self', ')', ':', 'if', 'not', 'hasattr', '(', 'self', ',', "'_key_file_public'", ')', ':', 'self', '.', 'key_file_public', '=', "'~/.ssh/{key}.pub'", '.', 'format', '(', 'key', '=', 'self', '.', 'key_name', ')', 'return', 'self', '.', '_key_file_public'] | str: path to the public key that will be uploaded to the cloud
provider (by default looks for a ``.pub`` file with name
:attr:`key_name <tmdeploy.config.CloudSection.key_name>` in ``~/.ssh``
directory) | ['str', ':', 'path', 'to', 'the', 'public', 'key', 'that', 'will', 'be', 'uploaded', 'to', 'the', 'cloud', 'provider', '(', 'by', 'default', 'looks', 'for', 'a', '.', 'pub', 'file', 'with', 'name', ':', 'attr', ':', 'key_name', '<tmdeploy', '.', 'config', '.', 'CloudSection', '.', 'key_name', '>', 'in', '~', '/', '.', 'ssh', 'directory', ')'] | train | https://github.com/TissueMAPS/TmDeploy/blob/f891b4ffb21431988bc4a063ae871da3bf284a45/tmdeploy/config.py#L310-L318 |
1,315 | log2timeline/dfvfs | dfvfs/file_io/gzip_file_io.py | GzipFile.read | def read(self, size=None):
"""Reads a byte string from the gzip file at the current offset.
The function will read a byte string up to the specified size or
all of the remaining data if no size was specified.
Args:
size (Optional[int]): number of bytes to read, where None is all
remaining data.
Returns:
bytes: data read.
Raises:
IOError: if the read failed.
OSError: if the read failed.
"""
data = b''
while ((size and len(data) < size) and
self._current_offset < self.uncompressed_data_size):
member = self._GetMemberForOffset(self._current_offset)
member_offset = self._current_offset - member.uncompressed_data_offset
data_read = member.ReadAtOffset(member_offset, size)
if data_read:
self._current_offset += len(data_read)
data = b''.join([data, data_read])
return data | python | def read(self, size=None):
"""Reads a byte string from the gzip file at the current offset.
The function will read a byte string up to the specified size or
all of the remaining data if no size was specified.
Args:
size (Optional[int]): number of bytes to read, where None is all
remaining data.
Returns:
bytes: data read.
Raises:
IOError: if the read failed.
OSError: if the read failed.
"""
data = b''
while ((size and len(data) < size) and
self._current_offset < self.uncompressed_data_size):
member = self._GetMemberForOffset(self._current_offset)
member_offset = self._current_offset - member.uncompressed_data_offset
data_read = member.ReadAtOffset(member_offset, size)
if data_read:
self._current_offset += len(data_read)
data = b''.join([data, data_read])
return data | ['def', 'read', '(', 'self', ',', 'size', '=', 'None', ')', ':', 'data', '=', "b''", 'while', '(', '(', 'size', 'and', 'len', '(', 'data', ')', '<', 'size', ')', 'and', 'self', '.', '_current_offset', '<', 'self', '.', 'uncompressed_data_size', ')', ':', 'member', '=', 'self', '.', '_GetMemberForOffset', '(', 'self', '.', '_current_offset', ')', 'member_offset', '=', 'self', '.', '_current_offset', '-', 'member', '.', 'uncompressed_data_offset', 'data_read', '=', 'member', '.', 'ReadAtOffset', '(', 'member_offset', ',', 'size', ')', 'if', 'data_read', ':', 'self', '.', '_current_offset', '+=', 'len', '(', 'data_read', ')', 'data', '=', "b''", '.', 'join', '(', '[', 'data', ',', 'data_read', ']', ')', 'return', 'data'] | Reads a byte string from the gzip file at the current offset.
The function will read a byte string up to the specified size or
all of the remaining data if no size was specified.
Args:
size (Optional[int]): number of bytes to read, where None is all
remaining data.
Returns:
bytes: data read.
Raises:
IOError: if the read failed.
OSError: if the read failed. | ['Reads', 'a', 'byte', 'string', 'from', 'the', 'gzip', 'file', 'at', 'the', 'current', 'offset', '.'] | train | https://github.com/log2timeline/dfvfs/blob/2b3ccd115f9901d89f383397d4a1376a873c83c4/dfvfs/file_io/gzip_file_io.py#L117-L144 |
1,316 | Esri/ArcREST | src/arcrest/manageags/administration.py | AGSAdministration.services | def services(self):
"""
Gets the services object which will provide the ArcGIS Server's
admin information about services and folders.
"""
if self._resources is None:
self.__init()
if "services" in self._resources:
url = self._url + "/services"
return _services.Services(url=url,
securityHandler=self._securityHandler,
proxy_url=self._proxy_url,
proxy_port=self._proxy_port,
initialize=True)
else:
return None | python | def services(self):
"""
Gets the services object which will provide the ArcGIS Server's
admin information about services and folders.
"""
if self._resources is None:
self.__init()
if "services" in self._resources:
url = self._url + "/services"
return _services.Services(url=url,
securityHandler=self._securityHandler,
proxy_url=self._proxy_url,
proxy_port=self._proxy_port,
initialize=True)
else:
return None | ['def', 'services', '(', 'self', ')', ':', 'if', 'self', '.', '_resources', 'is', 'None', ':', 'self', '.', '__init', '(', ')', 'if', '"services"', 'in', 'self', '.', '_resources', ':', 'url', '=', 'self', '.', '_url', '+', '"/services"', 'return', '_services', '.', 'Services', '(', 'url', '=', 'url', ',', 'securityHandler', '=', 'self', '.', '_securityHandler', ',', 'proxy_url', '=', 'self', '.', '_proxy_url', ',', 'proxy_port', '=', 'self', '.', '_proxy_port', ',', 'initialize', '=', 'True', ')', 'else', ':', 'return', 'None'] | Gets the services object which will provide the ArcGIS Server's
admin information about services and folders. | ['Gets', 'the', 'services', 'object', 'which', 'will', 'provide', 'the', 'ArcGIS', 'Server', 's', 'admin', 'information', 'about', 'services', 'and', 'folders', '.'] | train | https://github.com/Esri/ArcREST/blob/ab240fde2b0200f61d4a5f6df033516e53f2f416/src/arcrest/manageags/administration.py#L382-L397 |
1,317 | saltstack/salt | salt/netapi/__init__.py | NetapiClient.ssh | def ssh(self, *args, **kwargs):
'''
Run salt-ssh commands synchronously
Wraps :py:meth:`salt.client.ssh.client.SSHClient.cmd_sync`.
:return: Returns the result from the salt-ssh command
'''
ssh_client = salt.client.ssh.client.SSHClient(mopts=self.opts,
disable_custom_roster=True)
return ssh_client.cmd_sync(kwargs) | python | def ssh(self, *args, **kwargs):
'''
Run salt-ssh commands synchronously
Wraps :py:meth:`salt.client.ssh.client.SSHClient.cmd_sync`.
:return: Returns the result from the salt-ssh command
'''
ssh_client = salt.client.ssh.client.SSHClient(mopts=self.opts,
disable_custom_roster=True)
return ssh_client.cmd_sync(kwargs) | ['def', 'ssh', '(', 'self', ',', '*', 'args', ',', '*', '*', 'kwargs', ')', ':', 'ssh_client', '=', 'salt', '.', 'client', '.', 'ssh', '.', 'client', '.', 'SSHClient', '(', 'mopts', '=', 'self', '.', 'opts', ',', 'disable_custom_roster', '=', 'True', ')', 'return', 'ssh_client', '.', 'cmd_sync', '(', 'kwargs', ')'] | Run salt-ssh commands synchronously
Wraps :py:meth:`salt.client.ssh.client.SSHClient.cmd_sync`.
:return: Returns the result from the salt-ssh command | ['Run', 'salt', '-', 'ssh', 'commands', 'synchronously'] | train | https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/netapi/__init__.py#L136-L146 |
1,318 | boriel/zxbasic | zxbparser.py | p_let_arr_substr_in_args3 | def p_let_arr_substr_in_args3(p):
""" statement : LET ARRAY_ID LP arguments COMMA TO RP EQ expr
| ARRAY_ID LP arguments COMMA TO RP EQ expr
"""
i = 2 if p[1].upper() == 'LET' else 1
id_ = p[i]
arg_list = p[i + 2]
substr = (make_number(0, lineno=p.lineno(i + 4)),
make_number(gl.MAX_STRSLICE_IDX, lineno=p.lineno(i + 3)))
expr_ = p[i + 7]
p[0] = make_array_substr_assign(p.lineno(i), id_, arg_list, substr, expr_) | python | def p_let_arr_substr_in_args3(p):
""" statement : LET ARRAY_ID LP arguments COMMA TO RP EQ expr
| ARRAY_ID LP arguments COMMA TO RP EQ expr
"""
i = 2 if p[1].upper() == 'LET' else 1
id_ = p[i]
arg_list = p[i + 2]
substr = (make_number(0, lineno=p.lineno(i + 4)),
make_number(gl.MAX_STRSLICE_IDX, lineno=p.lineno(i + 3)))
expr_ = p[i + 7]
p[0] = make_array_substr_assign(p.lineno(i), id_, arg_list, substr, expr_) | ['def', 'p_let_arr_substr_in_args3', '(', 'p', ')', ':', 'i', '=', '2', 'if', 'p', '[', '1', ']', '.', 'upper', '(', ')', '==', "'LET'", 'else', '1', 'id_', '=', 'p', '[', 'i', ']', 'arg_list', '=', 'p', '[', 'i', '+', '2', ']', 'substr', '=', '(', 'make_number', '(', '0', ',', 'lineno', '=', 'p', '.', 'lineno', '(', 'i', '+', '4', ')', ')', ',', 'make_number', '(', 'gl', '.', 'MAX_STRSLICE_IDX', ',', 'lineno', '=', 'p', '.', 'lineno', '(', 'i', '+', '3', ')', ')', ')', 'expr_', '=', 'p', '[', 'i', '+', '7', ']', 'p', '[', '0', ']', '=', 'make_array_substr_assign', '(', 'p', '.', 'lineno', '(', 'i', ')', ',', 'id_', ',', 'arg_list', ',', 'substr', ',', 'expr_', ')'] | statement : LET ARRAY_ID LP arguments COMMA TO RP EQ expr
| ARRAY_ID LP arguments COMMA TO RP EQ expr | ['statement', ':', 'LET', 'ARRAY_ID', 'LP', 'arguments', 'COMMA', 'TO', 'RP', 'EQ', 'expr', '|', 'ARRAY_ID', 'LP', 'arguments', 'COMMA', 'TO', 'RP', 'EQ', 'expr'] | train | https://github.com/boriel/zxbasic/blob/23b28db10e41117805bdb3c0f78543590853b132/zxbparser.py#L2646-L2657 |
1,319 | andycasey/sick | sick/models/model.py | Model.infer | def infer(self, data, initial_proposal=None, full_output=False,**kwargs):
"""
Infer the model parameters, given the data.
auto_convergence=True,
walkers=100, burn=2000, sample=2000, minimum_sample=2000,
convergence_check_frequency=1000, a=2.0, threads=1,
"""
# Apply data masks now so we don't have to do it on the fly.
data, pixels_affected = self._apply_data_mask(data)
# Any channels / parameters to ignore?
matched_channels, missing_channels, ignore_parameters \
= self._match_channels_to_data(data)
parameters = [p for p in self.parameters if p not in ignore_parameters]
#parameters = list(set(self.parameters).difference(ignore_parameters))
logger.debug("Inferring {0} parameters: {1}".format(len(parameters),
", ".join(parameters)))
# What sampling behaviour will we have?
# - Auto-convergence:
# + Sample for `minimum_sample` (default 2000, 200 walkers)
# + Calculate the maximum exponential autocorrelation time for
# all parameters
# + For the rest of the chain, calculate the autocorrelation time
# + Ensure that the number of samples we have is more than
# `effectively_independent_samples` (default 100) times.
# - Specified convergence:
# + Burn for `burn` (default 2000) steps
# + Sample for `sample` (default 2000) steps
kwd = {
"auto_convergence": False, # TODO CHANGE ME
"walkers": 100,
"burn": 2000,
"sample": 2000,
# The minimum_sample, n_tau_exp_as_burn_in, minimum_eis are only
# used if auto_convergence is turned on.
"minimum_sample": 2000,
"maximum_sample": 100000,
"n_tau_exp_as_burn_in": 3,
"minimum_effective_independent_samples": 100,
"check_convergence_frequency": 1000,
"a": 2.0,
"threads": 1
}
# Update from the model, then update from any keyword arguments given.
kwd.update(self._configuration.get("infer", {}).copy())
kwd.update(**kwargs)
# Make some checks.
if kwd["walkers"] % 2 > 0 or kwd["walkers"] < 2 * len(parameters):
raise ValueError("the number of walkers must be an even number and "
"be at least twice the number of model parameters")
check_keywords = ["threads", "a"]
if kwd["auto_convergence"]:
logger.info("Convergence will be estimated automatically.")
check_keywords += ["minimum_sample", "check_convergence_frequency",
"minimum_effective_independent_samples", "n_tau_exp_as_burn_in",
"maximum_sample"]
else:
check_keywords += ["burn", "sample"]
logger.warn("No convergence checks will be done!")
logger.info("Burning for {0} steps and sampling for {1} with {2} "\
"walkers".format(kwd["burn"], kwd["sample"], kwd["walkers"]))
for keyword in check_keywords:
if kwd[keyword] < 1:
raise ValueError("keyword {} must be a positive value".format(
keyword))
# Check for non-standard proposal scales.
if kwd["a"] != 2.0:
logger.warn("Using proposal scale of {0:.2f}".format(kwd["a"]))
# If no initial proposal given, estimate the model parameters.
if initial_proposal is None:
initial_proposal = self.estimate(data)
# Initial proposal could be:
# - an array (N_walkers, N_dimensions)
# - a dictionary containing key/value pairs for the dimensions
if isinstance(initial_proposal, dict):
wavelengths_required = []
for channel, spectrum in zip(matched_channels, data):
if channel is None: continue
z = initial_proposal.get("z",
initial_proposal.get("z_{}".format(channel), 0))
wavelengths_required.append(
[spectrum.disp[0] * (1 - z), spectrum.disp[-1] * (1 - z)])
closest_point = [initial_proposal[p] \
for p in self.grid_points.dtype.names]
subset_bounds = self._initialise_approximator(
closest_point=closest_point,
wavelengths_required=wavelengths_required, force=True, **kwargs)
initial_proposal = self._initial_proposal_distribution(
parameters, initial_proposal, kwd["walkers"])
elif isinstance(initial_proposal, np.ndarray):
initial_proposal = np.atleast_2d(initial_proposal)
if initial_proposal.shape != (kwd["walkers"], len(parameters)):
raise ValueError("initial proposal must be an array of shape "\
"(N_parameters, N_walkers) ({0}, {1})".format(kwd["walkers"],
len(parameters)))
# Prepare the convolution functions.
self._create_convolution_functions(matched_channels, data, parameters)
# Create the sampler.
logger.info("Creating sampler with {0} walkers and {1} threads".format(
kwd["walkers"], kwd["threads"]))
debug = kwargs.get("debug", False)
sampler = emcee.EnsembleSampler(kwd["walkers"], len(parameters),
inference.ln_probability, a=kwd["a"], threads=kwd["threads"],
args=(parameters, self, data, debug),
kwargs={"matched_channels": matched_channels})
# Regardless of whether we automatically check for convergence or not,
# we will still need to burn in for some minimum amount of time.
if kwd["auto_convergence"]:
# Sample for `minimum_sample` period.
descr, iterations = "", kwd["minimum_sample"]
else:
# Sample for `burn` period
descr, iterations = "burn-in", kwd["burn"]
# Start sampling.
t_init = time()
acceptance_fractions = []
progress_bar = kwargs.get("__show_progress_bar", True)
sampler, init_acceptance_fractions, pos, lnprob, rstate, init_elapsed \
= self._sample(sampler, initial_proposal, iterations, descr=descr,
parameters=parameters, __show_progress_bar=progress_bar)
acceptance_fractions.append(init_acceptance_fractions)
# If we don't have to check for convergence, it's easy:
if not kwd["auto_convergence"]:
# Save the chain and log probabilities before we reset the chain.
burn, sample = kwd["burn"], kwd["sample"]
converged = None # we don't know!
burn_chains = sampler.chain
burn_ln_probabilities = sampler.lnprobability
# Reset the chain.
logger.debug("Resetting chain...")
sampler.reset()
# Sample the posterior.
sampler, prod_acceptance_fractions, pos, lnprob, rstate, t_elapsed \
= self._sample(sampler, pos, kwd["sample"], lnprob0=lnprob,
rstate0=rstate, descr="production", parameters=parameters,
__show_progress_bar=progress_bar)
production_chains = sampler.chain
production_ln_probabilities = sampler.lnprobability
acceptance_fractions.append(prod_acceptance_fractions)
else:
# Start checking for convergence at a frequency
# of check_convergence_frequency
last_state = [pos, lnprob, rstate]
converged, total_steps = False, 0 + iterations
min_eis_required = kwd["minimum_effective_independent_samples"]
while not converged and kwd["maximum_sample"] > total_steps:
# Check for convergence.
# Estimate the exponential autocorrelation time.
try:
tau_exp, rho, rho_max_fit \
= utils.estimate_tau_exp(sampler.chain)
except:
logger.exception("Exception occurred when trying to "
"estimate the exponential autocorrelation time:")
logger.info("To recover, we are temporarily setting tau_exp"
" to {0}".format(total_steps))
tau_exp = total_steps
logger.info("Estimated tau_exp at {0} is {1:.0f}".format(
total_steps, tau_exp))
# Grab everything n_tau_exp_as_burn_in times that.
burn = int(np.ceil(tau_exp)) * kwd["n_tau_exp_as_burn_in"]
sample = sampler.chain.shape[1] - burn
if 1 > sample:
logger.info("Sampler has not converged because {0}x the "
"estimated exponential autocorrelation time of {1:.0f}"
" is step {2}, and we are only at step {3}".format(
kwd["n_tau_exp_as_burn_in"], tau_exp, burn,
total_steps))
else:
# Calculate the integrated autocorrelation time in the
# remaining sample, for every parameter.
tau_int = utils.estimate_tau_int(sampler.chain[:, burn:])
# Calculate the effective number of independent samples in
# each parameter.
num_effective = (kwd["walkers"] * sample)/(2*tau_int)
logger.info("Effective number of independent samples in "
"each parameter:")
for parameter, n_eis in zip(parameters, num_effective):
logger.info("\t{0}: {1:.0f}".format(parameter, n_eis))
if num_effective.min() > min_eis_required:
# Converged.
converged = True
logger.info("Convergence achieved ({0:.0f} > {1:.0f})"\
.format(num_effective.min() > min_eis_required))
# Separate the samples into burn and production..
burn_chains = sampler.chain[:, :burn, :]
burn_ln_probabilities = sampler.lnprobability[:burn]
production_chains = sampler.chain[:, burn:, :]
production_ln_probabilities = sampler.lnprobability[burn:]
break
else:
# Nope.
logger.info("Sampler has not converged because it did "
"not meet the minimum number of effective "
"independent samples ({0:.0f})".format(kwd["n"]))
# Keep sampling.
iterations = kwd["check_convergence_frequency"]
logger.info("Trying for another {0} steps".format(iterations))
pos, lnprob, rstate = last_state
sampler, af, pos, lnprob, rstate, t_elapsed = self._sample(
sampler, pos, iterations, lnprob0=lnprob, rstate0=rstate,
descr="", parameters=parameters,
__show_progress_bar=progress_bar)
total_steps += iterations
acceptance_fractions.append(af)
last_state.extend(pos, lnprob, rstate)
del last_state[:3]
if not converged:
logger.warn("Maximum number of samples ({:.0f}) reached without"
"convergence!".format(kwd["maximum_sample"]))
logger.info("Total time elapsed: {0} seconds".format(time() - t_init))
if sampler.pool:
sampler.pool.close()
sampler.pool.join()
# Stack burn and production information together.
chains = np.hstack([burn_chains, production_chains])
lnprobability = np.hstack([
burn_ln_probabilities, production_ln_probabilities])
acceptance_fractions = np.hstack(acceptance_fractions)
chi_sq, dof, model_fluxes = self._chi_sq(dict(zip(parameters,
[np.percentile(chains[:, burn:, i], 50)
for i in range(len(parameters))])), data)
# Convert velocity scales.
symbol, scale, units = self._preferred_redshift_scale
labels = [] + parameters
scales = np.ones(len(parameters))
if symbol != "z":
for i, parameter in enumerate(parameters):
if parameter == "z" or parameter.startswith("z_"):
chains[:, :, i] *= scale
scales[i] = scale
if "_" in parameter:
labels[i] = "_".join([symbol, parameter.split("_")[1:]])
else:
labels[i] = symbol
logger.debug("Scaled {0} (now {1}) to units of {2}".format(
parameter, labels[i], units))
# Calculate MAP values and associated uncertainties.
theta = OrderedDict()
for i, label in enumerate(labels):
l, c, u = np.percentile(chains[:, burn:, i], [16, 50, 84])
theta[label] = (c, u-c, l-c)
# Re-arrange the chains to be in the same order as the model parameters.
indices = np.array([parameters.index(p) \
for p in self.parameters if p in parameters])
chains = chains[:, :, indices]
# Remove the convolution functions.
if not kwargs.get("__keep_convolution_functions", False):
self._destroy_convolution_functions()
if full_output:
metadata = {
"burn": burn,
"walkers": kwd["walkers"],
"sample": sample,
"parameters": labels,
"scales": scales,
"chi_sq": chi_sq,
"dof": dof
}
return (theta, chains, lnprobability, acceptance_fractions, sampler,
metadata)
return theta | python | def infer(self, data, initial_proposal=None, full_output=False,**kwargs):
"""
Infer the model parameters, given the data.
auto_convergence=True,
walkers=100, burn=2000, sample=2000, minimum_sample=2000,
convergence_check_frequency=1000, a=2.0, threads=1,
"""
# Apply data masks now so we don't have to do it on the fly.
data, pixels_affected = self._apply_data_mask(data)
# Any channels / parameters to ignore?
matched_channels, missing_channels, ignore_parameters \
= self._match_channels_to_data(data)
parameters = [p for p in self.parameters if p not in ignore_parameters]
#parameters = list(set(self.parameters).difference(ignore_parameters))
logger.debug("Inferring {0} parameters: {1}".format(len(parameters),
", ".join(parameters)))
# What sampling behaviour will we have?
# - Auto-convergence:
# + Sample for `minimum_sample` (default 2000, 200 walkers)
# + Calculate the maximum exponential autocorrelation time for
# all parameters
# + For the rest of the chain, calculate the autocorrelation time
# + Ensure that the number of samples we have is more than
# `effectively_independent_samples` (default 100) times.
# - Specified convergence:
# + Burn for `burn` (default 2000) steps
# + Sample for `sample` (default 2000) steps
kwd = {
"auto_convergence": False, # TODO CHANGE ME
"walkers": 100,
"burn": 2000,
"sample": 2000,
# The minimum_sample, n_tau_exp_as_burn_in, minimum_eis are only
# used if auto_convergence is turned on.
"minimum_sample": 2000,
"maximum_sample": 100000,
"n_tau_exp_as_burn_in": 3,
"minimum_effective_independent_samples": 100,
"check_convergence_frequency": 1000,
"a": 2.0,
"threads": 1
}
# Update from the model, then update from any keyword arguments given.
kwd.update(self._configuration.get("infer", {}).copy())
kwd.update(**kwargs)
# Make some checks.
if kwd["walkers"] % 2 > 0 or kwd["walkers"] < 2 * len(parameters):
raise ValueError("the number of walkers must be an even number and "
"be at least twice the number of model parameters")
check_keywords = ["threads", "a"]
if kwd["auto_convergence"]:
logger.info("Convergence will be estimated automatically.")
check_keywords += ["minimum_sample", "check_convergence_frequency",
"minimum_effective_independent_samples", "n_tau_exp_as_burn_in",
"maximum_sample"]
else:
check_keywords += ["burn", "sample"]
logger.warn("No convergence checks will be done!")
logger.info("Burning for {0} steps and sampling for {1} with {2} "\
"walkers".format(kwd["burn"], kwd["sample"], kwd["walkers"]))
for keyword in check_keywords:
if kwd[keyword] < 1:
raise ValueError("keyword {} must be a positive value".format(
keyword))
# Check for non-standard proposal scales.
if kwd["a"] != 2.0:
logger.warn("Using proposal scale of {0:.2f}".format(kwd["a"]))
# If no initial proposal given, estimate the model parameters.
if initial_proposal is None:
initial_proposal = self.estimate(data)
# Initial proposal could be:
# - an array (N_walkers, N_dimensions)
# - a dictionary containing key/value pairs for the dimensions
if isinstance(initial_proposal, dict):
wavelengths_required = []
for channel, spectrum in zip(matched_channels, data):
if channel is None: continue
z = initial_proposal.get("z",
initial_proposal.get("z_{}".format(channel), 0))
wavelengths_required.append(
[spectrum.disp[0] * (1 - z), spectrum.disp[-1] * (1 - z)])
closest_point = [initial_proposal[p] \
for p in self.grid_points.dtype.names]
subset_bounds = self._initialise_approximator(
closest_point=closest_point,
wavelengths_required=wavelengths_required, force=True, **kwargs)
initial_proposal = self._initial_proposal_distribution(
parameters, initial_proposal, kwd["walkers"])
elif isinstance(initial_proposal, np.ndarray):
initial_proposal = np.atleast_2d(initial_proposal)
if initial_proposal.shape != (kwd["walkers"], len(parameters)):
raise ValueError("initial proposal must be an array of shape "\
"(N_parameters, N_walkers) ({0}, {1})".format(kwd["walkers"],
len(parameters)))
# Prepare the convolution functions.
self._create_convolution_functions(matched_channels, data, parameters)
# Create the sampler.
logger.info("Creating sampler with {0} walkers and {1} threads".format(
kwd["walkers"], kwd["threads"]))
debug = kwargs.get("debug", False)
sampler = emcee.EnsembleSampler(kwd["walkers"], len(parameters),
inference.ln_probability, a=kwd["a"], threads=kwd["threads"],
args=(parameters, self, data, debug),
kwargs={"matched_channels": matched_channels})
# Regardless of whether we automatically check for convergence or not,
# we will still need to burn in for some minimum amount of time.
if kwd["auto_convergence"]:
# Sample for `minimum_sample` period.
descr, iterations = "", kwd["minimum_sample"]
else:
# Sample for `burn` period
descr, iterations = "burn-in", kwd["burn"]
# Start sampling.
t_init = time()
acceptance_fractions = []
progress_bar = kwargs.get("__show_progress_bar", True)
sampler, init_acceptance_fractions, pos, lnprob, rstate, init_elapsed \
= self._sample(sampler, initial_proposal, iterations, descr=descr,
parameters=parameters, __show_progress_bar=progress_bar)
acceptance_fractions.append(init_acceptance_fractions)
# If we don't have to check for convergence, it's easy:
if not kwd["auto_convergence"]:
# Save the chain and log probabilities before we reset the chain.
burn, sample = kwd["burn"], kwd["sample"]
converged = None # we don't know!
burn_chains = sampler.chain
burn_ln_probabilities = sampler.lnprobability
# Reset the chain.
logger.debug("Resetting chain...")
sampler.reset()
# Sample the posterior.
sampler, prod_acceptance_fractions, pos, lnprob, rstate, t_elapsed \
= self._sample(sampler, pos, kwd["sample"], lnprob0=lnprob,
rstate0=rstate, descr="production", parameters=parameters,
__show_progress_bar=progress_bar)
production_chains = sampler.chain
production_ln_probabilities = sampler.lnprobability
acceptance_fractions.append(prod_acceptance_fractions)
else:
# Start checking for convergence at a frequency
# of check_convergence_frequency
last_state = [pos, lnprob, rstate]
converged, total_steps = False, 0 + iterations
min_eis_required = kwd["minimum_effective_independent_samples"]
while not converged and kwd["maximum_sample"] > total_steps:
# Check for convergence.
# Estimate the exponential autocorrelation time.
try:
tau_exp, rho, rho_max_fit \
= utils.estimate_tau_exp(sampler.chain)
except:
logger.exception("Exception occurred when trying to "
"estimate the exponential autocorrelation time:")
logger.info("To recover, we are temporarily setting tau_exp"
" to {0}".format(total_steps))
tau_exp = total_steps
logger.info("Estimated tau_exp at {0} is {1:.0f}".format(
total_steps, tau_exp))
# Grab everything n_tau_exp_as_burn_in times that.
burn = int(np.ceil(tau_exp)) * kwd["n_tau_exp_as_burn_in"]
sample = sampler.chain.shape[1] - burn
if 1 > sample:
logger.info("Sampler has not converged because {0}x the "
"estimated exponential autocorrelation time of {1:.0f}"
" is step {2}, and we are only at step {3}".format(
kwd["n_tau_exp_as_burn_in"], tau_exp, burn,
total_steps))
else:
# Calculate the integrated autocorrelation time in the
# remaining sample, for every parameter.
tau_int = utils.estimate_tau_int(sampler.chain[:, burn:])
# Calculate the effective number of independent samples in
# each parameter.
num_effective = (kwd["walkers"] * sample)/(2*tau_int)
logger.info("Effective number of independent samples in "
"each parameter:")
for parameter, n_eis in zip(parameters, num_effective):
logger.info("\t{0}: {1:.0f}".format(parameter, n_eis))
if num_effective.min() > min_eis_required:
# Converged.
converged = True
logger.info("Convergence achieved ({0:.0f} > {1:.0f})"\
.format(num_effective.min() > min_eis_required))
# Separate the samples into burn and production..
burn_chains = sampler.chain[:, :burn, :]
burn_ln_probabilities = sampler.lnprobability[:burn]
production_chains = sampler.chain[:, burn:, :]
production_ln_probabilities = sampler.lnprobability[burn:]
break
else:
# Nope.
logger.info("Sampler has not converged because it did "
"not meet the minimum number of effective "
"independent samples ({0:.0f})".format(kwd["n"]))
# Keep sampling.
iterations = kwd["check_convergence_frequency"]
logger.info("Trying for another {0} steps".format(iterations))
pos, lnprob, rstate = last_state
sampler, af, pos, lnprob, rstate, t_elapsed = self._sample(
sampler, pos, iterations, lnprob0=lnprob, rstate0=rstate,
descr="", parameters=parameters,
__show_progress_bar=progress_bar)
total_steps += iterations
acceptance_fractions.append(af)
last_state.extend(pos, lnprob, rstate)
del last_state[:3]
if not converged:
logger.warn("Maximum number of samples ({:.0f}) reached without"
"convergence!".format(kwd["maximum_sample"]))
logger.info("Total time elapsed: {0} seconds".format(time() - t_init))
if sampler.pool:
sampler.pool.close()
sampler.pool.join()
# Stack burn and production information together.
chains = np.hstack([burn_chains, production_chains])
lnprobability = np.hstack([
burn_ln_probabilities, production_ln_probabilities])
acceptance_fractions = np.hstack(acceptance_fractions)
chi_sq, dof, model_fluxes = self._chi_sq(dict(zip(parameters,
[np.percentile(chains[:, burn:, i], 50)
for i in range(len(parameters))])), data)
# Convert velocity scales.
symbol, scale, units = self._preferred_redshift_scale
labels = [] + parameters
scales = np.ones(len(parameters))
if symbol != "z":
for i, parameter in enumerate(parameters):
if parameter == "z" or parameter.startswith("z_"):
chains[:, :, i] *= scale
scales[i] = scale
if "_" in parameter:
labels[i] = "_".join([symbol, parameter.split("_")[1:]])
else:
labels[i] = symbol
logger.debug("Scaled {0} (now {1}) to units of {2}".format(
parameter, labels[i], units))
# Calculate MAP values and associated uncertainties.
theta = OrderedDict()
for i, label in enumerate(labels):
l, c, u = np.percentile(chains[:, burn:, i], [16, 50, 84])
theta[label] = (c, u-c, l-c)
# Re-arrange the chains to be in the same order as the model parameters.
indices = np.array([parameters.index(p) \
for p in self.parameters if p in parameters])
chains = chains[:, :, indices]
# Remove the convolution functions.
if not kwargs.get("__keep_convolution_functions", False):
self._destroy_convolution_functions()
if full_output:
metadata = {
"burn": burn,
"walkers": kwd["walkers"],
"sample": sample,
"parameters": labels,
"scales": scales,
"chi_sq": chi_sq,
"dof": dof
}
return (theta, chains, lnprobability, acceptance_fractions, sampler,
metadata)
return theta | ['def', 'infer', '(', 'self', ',', 'data', ',', 'initial_proposal', '=', 'None', ',', 'full_output', '=', 'False', ',', '*', '*', 'kwargs', ')', ':', "# Apply data masks now so we don't have to do it on the fly.", 'data', ',', 'pixels_affected', '=', 'self', '.', '_apply_data_mask', '(', 'data', ')', '# Any channels / parameters to ignore?', 'matched_channels', ',', 'missing_channels', ',', 'ignore_parameters', '=', 'self', '.', '_match_channels_to_data', '(', 'data', ')', 'parameters', '=', '[', 'p', 'for', 'p', 'in', 'self', '.', 'parameters', 'if', 'p', 'not', 'in', 'ignore_parameters', ']', '#parameters = list(set(self.parameters).difference(ignore_parameters))', 'logger', '.', 'debug', '(', '"Inferring {0} parameters: {1}"', '.', 'format', '(', 'len', '(', 'parameters', ')', ',', '", "', '.', 'join', '(', 'parameters', ')', ')', ')', '# What sampling behaviour will we have?', '# - Auto-convergence:', '# + Sample for `minimum_sample` (default 2000, 200 walkers)', '# + Calculate the maximum exponential autocorrelation time for', '# all parameters', '# + For the rest of the chain, calculate the autocorrelation time', '# + Ensure that the number of samples we have is more than ', '# `effectively_independent_samples` (default 100) times.', '# - Specified convergence:', '# + Burn for `burn` (default 2000) steps', '# + Sample for `sample` (default 2000) steps', 'kwd', '=', '{', '"auto_convergence"', ':', 'False', ',', '# TODO CHANGE ME', '"walkers"', ':', '100', ',', '"burn"', ':', '2000', ',', '"sample"', ':', '2000', ',', '# The minimum_sample, n_tau_exp_as_burn_in, minimum_eis are only', '# used if auto_convergence is turned on.', '"minimum_sample"', ':', '2000', ',', '"maximum_sample"', ':', '100000', ',', '"n_tau_exp_as_burn_in"', ':', '3', ',', '"minimum_effective_independent_samples"', ':', '100', ',', '"check_convergence_frequency"', ':', '1000', ',', '"a"', ':', '2.0', ',', '"threads"', ':', '1', '}', '# Update from the model, then update from any keyword arguments given.', 'kwd', '.', 'update', '(', 'self', '.', '_configuration', '.', 'get', '(', '"infer"', ',', '{', '}', ')', '.', 'copy', '(', ')', ')', 'kwd', '.', 'update', '(', '*', '*', 'kwargs', ')', '# Make some checks.', 'if', 'kwd', '[', '"walkers"', ']', '%', '2', '>', '0', 'or', 'kwd', '[', '"walkers"', ']', '<', '2', '*', 'len', '(', 'parameters', ')', ':', 'raise', 'ValueError', '(', '"the number of walkers must be an even number and "', '"be at least twice the number of model parameters"', ')', 'check_keywords', '=', '[', '"threads"', ',', '"a"', ']', 'if', 'kwd', '[', '"auto_convergence"', ']', ':', 'logger', '.', 'info', '(', '"Convergence will be estimated automatically."', ')', 'check_keywords', '+=', '[', '"minimum_sample"', ',', '"check_convergence_frequency"', ',', '"minimum_effective_independent_samples"', ',', '"n_tau_exp_as_burn_in"', ',', '"maximum_sample"', ']', 'else', ':', 'check_keywords', '+=', '[', '"burn"', ',', '"sample"', ']', 'logger', '.', 'warn', '(', '"No convergence checks will be done!"', ')', 'logger', '.', 'info', '(', '"Burning for {0} steps and sampling for {1} with {2} "', '"walkers"', '.', 'format', '(', 'kwd', '[', '"burn"', ']', ',', 'kwd', '[', '"sample"', ']', ',', 'kwd', '[', '"walkers"', ']', ')', ')', 'for', 'keyword', 'in', 'check_keywords', ':', 'if', 'kwd', '[', 'keyword', ']', '<', '1', ':', 'raise', 'ValueError', '(', '"keyword {} must be a positive value"', '.', 'format', '(', 'keyword', ')', ')', '# Check for non-standard proposal scales.', 'if', 'kwd', '[', '"a"', ']', '!=', '2.0', ':', 'logger', '.', 'warn', '(', '"Using proposal scale of {0:.2f}"', '.', 'format', '(', 'kwd', '[', '"a"', ']', ')', ')', '# If no initial proposal given, estimate the model parameters.', 'if', 'initial_proposal', 'is', 'None', ':', 'initial_proposal', '=', 'self', '.', 'estimate', '(', 'data', ')', '# Initial proposal could be:', '# - an array (N_walkers, N_dimensions)', '# - a dictionary containing key/value pairs for the dimensions', 'if', 'isinstance', '(', 'initial_proposal', ',', 'dict', ')', ':', 'wavelengths_required', '=', '[', ']', 'for', 'channel', ',', 'spectrum', 'in', 'zip', '(', 'matched_channels', ',', 'data', ')', ':', 'if', 'channel', 'is', 'None', ':', 'continue', 'z', '=', 'initial_proposal', '.', 'get', '(', '"z"', ',', 'initial_proposal', '.', 'get', '(', '"z_{}"', '.', 'format', '(', 'channel', ')', ',', '0', ')', ')', 'wavelengths_required', '.', 'append', '(', '[', 'spectrum', '.', 'disp', '[', '0', ']', '*', '(', '1', '-', 'z', ')', ',', 'spectrum', '.', 'disp', '[', '-', '1', ']', '*', '(', '1', '-', 'z', ')', ']', ')', 'closest_point', '=', '[', 'initial_proposal', '[', 'p', ']', 'for', 'p', 'in', 'self', '.', 'grid_points', '.', 'dtype', '.', 'names', ']', 'subset_bounds', '=', 'self', '.', '_initialise_approximator', '(', 'closest_point', '=', 'closest_point', ',', 'wavelengths_required', '=', 'wavelengths_required', ',', 'force', '=', 'True', ',', '*', '*', 'kwargs', ')', 'initial_proposal', '=', 'self', '.', '_initial_proposal_distribution', '(', 'parameters', ',', 'initial_proposal', ',', 'kwd', '[', '"walkers"', ']', ')', 'elif', 'isinstance', '(', 'initial_proposal', ',', 'np', '.', 'ndarray', ')', ':', 'initial_proposal', '=', 'np', '.', 'atleast_2d', '(', 'initial_proposal', ')', 'if', 'initial_proposal', '.', 'shape', '!=', '(', 'kwd', '[', '"walkers"', ']', ',', 'len', '(', 'parameters', ')', ')', ':', 'raise', 'ValueError', '(', '"initial proposal must be an array of shape "', '"(N_parameters, N_walkers) ({0}, {1})"', '.', 'format', '(', 'kwd', '[', '"walkers"', ']', ',', 'len', '(', 'parameters', ')', ')', ')', '# Prepare the convolution functions.', 'self', '.', '_create_convolution_functions', '(', 'matched_channels', ',', 'data', ',', 'parameters', ')', '# Create the sampler.', 'logger', '.', 'info', '(', '"Creating sampler with {0} walkers and {1} threads"', '.', 'format', '(', 'kwd', '[', '"walkers"', ']', ',', 'kwd', '[', '"threads"', ']', ')', ')', 'debug', '=', 'kwargs', '.', 'get', '(', '"debug"', ',', 'False', ')', 'sampler', '=', 'emcee', '.', 'EnsembleSampler', '(', 'kwd', '[', '"walkers"', ']', ',', 'len', '(', 'parameters', ')', ',', 'inference', '.', 'ln_probability', ',', 'a', '=', 'kwd', '[', '"a"', ']', ',', 'threads', '=', 'kwd', '[', '"threads"', ']', ',', 'args', '=', '(', 'parameters', ',', 'self', ',', 'data', ',', 'debug', ')', ',', 'kwargs', '=', '{', '"matched_channels"', ':', 'matched_channels', '}', ')', '# Regardless of whether we automatically check for convergence or not,', '# we will still need to burn in for some minimum amount of time.', 'if', 'kwd', '[', '"auto_convergence"', ']', ':', '# Sample for `minimum_sample` period.', 'descr', ',', 'iterations', '=', '""', ',', 'kwd', '[', '"minimum_sample"', ']', 'else', ':', '# Sample for `burn` period', 'descr', ',', 'iterations', '=', '"burn-in"', ',', 'kwd', '[', '"burn"', ']', '# Start sampling.', 't_init', '=', 'time', '(', ')', 'acceptance_fractions', '=', '[', ']', 'progress_bar', '=', 'kwargs', '.', 'get', '(', '"__show_progress_bar"', ',', 'True', ')', 'sampler', ',', 'init_acceptance_fractions', ',', 'pos', ',', 'lnprob', ',', 'rstate', ',', 'init_elapsed', '=', 'self', '.', '_sample', '(', 'sampler', ',', 'initial_proposal', ',', 'iterations', ',', 'descr', '=', 'descr', ',', 'parameters', '=', 'parameters', ',', '__show_progress_bar', '=', 'progress_bar', ')', 'acceptance_fractions', '.', 'append', '(', 'init_acceptance_fractions', ')', "# If we don't have to check for convergence, it's easy:", 'if', 'not', 'kwd', '[', '"auto_convergence"', ']', ':', '# Save the chain and log probabilities before we reset the chain.', 'burn', ',', 'sample', '=', 'kwd', '[', '"burn"', ']', ',', 'kwd', '[', '"sample"', ']', 'converged', '=', 'None', "# we don't know!", 'burn_chains', '=', 'sampler', '.', 'chain', 'burn_ln_probabilities', '=', 'sampler', '.', 'lnprobability', '# Reset the chain.', 'logger', '.', 'debug', '(', '"Resetting chain..."', ')', 'sampler', '.', 'reset', '(', ')', '# Sample the posterior.', 'sampler', ',', 'prod_acceptance_fractions', ',', 'pos', ',', 'lnprob', ',', 'rstate', ',', 't_elapsed', '=', 'self', '.', '_sample', '(', 'sampler', ',', 'pos', ',', 'kwd', '[', '"sample"', ']', ',', 'lnprob0', '=', 'lnprob', ',', 'rstate0', '=', 'rstate', ',', 'descr', '=', '"production"', ',', 'parameters', '=', 'parameters', ',', '__show_progress_bar', '=', 'progress_bar', ')', 'production_chains', '=', 'sampler', '.', 'chain', 'production_ln_probabilities', '=', 'sampler', '.', 'lnprobability', 'acceptance_fractions', '.', 'append', '(', 'prod_acceptance_fractions', ')', 'else', ':', '# Start checking for convergence at a frequency', '# of check_convergence_frequency', 'last_state', '=', '[', 'pos', ',', 'lnprob', ',', 'rstate', ']', 'converged', ',', 'total_steps', '=', 'False', ',', '0', '+', 'iterations', 'min_eis_required', '=', 'kwd', '[', '"minimum_effective_independent_samples"', ']', 'while', 'not', 'converged', 'and', 'kwd', '[', '"maximum_sample"', ']', '>', 'total_steps', ':', '# Check for convergence.', '# Estimate the exponential autocorrelation time.', 'try', ':', 'tau_exp', ',', 'rho', ',', 'rho_max_fit', '=', 'utils', '.', 'estimate_tau_exp', '(', 'sampler', '.', 'chain', ')', 'except', ':', 'logger', '.', 'exception', '(', '"Exception occurred when trying to "', '"estimate the exponential autocorrelation time:"', ')', 'logger', '.', 'info', '(', '"To recover, we are temporarily setting tau_exp"', '" to {0}"', '.', 'format', '(', 'total_steps', ')', ')', 'tau_exp', '=', 'total_steps', 'logger', '.', 'info', '(', '"Estimated tau_exp at {0} is {1:.0f}"', '.', 'format', '(', 'total_steps', ',', 'tau_exp', ')', ')', '# Grab everything n_tau_exp_as_burn_in times that.', 'burn', '=', 'int', '(', 'np', '.', 'ceil', '(', 'tau_exp', ')', ')', '*', 'kwd', '[', '"n_tau_exp_as_burn_in"', ']', 'sample', '=', 'sampler', '.', 'chain', '.', 'shape', '[', '1', ']', '-', 'burn', 'if', '1', '>', 'sample', ':', 'logger', '.', 'info', '(', '"Sampler has not converged because {0}x the "', '"estimated exponential autocorrelation time of {1:.0f}"', '" is step {2}, and we are only at step {3}"', '.', 'format', '(', 'kwd', '[', '"n_tau_exp_as_burn_in"', ']', ',', 'tau_exp', ',', 'burn', ',', 'total_steps', ')', ')', 'else', ':', '# Calculate the integrated autocorrelation time in the ', '# remaining sample, for every parameter.', 'tau_int', '=', 'utils', '.', 'estimate_tau_int', '(', 'sampler', '.', 'chain', '[', ':', ',', 'burn', ':', ']', ')', '# Calculate the effective number of independent samples in ', '# each parameter.', 'num_effective', '=', '(', 'kwd', '[', '"walkers"', ']', '*', 'sample', ')', '/', '(', '2', '*', 'tau_int', ')', 'logger', '.', 'info', '(', '"Effective number of independent samples in "', '"each parameter:"', ')', 'for', 'parameter', ',', 'n_eis', 'in', 'zip', '(', 'parameters', ',', 'num_effective', ')', ':', 'logger', '.', 'info', '(', '"\\t{0}: {1:.0f}"', '.', 'format', '(', 'parameter', ',', 'n_eis', ')', ')', 'if', 'num_effective', '.', 'min', '(', ')', '>', 'min_eis_required', ':', '# Converged.', 'converged', '=', 'True', 'logger', '.', 'info', '(', '"Convergence achieved ({0:.0f} > {1:.0f})"', '.', 'format', '(', 'num_effective', '.', 'min', '(', ')', '>', 'min_eis_required', ')', ')', '# Separate the samples into burn and production..', 'burn_chains', '=', 'sampler', '.', 'chain', '[', ':', ',', ':', 'burn', ',', ':', ']', 'burn_ln_probabilities', '=', 'sampler', '.', 'lnprobability', '[', ':', 'burn', ']', 'production_chains', '=', 'sampler', '.', 'chain', '[', ':', ',', 'burn', ':', ',', ':', ']', 'production_ln_probabilities', '=', 'sampler', '.', 'lnprobability', '[', 'burn', ':', ']', 'break', 'else', ':', '# Nope.', 'logger', '.', 'info', '(', '"Sampler has not converged because it did "', '"not meet the minimum number of effective "', '"independent samples ({0:.0f})"', '.', 'format', '(', 'kwd', '[', '"n"', ']', ')', ')', '# Keep sampling.', 'iterations', '=', 'kwd', '[', '"check_convergence_frequency"', ']', 'logger', '.', 'info', '(', '"Trying for another {0} steps"', '.', 'format', '(', 'iterations', ')', ')', 'pos', ',', 'lnprob', ',', 'rstate', '=', 'last_state', 'sampler', ',', 'af', ',', 'pos', ',', 'lnprob', ',', 'rstate', ',', 't_elapsed', '=', 'self', '.', '_sample', '(', 'sampler', ',', 'pos', ',', 'iterations', ',', 'lnprob0', '=', 'lnprob', ',', 'rstate0', '=', 'rstate', ',', 'descr', '=', '""', ',', 'parameters', '=', 'parameters', ',', '__show_progress_bar', '=', 'progress_bar', ')', 'total_steps', '+=', 'iterations', 'acceptance_fractions', '.', 'append', '(', 'af', ')', 'last_state', '.', 'extend', '(', 'pos', ',', 'lnprob', ',', 'rstate', ')', 'del', 'last_state', '[', ':', '3', ']', 'if', 'not', 'converged', ':', 'logger', '.', 'warn', '(', '"Maximum number of samples ({:.0f}) reached without"', '"convergence!"', '.', 'format', '(', 'kwd', '[', '"maximum_sample"', ']', ')', ')', 'logger', '.', 'info', '(', '"Total time elapsed: {0} seconds"', '.', 'format', '(', 'time', '(', ')', '-', 't_init', ')', ')', 'if', 'sampler', '.', 'pool', ':', 'sampler', '.', 'pool', '.', 'close', '(', ')', 'sampler', '.', 'pool', '.', 'join', '(', ')', '# Stack burn and production information together.', 'chains', '=', 'np', '.', 'hstack', '(', '[', 'burn_chains', ',', 'production_chains', ']', ')', 'lnprobability', '=', 'np', '.', 'hstack', '(', '[', 'burn_ln_probabilities', ',', 'production_ln_probabilities', ']', ')', 'acceptance_fractions', '=', 'np', '.', 'hstack', '(', 'acceptance_fractions', ')', 'chi_sq', ',', 'dof', ',', 'model_fluxes', '=', 'self', '.', '_chi_sq', '(', 'dict', '(', 'zip', '(', 'parameters', ',', '[', 'np', '.', 'percentile', '(', 'chains', '[', ':', ',', 'burn', ':', ',', 'i', ']', ',', '50', ')', 'for', 'i', 'in', 'range', '(', 'len', '(', 'parameters', ')', ')', ']', ')', ')', ',', 'data', ')', '# Convert velocity scales.', 'symbol', ',', 'scale', ',', 'units', '=', 'self', '.', '_preferred_redshift_scale', 'labels', '=', '[', ']', '+', 'parameters', 'scales', '=', 'np', '.', 'ones', '(', 'len', '(', 'parameters', ')', ')', 'if', 'symbol', '!=', '"z"', ':', 'for', 'i', ',', 'parameter', 'in', 'enumerate', '(', 'parameters', ')', ':', 'if', 'parameter', '==', '"z"', 'or', 'parameter', '.', 'startswith', '(', '"z_"', ')', ':', 'chains', '[', ':', ',', ':', ',', 'i', ']', '*=', 'scale', 'scales', '[', 'i', ']', '=', 'scale', 'if', '"_"', 'in', 'parameter', ':', 'labels', '[', 'i', ']', '=', '"_"', '.', 'join', '(', '[', 'symbol', ',', 'parameter', '.', 'split', '(', '"_"', ')', '[', '1', ':', ']', ']', ')', 'else', ':', 'labels', '[', 'i', ']', '=', 'symbol', 'logger', '.', 'debug', '(', '"Scaled {0} (now {1}) to units of {2}"', '.', 'format', '(', 'parameter', ',', 'labels', '[', 'i', ']', ',', 'units', ')', ')', '# Calculate MAP values and associated uncertainties.', 'theta', '=', 'OrderedDict', '(', ')', 'for', 'i', ',', 'label', 'in', 'enumerate', '(', 'labels', ')', ':', 'l', ',', 'c', ',', 'u', '=', 'np', '.', 'percentile', '(', 'chains', '[', ':', ',', 'burn', ':', ',', 'i', ']', ',', '[', '16', ',', '50', ',', '84', ']', ')', 'theta', '[', 'label', ']', '=', '(', 'c', ',', 'u', '-', 'c', ',', 'l', '-', 'c', ')', '# Re-arrange the chains to be in the same order as the model parameters.', 'indices', '=', 'np', '.', 'array', '(', '[', 'parameters', '.', 'index', '(', 'p', ')', 'for', 'p', 'in', 'self', '.', 'parameters', 'if', 'p', 'in', 'parameters', ']', ')', 'chains', '=', 'chains', '[', ':', ',', ':', ',', 'indices', ']', '# Remove the convolution functions.', 'if', 'not', 'kwargs', '.', 'get', '(', '"__keep_convolution_functions"', ',', 'False', ')', ':', 'self', '.', '_destroy_convolution_functions', '(', ')', 'if', 'full_output', ':', 'metadata', '=', '{', '"burn"', ':', 'burn', ',', '"walkers"', ':', 'kwd', '[', '"walkers"', ']', ',', '"sample"', ':', 'sample', ',', '"parameters"', ':', 'labels', ',', '"scales"', ':', 'scales', ',', '"chi_sq"', ':', 'chi_sq', ',', '"dof"', ':', 'dof', '}', 'return', '(', 'theta', ',', 'chains', ',', 'lnprobability', ',', 'acceptance_fractions', ',', 'sampler', ',', 'metadata', ')', 'return', 'theta'] | Infer the model parameters, given the data.
auto_convergence=True,
walkers=100, burn=2000, sample=2000, minimum_sample=2000,
convergence_check_frequency=1000, a=2.0, threads=1, | ['Infer', 'the', 'model', 'parameters', 'given', 'the', 'data', '.', 'auto_convergence', '=', 'True', 'walkers', '=', '100', 'burn', '=', '2000', 'sample', '=', '2000', 'minimum_sample', '=', '2000', 'convergence_check_frequency', '=', '1000', 'a', '=', '2', '.', '0', 'threads', '=', '1'] | train | https://github.com/andycasey/sick/blob/6c37686182794c4cafea45abf7062b30b789b1a2/sick/models/model.py#L261-L578 |
1,320 | saltstack/salt | salt/daemons/masterapi.py | access_keys | def access_keys(opts):
'''
A key needs to be placed in the filesystem with permissions 0400 so
clients are required to run as root.
'''
# TODO: Need a way to get all available users for systems not supported by pwd module.
# For now users pattern matching will not work for publisher_acl.
keys = {}
publisher_acl = opts['publisher_acl']
acl_users = set(publisher_acl.keys())
if opts.get('user'):
acl_users.add(opts['user'])
acl_users.add(salt.utils.user.get_user())
for user in acl_users:
log.info('Preparing the %s key for local communication', user)
key = mk_key(opts, user)
if key is not None:
keys[user] = key
# Check other users matching ACL patterns
if opts['client_acl_verify'] and HAS_PWD:
log.profile('Beginning pwd.getpwall() call in masterapi access_keys function')
for user in pwd.getpwall():
user = user.pw_name
if user not in keys and salt.utils.stringutils.check_whitelist_blacklist(user, whitelist=acl_users):
keys[user] = mk_key(opts, user)
log.profile('End pwd.getpwall() call in masterapi access_keys function')
return keys | python | def access_keys(opts):
'''
A key needs to be placed in the filesystem with permissions 0400 so
clients are required to run as root.
'''
# TODO: Need a way to get all available users for systems not supported by pwd module.
# For now users pattern matching will not work for publisher_acl.
keys = {}
publisher_acl = opts['publisher_acl']
acl_users = set(publisher_acl.keys())
if opts.get('user'):
acl_users.add(opts['user'])
acl_users.add(salt.utils.user.get_user())
for user in acl_users:
log.info('Preparing the %s key for local communication', user)
key = mk_key(opts, user)
if key is not None:
keys[user] = key
# Check other users matching ACL patterns
if opts['client_acl_verify'] and HAS_PWD:
log.profile('Beginning pwd.getpwall() call in masterapi access_keys function')
for user in pwd.getpwall():
user = user.pw_name
if user not in keys and salt.utils.stringutils.check_whitelist_blacklist(user, whitelist=acl_users):
keys[user] = mk_key(opts, user)
log.profile('End pwd.getpwall() call in masterapi access_keys function')
return keys | ['def', 'access_keys', '(', 'opts', ')', ':', '# TODO: Need a way to get all available users for systems not supported by pwd module.', '# For now users pattern matching will not work for publisher_acl.', 'keys', '=', '{', '}', 'publisher_acl', '=', 'opts', '[', "'publisher_acl'", ']', 'acl_users', '=', 'set', '(', 'publisher_acl', '.', 'keys', '(', ')', ')', 'if', 'opts', '.', 'get', '(', "'user'", ')', ':', 'acl_users', '.', 'add', '(', 'opts', '[', "'user'", ']', ')', 'acl_users', '.', 'add', '(', 'salt', '.', 'utils', '.', 'user', '.', 'get_user', '(', ')', ')', 'for', 'user', 'in', 'acl_users', ':', 'log', '.', 'info', '(', "'Preparing the %s key for local communication'", ',', 'user', ')', 'key', '=', 'mk_key', '(', 'opts', ',', 'user', ')', 'if', 'key', 'is', 'not', 'None', ':', 'keys', '[', 'user', ']', '=', 'key', '# Check other users matching ACL patterns', 'if', 'opts', '[', "'client_acl_verify'", ']', 'and', 'HAS_PWD', ':', 'log', '.', 'profile', '(', "'Beginning pwd.getpwall() call in masterapi access_keys function'", ')', 'for', 'user', 'in', 'pwd', '.', 'getpwall', '(', ')', ':', 'user', '=', 'user', '.', 'pw_name', 'if', 'user', 'not', 'in', 'keys', 'and', 'salt', '.', 'utils', '.', 'stringutils', '.', 'check_whitelist_blacklist', '(', 'user', ',', 'whitelist', '=', 'acl_users', ')', ':', 'keys', '[', 'user', ']', '=', 'mk_key', '(', 'opts', ',', 'user', ')', 'log', '.', 'profile', '(', "'End pwd.getpwall() call in masterapi access_keys function'", ')', 'return', 'keys'] | A key needs to be placed in the filesystem with permissions 0400 so
clients are required to run as root. | ['A', 'key', 'needs', 'to', 'be', 'placed', 'in', 'the', 'filesystem', 'with', 'permissions', '0400', 'so', 'clients', 'are', 'required', 'to', 'run', 'as', 'root', '.'] | train | https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/daemons/masterapi.py#L259-L287 |
1,321 | molmod/molmod | molmod/graphs.py | EqualPattern.compare | def compare(self, vertex0, vertex1, subject_graph):
"""Returns true when the two vertices are of the same kind"""
return (
self.pattern_graph.vertex_fingerprints[vertex0] ==
subject_graph.vertex_fingerprints[vertex1]
).all() | python | def compare(self, vertex0, vertex1, subject_graph):
"""Returns true when the two vertices are of the same kind"""
return (
self.pattern_graph.vertex_fingerprints[vertex0] ==
subject_graph.vertex_fingerprints[vertex1]
).all() | ['def', 'compare', '(', 'self', ',', 'vertex0', ',', 'vertex1', ',', 'subject_graph', ')', ':', 'return', '(', 'self', '.', 'pattern_graph', '.', 'vertex_fingerprints', '[', 'vertex0', ']', '==', 'subject_graph', '.', 'vertex_fingerprints', '[', 'vertex1', ']', ')', '.', 'all', '(', ')'] | Returns true when the two vertices are of the same kind | ['Returns', 'true', 'when', 'the', 'two', 'vertices', 'are', 'of', 'the', 'same', 'kind'] | train | https://github.com/molmod/molmod/blob/a7b5b4364ed514ad4c465856c05b5eda1cb561e0/molmod/graphs.py#L1402-L1407 |
1,322 | tonybaloney/wily | wily/operators/__init__.py | resolve_metric_as_tuple | def resolve_metric_as_tuple(metric):
"""
Resolve metric key to a given target.
:param metric: the metric name.
:type metric: ``str``
:rtype: :class:`Metric`
"""
if "." in metric:
_, metric = metric.split(".")
r = [
(operator, match) for operator, match in ALL_METRICS if match[0] == metric
]
if not r or len(r) == 0:
raise ValueError(f"Metric {metric} not recognised.")
else:
return r[0] | python | def resolve_metric_as_tuple(metric):
"""
Resolve metric key to a given target.
:param metric: the metric name.
:type metric: ``str``
:rtype: :class:`Metric`
"""
if "." in metric:
_, metric = metric.split(".")
r = [
(operator, match) for operator, match in ALL_METRICS if match[0] == metric
]
if not r or len(r) == 0:
raise ValueError(f"Metric {metric} not recognised.")
else:
return r[0] | ['def', 'resolve_metric_as_tuple', '(', 'metric', ')', ':', 'if', '"."', 'in', 'metric', ':', '_', ',', 'metric', '=', 'metric', '.', 'split', '(', '"."', ')', 'r', '=', '[', '(', 'operator', ',', 'match', ')', 'for', 'operator', ',', 'match', 'in', 'ALL_METRICS', 'if', 'match', '[', '0', ']', '==', 'metric', ']', 'if', 'not', 'r', 'or', 'len', '(', 'r', ')', '==', '0', ':', 'raise', 'ValueError', '(', 'f"Metric {metric} not recognised."', ')', 'else', ':', 'return', 'r', '[', '0', ']'] | Resolve metric key to a given target.
:param metric: the metric name.
:type metric: ``str``
:rtype: :class:`Metric` | ['Resolve', 'metric', 'key', 'to', 'a', 'given', 'target', '.'] | train | https://github.com/tonybaloney/wily/blob/bae259354a91b57d56603f0ca7403186f086a84c/wily/operators/__init__.py#L170-L188 |
1,323 | DLR-RM/RAFCON | source/rafcon/core/global_variable_manager.py | GlobalVariableManager.delete_variable | def delete_variable(self, key):
"""Deletes a global variable
:param key: the key of the global variable to be deleted
:raises exceptions.AttributeError: if the global variable does not exist
"""
key = str(key)
if self.is_locked(key):
raise RuntimeError("Global variable is locked")
with self.__global_lock:
if key in self.__global_variable_dictionary:
access_key = self.lock_variable(key, block=True)
del self.__global_variable_dictionary[key]
self.unlock_variable(key, access_key)
del self.__variable_locks[key]
del self.__variable_references[key]
else:
raise AttributeError("Global variable %s does not exist!" % str(key))
logger.debug("Global variable %s was deleted!" % str(key)) | python | def delete_variable(self, key):
"""Deletes a global variable
:param key: the key of the global variable to be deleted
:raises exceptions.AttributeError: if the global variable does not exist
"""
key = str(key)
if self.is_locked(key):
raise RuntimeError("Global variable is locked")
with self.__global_lock:
if key in self.__global_variable_dictionary:
access_key = self.lock_variable(key, block=True)
del self.__global_variable_dictionary[key]
self.unlock_variable(key, access_key)
del self.__variable_locks[key]
del self.__variable_references[key]
else:
raise AttributeError("Global variable %s does not exist!" % str(key))
logger.debug("Global variable %s was deleted!" % str(key)) | ['def', 'delete_variable', '(', 'self', ',', 'key', ')', ':', 'key', '=', 'str', '(', 'key', ')', 'if', 'self', '.', 'is_locked', '(', 'key', ')', ':', 'raise', 'RuntimeError', '(', '"Global variable is locked"', ')', 'with', 'self', '.', '__global_lock', ':', 'if', 'key', 'in', 'self', '.', '__global_variable_dictionary', ':', 'access_key', '=', 'self', '.', 'lock_variable', '(', 'key', ',', 'block', '=', 'True', ')', 'del', 'self', '.', '__global_variable_dictionary', '[', 'key', ']', 'self', '.', 'unlock_variable', '(', 'key', ',', 'access_key', ')', 'del', 'self', '.', '__variable_locks', '[', 'key', ']', 'del', 'self', '.', '__variable_references', '[', 'key', ']', 'else', ':', 'raise', 'AttributeError', '(', '"Global variable %s does not exist!"', '%', 'str', '(', 'key', ')', ')', 'logger', '.', 'debug', '(', '"Global variable %s was deleted!"', '%', 'str', '(', 'key', ')', ')'] | Deletes a global variable
:param key: the key of the global variable to be deleted
:raises exceptions.AttributeError: if the global variable does not exist | ['Deletes', 'a', 'global', 'variable'] | train | https://github.com/DLR-RM/RAFCON/blob/24942ef1a904531f49ab8830a1dbb604441be498/source/rafcon/core/global_variable_manager.py#L159-L179 |
1,324 | spacetelescope/pysynphot | commissioning/extrap/extrap.py | classify_file | def classify_file(f):
"""Examine the column names to determine which type of file
this is. Return a tuple:
retvalue[0] = "file is non-parameterized"
retvalue[1] = "file contains error column"
"""
cols=f[1].columns
if len(cols) == 2:
#Then we must have a simple file
return (True,False)
elif len(cols) == 3 and ('ERROR' in cols.names):
return (True,True)
elif len(cols) > 2 and ('ERROR' not in cols.names):
return (True,False)
else:
return (False,True) | python | def classify_file(f):
"""Examine the column names to determine which type of file
this is. Return a tuple:
retvalue[0] = "file is non-parameterized"
retvalue[1] = "file contains error column"
"""
cols=f[1].columns
if len(cols) == 2:
#Then we must have a simple file
return (True,False)
elif len(cols) == 3 and ('ERROR' in cols.names):
return (True,True)
elif len(cols) > 2 and ('ERROR' not in cols.names):
return (True,False)
else:
return (False,True) | ['def', 'classify_file', '(', 'f', ')', ':', 'cols', '=', 'f', '[', '1', ']', '.', 'columns', 'if', 'len', '(', 'cols', ')', '==', '2', ':', '#Then we must have a simple file', 'return', '(', 'True', ',', 'False', ')', 'elif', 'len', '(', 'cols', ')', '==', '3', 'and', '(', "'ERROR'", 'in', 'cols', '.', 'names', ')', ':', 'return', '(', 'True', ',', 'True', ')', 'elif', 'len', '(', 'cols', ')', '>', '2', 'and', '(', "'ERROR'", 'not', 'in', 'cols', '.', 'names', ')', ':', 'return', '(', 'True', ',', 'False', ')', 'else', ':', 'return', '(', 'False', ',', 'True', ')'] | Examine the column names to determine which type of file
this is. Return a tuple:
retvalue[0] = "file is non-parameterized"
retvalue[1] = "file contains error column" | ['Examine', 'the', 'column', 'names', 'to', 'determine', 'which', 'type', 'of', 'file', 'this', 'is', '.', 'Return', 'a', 'tuple', ':', 'retvalue', '[', '0', ']', '=', 'file', 'is', 'non', '-', 'parameterized', 'retvalue', '[', '1', ']', '=', 'file', 'contains', 'error', 'column'] | train | https://github.com/spacetelescope/pysynphot/blob/a125ff956f4d94beb157bd51899747a13234bb97/commissioning/extrap/extrap.py#L22-L37 |
1,325 | pyvisa/pyvisa | pyvisa/shell.py | VisaShell.do_open | def do_open(self, args):
"""Open resource by number, resource name or alias: open 3"""
if not args:
print('A resource name must be specified.')
return
if self.current:
print('You can only open one resource at a time. Please close the current one first.')
return
if args.isdigit():
try:
args = self.resources[int(args)][0]
except IndexError:
print('Not a valid resource number. Use the command "list".')
return
try:
self.current = self.resource_manager.open_resource(args)
print('{} has been opened.\n'
'You can talk to the device using "write", "read" or "query".\n'
'The default end of message is added to each message.'.format(args))
self.py_attr = []
self.vi_attr = []
for attr in getattr(self.current, 'visa_attributes_classes', ()):
if attr.py_name:
self.py_attr.append(attr.py_name)
self.vi_attr.append(attr.visa_name)
self.prompt = '(open) '
except Exception as e:
print(e) | python | def do_open(self, args):
"""Open resource by number, resource name or alias: open 3"""
if not args:
print('A resource name must be specified.')
return
if self.current:
print('You can only open one resource at a time. Please close the current one first.')
return
if args.isdigit():
try:
args = self.resources[int(args)][0]
except IndexError:
print('Not a valid resource number. Use the command "list".')
return
try:
self.current = self.resource_manager.open_resource(args)
print('{} has been opened.\n'
'You can talk to the device using "write", "read" or "query".\n'
'The default end of message is added to each message.'.format(args))
self.py_attr = []
self.vi_attr = []
for attr in getattr(self.current, 'visa_attributes_classes', ()):
if attr.py_name:
self.py_attr.append(attr.py_name)
self.vi_attr.append(attr.visa_name)
self.prompt = '(open) '
except Exception as e:
print(e) | ['def', 'do_open', '(', 'self', ',', 'args', ')', ':', 'if', 'not', 'args', ':', 'print', '(', "'A resource name must be specified.'", ')', 'return', 'if', 'self', '.', 'current', ':', 'print', '(', "'You can only open one resource at a time. Please close the current one first.'", ')', 'return', 'if', 'args', '.', 'isdigit', '(', ')', ':', 'try', ':', 'args', '=', 'self', '.', 'resources', '[', 'int', '(', 'args', ')', ']', '[', '0', ']', 'except', 'IndexError', ':', 'print', '(', '\'Not a valid resource number. Use the command "list".\'', ')', 'return', 'try', ':', 'self', '.', 'current', '=', 'self', '.', 'resource_manager', '.', 'open_resource', '(', 'args', ')', 'print', '(', "'{} has been opened.\\n'", '\'You can talk to the device using "write", "read" or "query".\\n\'', "'The default end of message is added to each message.'", '.', 'format', '(', 'args', ')', ')', 'self', '.', 'py_attr', '=', '[', ']', 'self', '.', 'vi_attr', '=', '[', ']', 'for', 'attr', 'in', 'getattr', '(', 'self', '.', 'current', ',', "'visa_attributes_classes'", ',', '(', ')', ')', ':', 'if', 'attr', '.', 'py_name', ':', 'self', '.', 'py_attr', '.', 'append', '(', 'attr', '.', 'py_name', ')', 'self', '.', 'vi_attr', '.', 'append', '(', 'attr', '.', 'visa_name', ')', 'self', '.', 'prompt', '=', "'(open) '", 'except', 'Exception', 'as', 'e', ':', 'print', '(', 'e', ')'] | Open resource by number, resource name or alias: open 3 | ['Open', 'resource', 'by', 'number', 'resource', 'name', 'or', 'alias', ':', 'open', '3'] | train | https://github.com/pyvisa/pyvisa/blob/b8b2d4371e1f00782856aa9176ff1ced6bcb3798/pyvisa/shell.py#L138-L171 |
1,326 | Telefonica/toolium | toolium/driver_wrapper.py | DriverWrapper.configure_visual_baseline | def configure_visual_baseline(self):
"""Configure baseline directory"""
# Get baseline name
baseline_name = self.config.get_optional('VisualTests', 'baseline_name', '{Driver_type}')
for section in self.config.sections():
for option in self.config.options(section):
option_value = self.config.get(section, option)
baseline_name = baseline_name.replace('{{{0}_{1}}}'.format(section, option), option_value)
# Configure baseline directory if baseline name has changed
if self.baseline_name != baseline_name:
self.baseline_name = baseline_name
self.visual_baseline_directory = os.path.join(DriverWrappersPool.visual_baseline_directory,
get_valid_filename(baseline_name)) | python | def configure_visual_baseline(self):
"""Configure baseline directory"""
# Get baseline name
baseline_name = self.config.get_optional('VisualTests', 'baseline_name', '{Driver_type}')
for section in self.config.sections():
for option in self.config.options(section):
option_value = self.config.get(section, option)
baseline_name = baseline_name.replace('{{{0}_{1}}}'.format(section, option), option_value)
# Configure baseline directory if baseline name has changed
if self.baseline_name != baseline_name:
self.baseline_name = baseline_name
self.visual_baseline_directory = os.path.join(DriverWrappersPool.visual_baseline_directory,
get_valid_filename(baseline_name)) | ['def', 'configure_visual_baseline', '(', 'self', ')', ':', '# Get baseline name', 'baseline_name', '=', 'self', '.', 'config', '.', 'get_optional', '(', "'VisualTests'", ',', "'baseline_name'", ',', "'{Driver_type}'", ')', 'for', 'section', 'in', 'self', '.', 'config', '.', 'sections', '(', ')', ':', 'for', 'option', 'in', 'self', '.', 'config', '.', 'options', '(', 'section', ')', ':', 'option_value', '=', 'self', '.', 'config', '.', 'get', '(', 'section', ',', 'option', ')', 'baseline_name', '=', 'baseline_name', '.', 'replace', '(', "'{{{0}_{1}}}'", '.', 'format', '(', 'section', ',', 'option', ')', ',', 'option_value', ')', '# Configure baseline directory if baseline name has changed', 'if', 'self', '.', 'baseline_name', '!=', 'baseline_name', ':', 'self', '.', 'baseline_name', '=', 'baseline_name', 'self', '.', 'visual_baseline_directory', '=', 'os', '.', 'path', '.', 'join', '(', 'DriverWrappersPool', '.', 'visual_baseline_directory', ',', 'get_valid_filename', '(', 'baseline_name', ')', ')'] | Configure baseline directory | ['Configure', 'baseline', 'directory'] | train | https://github.com/Telefonica/toolium/blob/56847c243b3a98876df74c184b75e43f8810e475/toolium/driver_wrapper.py#L133-L146 |
1,327 | saltstack/salt | salt/states/zk_concurrency.py | lock | def lock(name,
zk_hosts=None,
identifier=None,
max_concurrency=1,
timeout=None,
ephemeral_lease=False,
profile=None,
scheme=None,
username=None,
password=None,
default_acl=None):
'''
Block state execution until you are able to get the lock (or hit the timeout)
'''
ret = {'name': name,
'changes': {},
'result': False,
'comment': ''}
conn_kwargs = {'profile': profile, 'scheme': scheme,
'username': username, 'password': password, 'default_acl': default_acl}
if __opts__['test']:
ret['result'] = None
ret['comment'] = 'Attempt to acquire lock'
return ret
if identifier is None:
identifier = __grains__['id']
locked = __salt__['zk_concurrency.lock'](name,
zk_hosts,
identifier=identifier,
max_concurrency=max_concurrency,
timeout=timeout,
ephemeral_lease=ephemeral_lease,
**conn_kwargs)
if locked:
ret['result'] = True
ret['comment'] = 'lock acquired'
else:
ret['comment'] = 'Unable to acquire lock'
return ret | python | def lock(name,
zk_hosts=None,
identifier=None,
max_concurrency=1,
timeout=None,
ephemeral_lease=False,
profile=None,
scheme=None,
username=None,
password=None,
default_acl=None):
'''
Block state execution until you are able to get the lock (or hit the timeout)
'''
ret = {'name': name,
'changes': {},
'result': False,
'comment': ''}
conn_kwargs = {'profile': profile, 'scheme': scheme,
'username': username, 'password': password, 'default_acl': default_acl}
if __opts__['test']:
ret['result'] = None
ret['comment'] = 'Attempt to acquire lock'
return ret
if identifier is None:
identifier = __grains__['id']
locked = __salt__['zk_concurrency.lock'](name,
zk_hosts,
identifier=identifier,
max_concurrency=max_concurrency,
timeout=timeout,
ephemeral_lease=ephemeral_lease,
**conn_kwargs)
if locked:
ret['result'] = True
ret['comment'] = 'lock acquired'
else:
ret['comment'] = 'Unable to acquire lock'
return ret | ['def', 'lock', '(', 'name', ',', 'zk_hosts', '=', 'None', ',', 'identifier', '=', 'None', ',', 'max_concurrency', '=', '1', ',', 'timeout', '=', 'None', ',', 'ephemeral_lease', '=', 'False', ',', 'profile', '=', 'None', ',', 'scheme', '=', 'None', ',', 'username', '=', 'None', ',', 'password', '=', 'None', ',', 'default_acl', '=', 'None', ')', ':', 'ret', '=', '{', "'name'", ':', 'name', ',', "'changes'", ':', '{', '}', ',', "'result'", ':', 'False', ',', "'comment'", ':', "''", '}', 'conn_kwargs', '=', '{', "'profile'", ':', 'profile', ',', "'scheme'", ':', 'scheme', ',', "'username'", ':', 'username', ',', "'password'", ':', 'password', ',', "'default_acl'", ':', 'default_acl', '}', 'if', '__opts__', '[', "'test'", ']', ':', 'ret', '[', "'result'", ']', '=', 'None', 'ret', '[', "'comment'", ']', '=', "'Attempt to acquire lock'", 'return', 'ret', 'if', 'identifier', 'is', 'None', ':', 'identifier', '=', '__grains__', '[', "'id'", ']', 'locked', '=', '__salt__', '[', "'zk_concurrency.lock'", ']', '(', 'name', ',', 'zk_hosts', ',', 'identifier', '=', 'identifier', ',', 'max_concurrency', '=', 'max_concurrency', ',', 'timeout', '=', 'timeout', ',', 'ephemeral_lease', '=', 'ephemeral_lease', ',', '*', '*', 'conn_kwargs', ')', 'if', 'locked', ':', 'ret', '[', "'result'", ']', '=', 'True', 'ret', '[', "'comment'", ']', '=', "'lock acquired'", 'else', ':', 'ret', '[', "'comment'", ']', '=', "'Unable to acquire lock'", 'return', 'ret'] | Block state execution until you are able to get the lock (or hit the timeout) | ['Block', 'state', 'execution', 'until', 'you', 'are', 'able', 'to', 'get', 'the', 'lock', '(', 'or', 'hit', 'the', 'timeout', ')'] | train | https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/states/zk_concurrency.py#L69-L112 |
1,328 | trevisanj/a99 | a99/gui/a_WConfigEditor.py | WConfigEditor._update_fobj | def _update_fobj(self):
"""Updates fobj from GUI. Opposite of _update_gui()."""
# print("PPPPPPPPPPPPPPPPPPPRINTANDO O STACK")
# traceback.print_stack()
emsg, flag_error = "", False
fieldname = None
try:
self._before_update_fobj()
for item in self._map:
self._f.obj[item.fieldname] = item.get_value()
self._after_update_fobj()
except Exception as E:
flag_error = True
if fieldname is not None:
emsg = "Field '{}': {}".format(fieldname, str(E))
else:
emsg = str(E)
self.add_log_error(emsg)
self._flag_valid = not flag_error
if not flag_error:
self.status("") | python | def _update_fobj(self):
"""Updates fobj from GUI. Opposite of _update_gui()."""
# print("PPPPPPPPPPPPPPPPPPPRINTANDO O STACK")
# traceback.print_stack()
emsg, flag_error = "", False
fieldname = None
try:
self._before_update_fobj()
for item in self._map:
self._f.obj[item.fieldname] = item.get_value()
self._after_update_fobj()
except Exception as E:
flag_error = True
if fieldname is not None:
emsg = "Field '{}': {}".format(fieldname, str(E))
else:
emsg = str(E)
self.add_log_error(emsg)
self._flag_valid = not flag_error
if not flag_error:
self.status("") | ['def', '_update_fobj', '(', 'self', ')', ':', '# print("PPPPPPPPPPPPPPPPPPPRINTANDO O STACK")\r', '# traceback.print_stack()\r', 'emsg', ',', 'flag_error', '=', '""', ',', 'False', 'fieldname', '=', 'None', 'try', ':', 'self', '.', '_before_update_fobj', '(', ')', 'for', 'item', 'in', 'self', '.', '_map', ':', 'self', '.', '_f', '.', 'obj', '[', 'item', '.', 'fieldname', ']', '=', 'item', '.', 'get_value', '(', ')', 'self', '.', '_after_update_fobj', '(', ')', 'except', 'Exception', 'as', 'E', ':', 'flag_error', '=', 'True', 'if', 'fieldname', 'is', 'not', 'None', ':', 'emsg', '=', '"Field \'{}\': {}"', '.', 'format', '(', 'fieldname', ',', 'str', '(', 'E', ')', ')', 'else', ':', 'emsg', '=', 'str', '(', 'E', ')', 'self', '.', 'add_log_error', '(', 'emsg', ')', 'self', '.', '_flag_valid', '=', 'not', 'flag_error', 'if', 'not', 'flag_error', ':', 'self', '.', 'status', '(', '""', ')'] | Updates fobj from GUI. Opposite of _update_gui(). | ['Updates', 'fobj', 'from', 'GUI', '.', 'Opposite', 'of', '_update_gui', '()', '.'] | train | https://github.com/trevisanj/a99/blob/193e6e3c9b3e4f4a0ba7eb3eece846fe7045c539/a99/gui/a_WConfigEditor.py#L119-L146 |
1,329 | bukun/TorCMS | torcms/model/post_model.py | MPost.query_most_pic | def query_most_pic(num, kind='1'):
'''
Query most pics.
'''
return TabPost.select().where(
(TabPost.kind == kind) & (TabPost.logo != "")
).order_by(TabPost.view_count.desc()).limit(num) | python | def query_most_pic(num, kind='1'):
'''
Query most pics.
'''
return TabPost.select().where(
(TabPost.kind == kind) & (TabPost.logo != "")
).order_by(TabPost.view_count.desc()).limit(num) | ['def', 'query_most_pic', '(', 'num', ',', 'kind', '=', "'1'", ')', ':', 'return', 'TabPost', '.', 'select', '(', ')', '.', 'where', '(', '(', 'TabPost', '.', 'kind', '==', 'kind', ')', '&', '(', 'TabPost', '.', 'logo', '!=', '""', ')', ')', '.', 'order_by', '(', 'TabPost', '.', 'view_count', '.', 'desc', '(', ')', ')', '.', 'limit', '(', 'num', ')'] | Query most pics. | ['Query', 'most', 'pics', '.'] | train | https://github.com/bukun/TorCMS/blob/6567c7fe2604a1d646d4570c017840958630ed2b/torcms/model/post_model.py#L352-L358 |
1,330 | molmod/molmod | molmod/graphs.py | Graph.full_match | def full_match(self, other):
"""Find the mapping between vertex indexes in self and other.
This also works on disconnected graphs. Derived classes should just
implement get_vertex_string and get_edge_string to make this method
aware of the different nature of certain vertices. In case molecules,
this would make the algorithm sensitive to atom numbers etc.
"""
# we need normalize subgraphs because these graphs are used as patterns.
graphs0 = [
self.get_subgraph(group, normalize=True)
for group in self.independent_vertices
]
graphs1 = [
other.get_subgraph(group)
for group in other.independent_vertices
]
if len(graphs0) != len(graphs1):
return
matches = []
for graph0 in graphs0:
pattern = EqualPattern(graph0)
found_match = False
for i, graph1 in enumerate(graphs1):
local_matches = list(GraphSearch(pattern)(graph1, one_match=True))
if len(local_matches) == 1:
match = local_matches[0]
# we need to restore the relation between the normalized
# graph0 and its original indexes
old_to_new = OneToOne((
(j, i) for i, j
in enumerate(graph0._old_vertex_indexes)
))
matches.append(match * old_to_new)
del graphs1[i]
found_match = True
break
if not found_match:
return
result = OneToOne()
for match in matches:
result.add_relations(match.forward.items())
return result | python | def full_match(self, other):
"""Find the mapping between vertex indexes in self and other.
This also works on disconnected graphs. Derived classes should just
implement get_vertex_string and get_edge_string to make this method
aware of the different nature of certain vertices. In case molecules,
this would make the algorithm sensitive to atom numbers etc.
"""
# we need normalize subgraphs because these graphs are used as patterns.
graphs0 = [
self.get_subgraph(group, normalize=True)
for group in self.independent_vertices
]
graphs1 = [
other.get_subgraph(group)
for group in other.independent_vertices
]
if len(graphs0) != len(graphs1):
return
matches = []
for graph0 in graphs0:
pattern = EqualPattern(graph0)
found_match = False
for i, graph1 in enumerate(graphs1):
local_matches = list(GraphSearch(pattern)(graph1, one_match=True))
if len(local_matches) == 1:
match = local_matches[0]
# we need to restore the relation between the normalized
# graph0 and its original indexes
old_to_new = OneToOne((
(j, i) for i, j
in enumerate(graph0._old_vertex_indexes)
))
matches.append(match * old_to_new)
del graphs1[i]
found_match = True
break
if not found_match:
return
result = OneToOne()
for match in matches:
result.add_relations(match.forward.items())
return result | ['def', 'full_match', '(', 'self', ',', 'other', ')', ':', '# we need normalize subgraphs because these graphs are used as patterns.', 'graphs0', '=', '[', 'self', '.', 'get_subgraph', '(', 'group', ',', 'normalize', '=', 'True', ')', 'for', 'group', 'in', 'self', '.', 'independent_vertices', ']', 'graphs1', '=', '[', 'other', '.', 'get_subgraph', '(', 'group', ')', 'for', 'group', 'in', 'other', '.', 'independent_vertices', ']', 'if', 'len', '(', 'graphs0', ')', '!=', 'len', '(', 'graphs1', ')', ':', 'return', 'matches', '=', '[', ']', 'for', 'graph0', 'in', 'graphs0', ':', 'pattern', '=', 'EqualPattern', '(', 'graph0', ')', 'found_match', '=', 'False', 'for', 'i', ',', 'graph1', 'in', 'enumerate', '(', 'graphs1', ')', ':', 'local_matches', '=', 'list', '(', 'GraphSearch', '(', 'pattern', ')', '(', 'graph1', ',', 'one_match', '=', 'True', ')', ')', 'if', 'len', '(', 'local_matches', ')', '==', '1', ':', 'match', '=', 'local_matches', '[', '0', ']', '# we need to restore the relation between the normalized', '# graph0 and its original indexes', 'old_to_new', '=', 'OneToOne', '(', '(', '(', 'j', ',', 'i', ')', 'for', 'i', ',', 'j', 'in', 'enumerate', '(', 'graph0', '.', '_old_vertex_indexes', ')', ')', ')', 'matches', '.', 'append', '(', 'match', '*', 'old_to_new', ')', 'del', 'graphs1', '[', 'i', ']', 'found_match', '=', 'True', 'break', 'if', 'not', 'found_match', ':', 'return', 'result', '=', 'OneToOne', '(', ')', 'for', 'match', 'in', 'matches', ':', 'result', '.', 'add_relations', '(', 'match', '.', 'forward', '.', 'items', '(', ')', ')', 'return', 'result'] | Find the mapping between vertex indexes in self and other.
This also works on disconnected graphs. Derived classes should just
implement get_vertex_string and get_edge_string to make this method
aware of the different nature of certain vertices. In case molecules,
this would make the algorithm sensitive to atom numbers etc. | ['Find', 'the', 'mapping', 'between', 'vertex', 'indexes', 'in', 'self', 'and', 'other', '.'] | train | https://github.com/molmod/molmod/blob/a7b5b4364ed514ad4c465856c05b5eda1cb561e0/molmod/graphs.py#L782-L828 |
1,331 | openego/eDisGo | edisgo/grid/network.py | Results.save | def save(self, directory, parameters='all'):
"""
Saves results to disk.
Depending on which results are selected and if they exist, the
following directories and files are created:
* `powerflow_results` directory
* `voltages_pu.csv`
See :py:attr:`~pfa_v_mag_pu` for more information.
* `currents.csv`
See :func:`~i_res` for more information.
* `active_powers.csv`
See :py:attr:`~pfa_p` for more information.
* `reactive_powers.csv`
See :py:attr:`~pfa_q` for more information.
* `apparent_powers.csv`
See :func:`~s_res` for more information.
* `grid_losses.csv`
See :py:attr:`~grid_losses` for more information.
* `hv_mv_exchanges.csv`
See :py:attr:`~hv_mv_exchanges` for more information.
* `pypsa_network` directory
See :py:func:`pypsa.Network.export_to_csv_folder`
* `grid_expansion_results` directory
* `grid_expansion_costs.csv`
See :py:attr:`~grid_expansion_costs` for more information.
* `equipment_changes.csv`
See :py:attr:`~equipment_changes` for more information.
* `unresolved_issues.csv`
See :py:attr:`~unresolved_issues` for more information.
* `curtailment_results` directory
Files depend on curtailment specifications. There will be one file
for each curtailment specification, that is for every key in
:py:attr:`~curtailment` dictionary.
* `storage_integration_results` directory
* `storages.csv`
See :func:`~storages` for more information.
Parameters
----------
directory : :obj:`str`
Directory to save the results in.
parameters : :obj:`str` or :obj:`list` of :obj:`str`
Specifies which results will be saved. By default all results are
saved. To only save certain results set `parameters` to one of the
following options or choose several options by providing a list:
* 'pypsa_network'
* 'powerflow_results'
* 'grid_expansion_results'
* 'curtailment_results'
* 'storage_integration_results'
"""
def _save_power_flow_results(target_dir):
if self.pfa_v_mag_pu is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
# voltage
self.pfa_v_mag_pu.to_csv(
os.path.join(target_dir, 'voltages_pu.csv'))
# current
self.i_res.to_csv(
os.path.join(target_dir, 'currents.csv'))
# active power
self.pfa_p.to_csv(
os.path.join(target_dir, 'active_powers.csv'))
# reactive power
self.pfa_q.to_csv(
os.path.join(target_dir, 'reactive_powers.csv'))
# apparent power
self.s_res().to_csv(
os.path.join(target_dir, 'apparent_powers.csv'))
# grid losses
self.grid_losses.to_csv(
os.path.join(target_dir, 'grid_losses.csv'))
# grid exchanges
self.hv_mv_exchanges.to_csv(os.path.join(
target_dir, 'hv_mv_exchanges.csv'))
def _save_pypsa_network(target_dir):
if self.network.pypsa:
# create directory
os.makedirs(target_dir, exist_ok=True)
self.network.pypsa.export_to_csv_folder(target_dir)
def _save_grid_expansion_results(target_dir):
if self.grid_expansion_costs is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
# grid expansion costs
self.grid_expansion_costs.to_csv(os.path.join(
target_dir, 'grid_expansion_costs.csv'))
# unresolved issues
pd.DataFrame(self.unresolved_issues).to_csv(os.path.join(
target_dir, 'unresolved_issues.csv'))
# equipment changes
self.equipment_changes.to_csv(os.path.join(
target_dir, 'equipment_changes.csv'))
def _save_curtailment_results(target_dir):
if self.curtailment is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
for key, curtailment_df in self.curtailment.items():
if type(key) == tuple:
type_prefix = '-'.join([key[0], str(key[1])])
elif type(key) == str:
type_prefix = key
else:
raise KeyError("Unknown key type {} for key {}".format(
type(key), key))
filename = os.path.join(
target_dir, '{}.csv'.format(type_prefix))
curtailment_df.to_csv(filename, index_label=type_prefix)
def _save_storage_integration_results(target_dir):
storages = self.storages
if not storages.empty:
# create directory
os.makedirs(target_dir, exist_ok=True)
# general storage information
storages.to_csv(os.path.join(target_dir, 'storages.csv'))
# storages time series
ts_p, ts_q = self.storages_timeseries()
ts_p.to_csv(os.path.join(
target_dir, 'storages_active_power.csv'))
ts_q.to_csv(os.path.join(
target_dir, 'storages_reactive_power.csv'))
if not self.storages_costs_reduction is None:
self.storages_costs_reduction.to_csv(
os.path.join(target_dir,
'storages_costs_reduction.csv'))
# dictionary with function to call to save each parameter
func_dict = {
'powerflow_results': _save_power_flow_results,
'pypsa_network': _save_pypsa_network,
'grid_expansion_results': _save_grid_expansion_results,
'curtailment_results': _save_curtailment_results,
'storage_integration_results': _save_storage_integration_results
}
# if string is given convert to list
if isinstance(parameters, str):
if parameters == 'all':
parameters = ['powerflow_results', 'pypsa_network',
'grid_expansion_results', 'curtailment_results',
'storage_integration_results']
else:
parameters = [parameters]
# save each parameter
for parameter in parameters:
try:
func_dict[parameter](os.path.join(directory, parameter))
except KeyError:
message = "Invalid input {} for `parameters` when saving " \
"results. Must be any or a list of the following: " \
"'pypsa_network', 'powerflow_results', " \
"'grid_expansion_results', 'curtailment_results', " \
"'storage_integration_results'.".format(parameter)
logger.error(message)
raise KeyError(message)
except:
raise
# save measures
pd.DataFrame(data={'measure': self.measures}).to_csv(
os.path.join(directory, 'measures.csv'))
# save configs
with open(os.path.join(directory, 'configs.csv'), 'w') as f:
writer = csv.writer(f)
rows = [
['{}'.format(key)] + [value for item in values.items()
for value in item]
for key, values in self.network.config._data.items()]
writer.writerows(rows) | python | def save(self, directory, parameters='all'):
"""
Saves results to disk.
Depending on which results are selected and if they exist, the
following directories and files are created:
* `powerflow_results` directory
* `voltages_pu.csv`
See :py:attr:`~pfa_v_mag_pu` for more information.
* `currents.csv`
See :func:`~i_res` for more information.
* `active_powers.csv`
See :py:attr:`~pfa_p` for more information.
* `reactive_powers.csv`
See :py:attr:`~pfa_q` for more information.
* `apparent_powers.csv`
See :func:`~s_res` for more information.
* `grid_losses.csv`
See :py:attr:`~grid_losses` for more information.
* `hv_mv_exchanges.csv`
See :py:attr:`~hv_mv_exchanges` for more information.
* `pypsa_network` directory
See :py:func:`pypsa.Network.export_to_csv_folder`
* `grid_expansion_results` directory
* `grid_expansion_costs.csv`
See :py:attr:`~grid_expansion_costs` for more information.
* `equipment_changes.csv`
See :py:attr:`~equipment_changes` for more information.
* `unresolved_issues.csv`
See :py:attr:`~unresolved_issues` for more information.
* `curtailment_results` directory
Files depend on curtailment specifications. There will be one file
for each curtailment specification, that is for every key in
:py:attr:`~curtailment` dictionary.
* `storage_integration_results` directory
* `storages.csv`
See :func:`~storages` for more information.
Parameters
----------
directory : :obj:`str`
Directory to save the results in.
parameters : :obj:`str` or :obj:`list` of :obj:`str`
Specifies which results will be saved. By default all results are
saved. To only save certain results set `parameters` to one of the
following options or choose several options by providing a list:
* 'pypsa_network'
* 'powerflow_results'
* 'grid_expansion_results'
* 'curtailment_results'
* 'storage_integration_results'
"""
def _save_power_flow_results(target_dir):
if self.pfa_v_mag_pu is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
# voltage
self.pfa_v_mag_pu.to_csv(
os.path.join(target_dir, 'voltages_pu.csv'))
# current
self.i_res.to_csv(
os.path.join(target_dir, 'currents.csv'))
# active power
self.pfa_p.to_csv(
os.path.join(target_dir, 'active_powers.csv'))
# reactive power
self.pfa_q.to_csv(
os.path.join(target_dir, 'reactive_powers.csv'))
# apparent power
self.s_res().to_csv(
os.path.join(target_dir, 'apparent_powers.csv'))
# grid losses
self.grid_losses.to_csv(
os.path.join(target_dir, 'grid_losses.csv'))
# grid exchanges
self.hv_mv_exchanges.to_csv(os.path.join(
target_dir, 'hv_mv_exchanges.csv'))
def _save_pypsa_network(target_dir):
if self.network.pypsa:
# create directory
os.makedirs(target_dir, exist_ok=True)
self.network.pypsa.export_to_csv_folder(target_dir)
def _save_grid_expansion_results(target_dir):
if self.grid_expansion_costs is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
# grid expansion costs
self.grid_expansion_costs.to_csv(os.path.join(
target_dir, 'grid_expansion_costs.csv'))
# unresolved issues
pd.DataFrame(self.unresolved_issues).to_csv(os.path.join(
target_dir, 'unresolved_issues.csv'))
# equipment changes
self.equipment_changes.to_csv(os.path.join(
target_dir, 'equipment_changes.csv'))
def _save_curtailment_results(target_dir):
if self.curtailment is not None:
# create directory
os.makedirs(target_dir, exist_ok=True)
for key, curtailment_df in self.curtailment.items():
if type(key) == tuple:
type_prefix = '-'.join([key[0], str(key[1])])
elif type(key) == str:
type_prefix = key
else:
raise KeyError("Unknown key type {} for key {}".format(
type(key), key))
filename = os.path.join(
target_dir, '{}.csv'.format(type_prefix))
curtailment_df.to_csv(filename, index_label=type_prefix)
def _save_storage_integration_results(target_dir):
storages = self.storages
if not storages.empty:
# create directory
os.makedirs(target_dir, exist_ok=True)
# general storage information
storages.to_csv(os.path.join(target_dir, 'storages.csv'))
# storages time series
ts_p, ts_q = self.storages_timeseries()
ts_p.to_csv(os.path.join(
target_dir, 'storages_active_power.csv'))
ts_q.to_csv(os.path.join(
target_dir, 'storages_reactive_power.csv'))
if not self.storages_costs_reduction is None:
self.storages_costs_reduction.to_csv(
os.path.join(target_dir,
'storages_costs_reduction.csv'))
# dictionary with function to call to save each parameter
func_dict = {
'powerflow_results': _save_power_flow_results,
'pypsa_network': _save_pypsa_network,
'grid_expansion_results': _save_grid_expansion_results,
'curtailment_results': _save_curtailment_results,
'storage_integration_results': _save_storage_integration_results
}
# if string is given convert to list
if isinstance(parameters, str):
if parameters == 'all':
parameters = ['powerflow_results', 'pypsa_network',
'grid_expansion_results', 'curtailment_results',
'storage_integration_results']
else:
parameters = [parameters]
# save each parameter
for parameter in parameters:
try:
func_dict[parameter](os.path.join(directory, parameter))
except KeyError:
message = "Invalid input {} for `parameters` when saving " \
"results. Must be any or a list of the following: " \
"'pypsa_network', 'powerflow_results', " \
"'grid_expansion_results', 'curtailment_results', " \
"'storage_integration_results'.".format(parameter)
logger.error(message)
raise KeyError(message)
except:
raise
# save measures
pd.DataFrame(data={'measure': self.measures}).to_csv(
os.path.join(directory, 'measures.csv'))
# save configs
with open(os.path.join(directory, 'configs.csv'), 'w') as f:
writer = csv.writer(f)
rows = [
['{}'.format(key)] + [value for item in values.items()
for value in item]
for key, values in self.network.config._data.items()]
writer.writerows(rows) | ['def', 'save', '(', 'self', ',', 'directory', ',', 'parameters', '=', "'all'", ')', ':', 'def', '_save_power_flow_results', '(', 'target_dir', ')', ':', 'if', 'self', '.', 'pfa_v_mag_pu', 'is', 'not', 'None', ':', '# create directory', 'os', '.', 'makedirs', '(', 'target_dir', ',', 'exist_ok', '=', 'True', ')', '# voltage', 'self', '.', 'pfa_v_mag_pu', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'voltages_pu.csv'", ')', ')', '# current', 'self', '.', 'i_res', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'currents.csv'", ')', ')', '# active power', 'self', '.', 'pfa_p', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'active_powers.csv'", ')', ')', '# reactive power', 'self', '.', 'pfa_q', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'reactive_powers.csv'", ')', ')', '# apparent power', 'self', '.', 's_res', '(', ')', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'apparent_powers.csv'", ')', ')', '# grid losses', 'self', '.', 'grid_losses', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'grid_losses.csv'", ')', ')', '# grid exchanges', 'self', '.', 'hv_mv_exchanges', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'hv_mv_exchanges.csv'", ')', ')', 'def', '_save_pypsa_network', '(', 'target_dir', ')', ':', 'if', 'self', '.', 'network', '.', 'pypsa', ':', '# create directory', 'os', '.', 'makedirs', '(', 'target_dir', ',', 'exist_ok', '=', 'True', ')', 'self', '.', 'network', '.', 'pypsa', '.', 'export_to_csv_folder', '(', 'target_dir', ')', 'def', '_save_grid_expansion_results', '(', 'target_dir', ')', ':', 'if', 'self', '.', 'grid_expansion_costs', 'is', 'not', 'None', ':', '# create directory', 'os', '.', 'makedirs', '(', 'target_dir', ',', 'exist_ok', '=', 'True', ')', '# grid expansion costs', 'self', '.', 'grid_expansion_costs', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'grid_expansion_costs.csv'", ')', ')', '# unresolved issues', 'pd', '.', 'DataFrame', '(', 'self', '.', 'unresolved_issues', ')', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'unresolved_issues.csv'", ')', ')', '# equipment changes', 'self', '.', 'equipment_changes', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'equipment_changes.csv'", ')', ')', 'def', '_save_curtailment_results', '(', 'target_dir', ')', ':', 'if', 'self', '.', 'curtailment', 'is', 'not', 'None', ':', '# create directory', 'os', '.', 'makedirs', '(', 'target_dir', ',', 'exist_ok', '=', 'True', ')', 'for', 'key', ',', 'curtailment_df', 'in', 'self', '.', 'curtailment', '.', 'items', '(', ')', ':', 'if', 'type', '(', 'key', ')', '==', 'tuple', ':', 'type_prefix', '=', "'-'", '.', 'join', '(', '[', 'key', '[', '0', ']', ',', 'str', '(', 'key', '[', '1', ']', ')', ']', ')', 'elif', 'type', '(', 'key', ')', '==', 'str', ':', 'type_prefix', '=', 'key', 'else', ':', 'raise', 'KeyError', '(', '"Unknown key type {} for key {}"', '.', 'format', '(', 'type', '(', 'key', ')', ',', 'key', ')', ')', 'filename', '=', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'{}.csv'", '.', 'format', '(', 'type_prefix', ')', ')', 'curtailment_df', '.', 'to_csv', '(', 'filename', ',', 'index_label', '=', 'type_prefix', ')', 'def', '_save_storage_integration_results', '(', 'target_dir', ')', ':', 'storages', '=', 'self', '.', 'storages', 'if', 'not', 'storages', '.', 'empty', ':', '# create directory', 'os', '.', 'makedirs', '(', 'target_dir', ',', 'exist_ok', '=', 'True', ')', '# general storage information', 'storages', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'storages.csv'", ')', ')', '# storages time series', 'ts_p', ',', 'ts_q', '=', 'self', '.', 'storages_timeseries', '(', ')', 'ts_p', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'storages_active_power.csv'", ')', ')', 'ts_q', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'storages_reactive_power.csv'", ')', ')', 'if', 'not', 'self', '.', 'storages_costs_reduction', 'is', 'None', ':', 'self', '.', 'storages_costs_reduction', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'target_dir', ',', "'storages_costs_reduction.csv'", ')', ')', '# dictionary with function to call to save each parameter', 'func_dict', '=', '{', "'powerflow_results'", ':', '_save_power_flow_results', ',', "'pypsa_network'", ':', '_save_pypsa_network', ',', "'grid_expansion_results'", ':', '_save_grid_expansion_results', ',', "'curtailment_results'", ':', '_save_curtailment_results', ',', "'storage_integration_results'", ':', '_save_storage_integration_results', '}', '# if string is given convert to list', 'if', 'isinstance', '(', 'parameters', ',', 'str', ')', ':', 'if', 'parameters', '==', "'all'", ':', 'parameters', '=', '[', "'powerflow_results'", ',', "'pypsa_network'", ',', "'grid_expansion_results'", ',', "'curtailment_results'", ',', "'storage_integration_results'", ']', 'else', ':', 'parameters', '=', '[', 'parameters', ']', '# save each parameter', 'for', 'parameter', 'in', 'parameters', ':', 'try', ':', 'func_dict', '[', 'parameter', ']', '(', 'os', '.', 'path', '.', 'join', '(', 'directory', ',', 'parameter', ')', ')', 'except', 'KeyError', ':', 'message', '=', '"Invalid input {} for `parameters` when saving "', '"results. Must be any or a list of the following: "', '"\'pypsa_network\', \'powerflow_results\', "', '"\'grid_expansion_results\', \'curtailment_results\', "', '"\'storage_integration_results\'."', '.', 'format', '(', 'parameter', ')', 'logger', '.', 'error', '(', 'message', ')', 'raise', 'KeyError', '(', 'message', ')', 'except', ':', 'raise', '# save measures', 'pd', '.', 'DataFrame', '(', 'data', '=', '{', "'measure'", ':', 'self', '.', 'measures', '}', ')', '.', 'to_csv', '(', 'os', '.', 'path', '.', 'join', '(', 'directory', ',', "'measures.csv'", ')', ')', '# save configs', 'with', 'open', '(', 'os', '.', 'path', '.', 'join', '(', 'directory', ',', "'configs.csv'", ')', ',', "'w'", ')', 'as', 'f', ':', 'writer', '=', 'csv', '.', 'writer', '(', 'f', ')', 'rows', '=', '[', '[', "'{}'", '.', 'format', '(', 'key', ')', ']', '+', '[', 'value', 'for', 'item', 'in', 'values', '.', 'items', '(', ')', 'for', 'value', 'in', 'item', ']', 'for', 'key', ',', 'values', 'in', 'self', '.', 'network', '.', 'config', '.', '_data', '.', 'items', '(', ')', ']', 'writer', '.', 'writerows', '(', 'rows', ')'] | Saves results to disk.
Depending on which results are selected and if they exist, the
following directories and files are created:
* `powerflow_results` directory
* `voltages_pu.csv`
See :py:attr:`~pfa_v_mag_pu` for more information.
* `currents.csv`
See :func:`~i_res` for more information.
* `active_powers.csv`
See :py:attr:`~pfa_p` for more information.
* `reactive_powers.csv`
See :py:attr:`~pfa_q` for more information.
* `apparent_powers.csv`
See :func:`~s_res` for more information.
* `grid_losses.csv`
See :py:attr:`~grid_losses` for more information.
* `hv_mv_exchanges.csv`
See :py:attr:`~hv_mv_exchanges` for more information.
* `pypsa_network` directory
See :py:func:`pypsa.Network.export_to_csv_folder`
* `grid_expansion_results` directory
* `grid_expansion_costs.csv`
See :py:attr:`~grid_expansion_costs` for more information.
* `equipment_changes.csv`
See :py:attr:`~equipment_changes` for more information.
* `unresolved_issues.csv`
See :py:attr:`~unresolved_issues` for more information.
* `curtailment_results` directory
Files depend on curtailment specifications. There will be one file
for each curtailment specification, that is for every key in
:py:attr:`~curtailment` dictionary.
* `storage_integration_results` directory
* `storages.csv`
See :func:`~storages` for more information.
Parameters
----------
directory : :obj:`str`
Directory to save the results in.
parameters : :obj:`str` or :obj:`list` of :obj:`str`
Specifies which results will be saved. By default all results are
saved. To only save certain results set `parameters` to one of the
following options or choose several options by providing a list:
* 'pypsa_network'
* 'powerflow_results'
* 'grid_expansion_results'
* 'curtailment_results'
* 'storage_integration_results' | ['Saves', 'results', 'to', 'disk', '.'] | train | https://github.com/openego/eDisGo/blob/e6245bdaf236f9c49dbda5a18c1c458290f41e2b/edisgo/grid/network.py#L2996-L3209 |
1,332 | SKA-ScienceDataProcessor/integration-prototype | sip/tango_control/tango_master/app/sdp_master_device.py | SDPMasterDevice._get_service_state | def _get_service_state(service_id: str):
"""Get the Service state object for the specified id."""
LOG.debug('Getting state of service %s', service_id)
services = get_service_id_list()
service_ids = [s for s in services if service_id in s]
if len(service_ids) != 1:
return 'Service not found! services = {}'.format(str(services))
subsystem, name, version = service_ids[0].split(':')
return ServiceState(subsystem, name, version) | python | def _get_service_state(service_id: str):
"""Get the Service state object for the specified id."""
LOG.debug('Getting state of service %s', service_id)
services = get_service_id_list()
service_ids = [s for s in services if service_id in s]
if len(service_ids) != 1:
return 'Service not found! services = {}'.format(str(services))
subsystem, name, version = service_ids[0].split(':')
return ServiceState(subsystem, name, version) | ['def', '_get_service_state', '(', 'service_id', ':', 'str', ')', ':', 'LOG', '.', 'debug', '(', "'Getting state of service %s'", ',', 'service_id', ')', 'services', '=', 'get_service_id_list', '(', ')', 'service_ids', '=', '[', 's', 'for', 's', 'in', 'services', 'if', 'service_id', 'in', 's', ']', 'if', 'len', '(', 'service_ids', ')', '!=', '1', ':', 'return', "'Service not found! services = {}'", '.', 'format', '(', 'str', '(', 'services', ')', ')', 'subsystem', ',', 'name', ',', 'version', '=', 'service_ids', '[', '0', ']', '.', 'split', '(', "':'", ')', 'return', 'ServiceState', '(', 'subsystem', ',', 'name', ',', 'version', ')'] | Get the Service state object for the specified id. | ['Get', 'the', 'Service', 'state', 'object', 'for', 'the', 'specified', 'id', '.'] | train | https://github.com/SKA-ScienceDataProcessor/integration-prototype/blob/8c8006de6ad71dcd44114b0338780738079c87d4/sip/tango_control/tango_master/app/sdp_master_device.py#L118-L126 |
1,333 | python-rope/rope | rope/base/history.py | History.do | def do(self, changes, task_handle=taskhandle.NullTaskHandle()):
"""Perform the change and add it to the `self.undo_list`
Note that uninteresting changes (changes to ignored files)
will not be appended to `self.undo_list`.
"""
try:
self.current_change = changes
changes.do(change.create_job_set(task_handle, changes))
finally:
self.current_change = None
if self._is_change_interesting(changes):
self.undo_list.append(changes)
self._remove_extra_items()
del self.redo_list[:] | python | def do(self, changes, task_handle=taskhandle.NullTaskHandle()):
"""Perform the change and add it to the `self.undo_list`
Note that uninteresting changes (changes to ignored files)
will not be appended to `self.undo_list`.
"""
try:
self.current_change = changes
changes.do(change.create_job_set(task_handle, changes))
finally:
self.current_change = None
if self._is_change_interesting(changes):
self.undo_list.append(changes)
self._remove_extra_items()
del self.redo_list[:] | ['def', 'do', '(', 'self', ',', 'changes', ',', 'task_handle', '=', 'taskhandle', '.', 'NullTaskHandle', '(', ')', ')', ':', 'try', ':', 'self', '.', 'current_change', '=', 'changes', 'changes', '.', 'do', '(', 'change', '.', 'create_job_set', '(', 'task_handle', ',', 'changes', ')', ')', 'finally', ':', 'self', '.', 'current_change', '=', 'None', 'if', 'self', '.', '_is_change_interesting', '(', 'changes', ')', ':', 'self', '.', 'undo_list', '.', 'append', '(', 'changes', ')', 'self', '.', '_remove_extra_items', '(', ')', 'del', 'self', '.', 'redo_list', '[', ':', ']'] | Perform the change and add it to the `self.undo_list`
Note that uninteresting changes (changes to ignored files)
will not be appended to `self.undo_list`. | ['Perform', 'the', 'change', 'and', 'add', 'it', 'to', 'the', 'self', '.', 'undo_list'] | train | https://github.com/python-rope/rope/blob/1c9f9cd5964b099a99a9111e998f0dc728860688/rope/base/history.py#L27-L42 |
1,334 | glitchassassin/lackey | lackey/RegionMatching.py | Region.stopObserver | def stopObserver(self):
""" Stops this region's observer loop.
If this is running in a subprocess, the subprocess will end automatically.
"""
self._observer.isStopped = True
self._observer.isRunning = False | python | def stopObserver(self):
""" Stops this region's observer loop.
If this is running in a subprocess, the subprocess will end automatically.
"""
self._observer.isStopped = True
self._observer.isRunning = False | ['def', 'stopObserver', '(', 'self', ')', ':', 'self', '.', '_observer', '.', 'isStopped', '=', 'True', 'self', '.', '_observer', '.', 'isRunning', '=', 'False'] | Stops this region's observer loop.
If this is running in a subprocess, the subprocess will end automatically. | ['Stops', 'this', 'region', 's', 'observer', 'loop', '.'] | train | https://github.com/glitchassassin/lackey/blob/7adadfacd7f45d81186710be992f5668b15399fe/lackey/RegionMatching.py#L1486-L1492 |
1,335 | EUDAT-B2SAFE/B2HANDLE | b2handle/utilhandle.py | create_authentication_string | def create_authentication_string(username, password):
'''
Creates an authentication string from the username and password.
:username: Username.
:password: Password.
:return: The encoded string.
'''
username_utf8 = username.encode('utf-8')
userpw_utf8 = password.encode('utf-8')
username_perc = quote(username_utf8)
userpw_perc = quote(userpw_utf8)
authinfostring = username_perc + ':' + userpw_perc
authinfostring_base64 = base64.b64encode(authinfostring.encode('utf-8')).decode('utf-8')
return authinfostring_base64 | python | def create_authentication_string(username, password):
'''
Creates an authentication string from the username and password.
:username: Username.
:password: Password.
:return: The encoded string.
'''
username_utf8 = username.encode('utf-8')
userpw_utf8 = password.encode('utf-8')
username_perc = quote(username_utf8)
userpw_perc = quote(userpw_utf8)
authinfostring = username_perc + ':' + userpw_perc
authinfostring_base64 = base64.b64encode(authinfostring.encode('utf-8')).decode('utf-8')
return authinfostring_base64 | ['def', 'create_authentication_string', '(', 'username', ',', 'password', ')', ':', 'username_utf8', '=', 'username', '.', 'encode', '(', "'utf-8'", ')', 'userpw_utf8', '=', 'password', '.', 'encode', '(', "'utf-8'", ')', 'username_perc', '=', 'quote', '(', 'username_utf8', ')', 'userpw_perc', '=', 'quote', '(', 'userpw_utf8', ')', 'authinfostring', '=', 'username_perc', '+', "':'", '+', 'userpw_perc', 'authinfostring_base64', '=', 'base64', '.', 'b64encode', '(', 'authinfostring', '.', 'encode', '(', "'utf-8'", ')', ')', '.', 'decode', '(', "'utf-8'", ')', 'return', 'authinfostring_base64'] | Creates an authentication string from the username and password.
:username: Username.
:password: Password.
:return: The encoded string. | ['Creates', 'an', 'authentication', 'string', 'from', 'the', 'username', 'and', 'password', '.'] | train | https://github.com/EUDAT-B2SAFE/B2HANDLE/blob/a6d216d459644e01fbdfd5b318a535950bc5cdbb/b2handle/utilhandle.py#L102-L118 |
1,336 | brechtm/rinohtype | src/rinoh/hyphenator.py | Hyph_dict.positions | def positions(self, word):
"""
Returns a list of positions where the word can be hyphenated.
E.g. for the dutch word 'lettergrepen' this method returns
the list [3, 6, 9].
Each position is a 'data int' (dint) with a data attribute.
If the data attribute is not None, it contains a tuple with
information about nonstandard hyphenation at that point:
(change, index, cut)
change: is a string like 'ff=f', that describes how hyphenation
should take place.
index: where to substitute the change, counting from the current
point
cut: how many characters to remove while substituting the nonstandard
hyphenation
"""
word = word.lower()
points = self.cache.get(word)
if points is None:
prepWord = '.%s.' % word
res = [0] * (len(prepWord) + 1)
for i in range(len(prepWord) - 1):
for j in range(i + 1, min(i + self.maxlen, len(prepWord)) + 1):
p = self.patterns.get(prepWord[i:j])
if p:
offset, value = p
s = slice(i + offset, i + offset + len(value))
res[s] = map(max, value, res[s])
points = [dint(i - 1, ref=r) for i, r in enumerate(res) if r % 2]
self.cache[word] = points
return points | python | def positions(self, word):
"""
Returns a list of positions where the word can be hyphenated.
E.g. for the dutch word 'lettergrepen' this method returns
the list [3, 6, 9].
Each position is a 'data int' (dint) with a data attribute.
If the data attribute is not None, it contains a tuple with
information about nonstandard hyphenation at that point:
(change, index, cut)
change: is a string like 'ff=f', that describes how hyphenation
should take place.
index: where to substitute the change, counting from the current
point
cut: how many characters to remove while substituting the nonstandard
hyphenation
"""
word = word.lower()
points = self.cache.get(word)
if points is None:
prepWord = '.%s.' % word
res = [0] * (len(prepWord) + 1)
for i in range(len(prepWord) - 1):
for j in range(i + 1, min(i + self.maxlen, len(prepWord)) + 1):
p = self.patterns.get(prepWord[i:j])
if p:
offset, value = p
s = slice(i + offset, i + offset + len(value))
res[s] = map(max, value, res[s])
points = [dint(i - 1, ref=r) for i, r in enumerate(res) if r % 2]
self.cache[word] = points
return points | ['def', 'positions', '(', 'self', ',', 'word', ')', ':', 'word', '=', 'word', '.', 'lower', '(', ')', 'points', '=', 'self', '.', 'cache', '.', 'get', '(', 'word', ')', 'if', 'points', 'is', 'None', ':', 'prepWord', '=', "'.%s.'", '%', 'word', 'res', '=', '[', '0', ']', '*', '(', 'len', '(', 'prepWord', ')', '+', '1', ')', 'for', 'i', 'in', 'range', '(', 'len', '(', 'prepWord', ')', '-', '1', ')', ':', 'for', 'j', 'in', 'range', '(', 'i', '+', '1', ',', 'min', '(', 'i', '+', 'self', '.', 'maxlen', ',', 'len', '(', 'prepWord', ')', ')', '+', '1', ')', ':', 'p', '=', 'self', '.', 'patterns', '.', 'get', '(', 'prepWord', '[', 'i', ':', 'j', ']', ')', 'if', 'p', ':', 'offset', ',', 'value', '=', 'p', 's', '=', 'slice', '(', 'i', '+', 'offset', ',', 'i', '+', 'offset', '+', 'len', '(', 'value', ')', ')', 'res', '[', 's', ']', '=', 'map', '(', 'max', ',', 'value', ',', 'res', '[', 's', ']', ')', 'points', '=', '[', 'dint', '(', 'i', '-', '1', ',', 'ref', '=', 'r', ')', 'for', 'i', ',', 'r', 'in', 'enumerate', '(', 'res', ')', 'if', 'r', '%', '2', ']', 'self', '.', 'cache', '[', 'word', ']', '=', 'points', 'return', 'points'] | Returns a list of positions where the word can be hyphenated.
E.g. for the dutch word 'lettergrepen' this method returns
the list [3, 6, 9].
Each position is a 'data int' (dint) with a data attribute.
If the data attribute is not None, it contains a tuple with
information about nonstandard hyphenation at that point:
(change, index, cut)
change: is a string like 'ff=f', that describes how hyphenation
should take place.
index: where to substitute the change, counting from the current
point
cut: how many characters to remove while substituting the nonstandard
hyphenation | ['Returns', 'a', 'list', 'of', 'positions', 'where', 'the', 'word', 'can', 'be', 'hyphenated', '.', 'E', '.', 'g', '.', 'for', 'the', 'dutch', 'word', 'lettergrepen', 'this', 'method', 'returns', 'the', 'list', '[', '3', '6', '9', ']', '.'] | train | https://github.com/brechtm/rinohtype/blob/40a63c4e5ad7550f62b6860f1812cb67cafb9dc7/src/rinoh/hyphenator.py#L114-L147 |
1,337 | ensime/ensime-vim | ensime_shared/ticker.py | Ticker._start_refresh_timer | def _start_refresh_timer(self):
"""Start the Vim timer. """
if not self._timer:
self._timer = self._vim.eval(
"timer_start({}, 'EnTick', {{'repeat': -1}})"
.format(REFRESH_TIMER)
) | python | def _start_refresh_timer(self):
"""Start the Vim timer. """
if not self._timer:
self._timer = self._vim.eval(
"timer_start({}, 'EnTick', {{'repeat': -1}})"
.format(REFRESH_TIMER)
) | ['def', '_start_refresh_timer', '(', 'self', ')', ':', 'if', 'not', 'self', '.', '_timer', ':', 'self', '.', '_timer', '=', 'self', '.', '_vim', '.', 'eval', '(', '"timer_start({}, \'EnTick\', {{\'repeat\': -1}})"', '.', 'format', '(', 'REFRESH_TIMER', ')', ')'] | Start the Vim timer. | ['Start', 'the', 'Vim', 'timer', '.'] | train | https://github.com/ensime/ensime-vim/blob/caa734e84f002b25446c615706283a74edd4ecfe/ensime_shared/ticker.py#L30-L36 |
1,338 | arviz-devs/arviz | arviz/stats/stats.py | loo | def loo(data, pointwise=False, reff=None, scale="deviance"):
"""Pareto-smoothed importance sampling leave-one-out cross-validation.
Calculates leave-one-out (LOO) cross-validation for out of sample predictive model fit,
following Vehtari et al. (2017). Cross-validation is computed using Pareto-smoothed
importance sampling (PSIS).
Parameters
----------
data : result of MCMC run
pointwise: bool, optional
if True the pointwise predictive accuracy will be returned. Defaults to False
reff : float, optional
Relative MCMC efficiency, `effective_n / n` i.e. number of effective samples divided by
the number of actual samples. Computed from trace by default.
scale : str
Output scale for loo. Available options are:
- `deviance` : (default) -2 * (log-score)
- `log` : 1 * log-score (after Vehtari et al. (2017))
- `negative_log` : -1 * (log-score)
Returns
-------
pandas.Series with the following columns:
loo: approximated Leave-one-out cross-validation
loo_se: standard error of loo
p_loo: effective number of parameters
shape_warn: 1 if the estimated shape parameter of
Pareto distribution is greater than 0.7 for one or more samples
loo_i: array of pointwise predictive accuracy, only if pointwise True
pareto_k: array of Pareto shape values, only if pointwise True
loo_scale: scale of the loo results
"""
inference_data = convert_to_inference_data(data)
for group in ("posterior", "sample_stats"):
if not hasattr(inference_data, group):
raise TypeError(
"Must be able to extract a {group}" "group from data!".format(group=group)
)
if "log_likelihood" not in inference_data.sample_stats:
raise TypeError("Data must include log_likelihood in sample_stats")
posterior = inference_data.posterior
log_likelihood = inference_data.sample_stats.log_likelihood
n_samples = log_likelihood.chain.size * log_likelihood.draw.size
new_shape = (n_samples,) + log_likelihood.shape[2:]
log_likelihood = log_likelihood.values.reshape(*new_shape)
if scale.lower() == "deviance":
scale_value = -2
elif scale.lower() == "log":
scale_value = 1
elif scale.lower() == "negative_log":
scale_value = -1
else:
raise TypeError('Valid scale values are "deviance", "log", "negative_log"')
if reff is None:
n_chains = len(posterior.chain)
if n_chains == 1:
reff = 1.0
else:
ess = effective_sample_size(posterior)
# this mean is over all data variables
reff = np.hstack([ess[v].values.flatten() for v in ess.data_vars]).mean() / n_samples
log_weights, pareto_shape = psislw(-log_likelihood, reff)
log_weights += log_likelihood
warn_mg = 0
if np.any(pareto_shape > 0.7):
warnings.warn(
"""Estimated shape parameter of Pareto distribution is greater than 0.7 for
one or more samples. You should consider using a more robust model, this is because
importance sampling is less likely to work well if the marginal posterior and LOO posterior
are very different. This is more likely to happen with a non-robust model and highly
influential observations."""
)
warn_mg = 1
loo_lppd_i = scale_value * _logsumexp(log_weights, axis=0)
loo_lppd = loo_lppd_i.sum()
loo_lppd_se = (len(loo_lppd_i) * np.var(loo_lppd_i)) ** 0.5
lppd = np.sum(_logsumexp(log_likelihood, axis=0, b_inv=log_likelihood.shape[0]))
p_loo = lppd - loo_lppd / scale_value
if pointwise:
if np.equal(loo_lppd, loo_lppd_i).all(): # pylint: disable=no-member
warnings.warn(
"""The point-wise LOO is the same with the sum LOO, please double check
the Observed RV in your model to make sure it returns element-wise logp.
"""
)
return pd.Series(
data=[loo_lppd, loo_lppd_se, p_loo, warn_mg, loo_lppd_i, pareto_shape, scale],
index=["loo", "loo_se", "p_loo", "warning", "loo_i", "pareto_k", "loo_scale"],
)
else:
return pd.Series(
data=[loo_lppd, loo_lppd_se, p_loo, warn_mg, scale],
index=["loo", "loo_se", "p_loo", "warning", "loo_scale"],
) | python | def loo(data, pointwise=False, reff=None, scale="deviance"):
"""Pareto-smoothed importance sampling leave-one-out cross-validation.
Calculates leave-one-out (LOO) cross-validation for out of sample predictive model fit,
following Vehtari et al. (2017). Cross-validation is computed using Pareto-smoothed
importance sampling (PSIS).
Parameters
----------
data : result of MCMC run
pointwise: bool, optional
if True the pointwise predictive accuracy will be returned. Defaults to False
reff : float, optional
Relative MCMC efficiency, `effective_n / n` i.e. number of effective samples divided by
the number of actual samples. Computed from trace by default.
scale : str
Output scale for loo. Available options are:
- `deviance` : (default) -2 * (log-score)
- `log` : 1 * log-score (after Vehtari et al. (2017))
- `negative_log` : -1 * (log-score)
Returns
-------
pandas.Series with the following columns:
loo: approximated Leave-one-out cross-validation
loo_se: standard error of loo
p_loo: effective number of parameters
shape_warn: 1 if the estimated shape parameter of
Pareto distribution is greater than 0.7 for one or more samples
loo_i: array of pointwise predictive accuracy, only if pointwise True
pareto_k: array of Pareto shape values, only if pointwise True
loo_scale: scale of the loo results
"""
inference_data = convert_to_inference_data(data)
for group in ("posterior", "sample_stats"):
if not hasattr(inference_data, group):
raise TypeError(
"Must be able to extract a {group}" "group from data!".format(group=group)
)
if "log_likelihood" not in inference_data.sample_stats:
raise TypeError("Data must include log_likelihood in sample_stats")
posterior = inference_data.posterior
log_likelihood = inference_data.sample_stats.log_likelihood
n_samples = log_likelihood.chain.size * log_likelihood.draw.size
new_shape = (n_samples,) + log_likelihood.shape[2:]
log_likelihood = log_likelihood.values.reshape(*new_shape)
if scale.lower() == "deviance":
scale_value = -2
elif scale.lower() == "log":
scale_value = 1
elif scale.lower() == "negative_log":
scale_value = -1
else:
raise TypeError('Valid scale values are "deviance", "log", "negative_log"')
if reff is None:
n_chains = len(posterior.chain)
if n_chains == 1:
reff = 1.0
else:
ess = effective_sample_size(posterior)
# this mean is over all data variables
reff = np.hstack([ess[v].values.flatten() for v in ess.data_vars]).mean() / n_samples
log_weights, pareto_shape = psislw(-log_likelihood, reff)
log_weights += log_likelihood
warn_mg = 0
if np.any(pareto_shape > 0.7):
warnings.warn(
"""Estimated shape parameter of Pareto distribution is greater than 0.7 for
one or more samples. You should consider using a more robust model, this is because
importance sampling is less likely to work well if the marginal posterior and LOO posterior
are very different. This is more likely to happen with a non-robust model and highly
influential observations."""
)
warn_mg = 1
loo_lppd_i = scale_value * _logsumexp(log_weights, axis=0)
loo_lppd = loo_lppd_i.sum()
loo_lppd_se = (len(loo_lppd_i) * np.var(loo_lppd_i)) ** 0.5
lppd = np.sum(_logsumexp(log_likelihood, axis=0, b_inv=log_likelihood.shape[0]))
p_loo = lppd - loo_lppd / scale_value
if pointwise:
if np.equal(loo_lppd, loo_lppd_i).all(): # pylint: disable=no-member
warnings.warn(
"""The point-wise LOO is the same with the sum LOO, please double check
the Observed RV in your model to make sure it returns element-wise logp.
"""
)
return pd.Series(
data=[loo_lppd, loo_lppd_se, p_loo, warn_mg, loo_lppd_i, pareto_shape, scale],
index=["loo", "loo_se", "p_loo", "warning", "loo_i", "pareto_k", "loo_scale"],
)
else:
return pd.Series(
data=[loo_lppd, loo_lppd_se, p_loo, warn_mg, scale],
index=["loo", "loo_se", "p_loo", "warning", "loo_scale"],
) | ['def', 'loo', '(', 'data', ',', 'pointwise', '=', 'False', ',', 'reff', '=', 'None', ',', 'scale', '=', '"deviance"', ')', ':', 'inference_data', '=', 'convert_to_inference_data', '(', 'data', ')', 'for', 'group', 'in', '(', '"posterior"', ',', '"sample_stats"', ')', ':', 'if', 'not', 'hasattr', '(', 'inference_data', ',', 'group', ')', ':', 'raise', 'TypeError', '(', '"Must be able to extract a {group}"', '"group from data!"', '.', 'format', '(', 'group', '=', 'group', ')', ')', 'if', '"log_likelihood"', 'not', 'in', 'inference_data', '.', 'sample_stats', ':', 'raise', 'TypeError', '(', '"Data must include log_likelihood in sample_stats"', ')', 'posterior', '=', 'inference_data', '.', 'posterior', 'log_likelihood', '=', 'inference_data', '.', 'sample_stats', '.', 'log_likelihood', 'n_samples', '=', 'log_likelihood', '.', 'chain', '.', 'size', '*', 'log_likelihood', '.', 'draw', '.', 'size', 'new_shape', '=', '(', 'n_samples', ',', ')', '+', 'log_likelihood', '.', 'shape', '[', '2', ':', ']', 'log_likelihood', '=', 'log_likelihood', '.', 'values', '.', 'reshape', '(', '*', 'new_shape', ')', 'if', 'scale', '.', 'lower', '(', ')', '==', '"deviance"', ':', 'scale_value', '=', '-', '2', 'elif', 'scale', '.', 'lower', '(', ')', '==', '"log"', ':', 'scale_value', '=', '1', 'elif', 'scale', '.', 'lower', '(', ')', '==', '"negative_log"', ':', 'scale_value', '=', '-', '1', 'else', ':', 'raise', 'TypeError', '(', '\'Valid scale values are "deviance", "log", "negative_log"\'', ')', 'if', 'reff', 'is', 'None', ':', 'n_chains', '=', 'len', '(', 'posterior', '.', 'chain', ')', 'if', 'n_chains', '==', '1', ':', 'reff', '=', '1.0', 'else', ':', 'ess', '=', 'effective_sample_size', '(', 'posterior', ')', '# this mean is over all data variables', 'reff', '=', 'np', '.', 'hstack', '(', '[', 'ess', '[', 'v', ']', '.', 'values', '.', 'flatten', '(', ')', 'for', 'v', 'in', 'ess', '.', 'data_vars', ']', ')', '.', 'mean', '(', ')', '/', 'n_samples', 'log_weights', ',', 'pareto_shape', '=', 'psislw', '(', '-', 'log_likelihood', ',', 'reff', ')', 'log_weights', '+=', 'log_likelihood', 'warn_mg', '=', '0', 'if', 'np', '.', 'any', '(', 'pareto_shape', '>', '0.7', ')', ':', 'warnings', '.', 'warn', '(', '"""Estimated shape parameter of Pareto distribution is greater than 0.7 for\n one or more samples. You should consider using a more robust model, this is because\n importance sampling is less likely to work well if the marginal posterior and LOO posterior\n are very different. This is more likely to happen with a non-robust model and highly\n influential observations."""', ')', 'warn_mg', '=', '1', 'loo_lppd_i', '=', 'scale_value', '*', '_logsumexp', '(', 'log_weights', ',', 'axis', '=', '0', ')', 'loo_lppd', '=', 'loo_lppd_i', '.', 'sum', '(', ')', 'loo_lppd_se', '=', '(', 'len', '(', 'loo_lppd_i', ')', '*', 'np', '.', 'var', '(', 'loo_lppd_i', ')', ')', '**', '0.5', 'lppd', '=', 'np', '.', 'sum', '(', '_logsumexp', '(', 'log_likelihood', ',', 'axis', '=', '0', ',', 'b_inv', '=', 'log_likelihood', '.', 'shape', '[', '0', ']', ')', ')', 'p_loo', '=', 'lppd', '-', 'loo_lppd', '/', 'scale_value', 'if', 'pointwise', ':', 'if', 'np', '.', 'equal', '(', 'loo_lppd', ',', 'loo_lppd_i', ')', '.', 'all', '(', ')', ':', '# pylint: disable=no-member', 'warnings', '.', 'warn', '(', '"""The point-wise LOO is the same with the sum LOO, please double check\n the Observed RV in your model to make sure it returns element-wise logp.\n """', ')', 'return', 'pd', '.', 'Series', '(', 'data', '=', '[', 'loo_lppd', ',', 'loo_lppd_se', ',', 'p_loo', ',', 'warn_mg', ',', 'loo_lppd_i', ',', 'pareto_shape', ',', 'scale', ']', ',', 'index', '=', '[', '"loo"', ',', '"loo_se"', ',', '"p_loo"', ',', '"warning"', ',', '"loo_i"', ',', '"pareto_k"', ',', '"loo_scale"', ']', ',', ')', 'else', ':', 'return', 'pd', '.', 'Series', '(', 'data', '=', '[', 'loo_lppd', ',', 'loo_lppd_se', ',', 'p_loo', ',', 'warn_mg', ',', 'scale', ']', ',', 'index', '=', '[', '"loo"', ',', '"loo_se"', ',', '"p_loo"', ',', '"warning"', ',', '"loo_scale"', ']', ',', ')'] | Pareto-smoothed importance sampling leave-one-out cross-validation.
Calculates leave-one-out (LOO) cross-validation for out of sample predictive model fit,
following Vehtari et al. (2017). Cross-validation is computed using Pareto-smoothed
importance sampling (PSIS).
Parameters
----------
data : result of MCMC run
pointwise: bool, optional
if True the pointwise predictive accuracy will be returned. Defaults to False
reff : float, optional
Relative MCMC efficiency, `effective_n / n` i.e. number of effective samples divided by
the number of actual samples. Computed from trace by default.
scale : str
Output scale for loo. Available options are:
- `deviance` : (default) -2 * (log-score)
- `log` : 1 * log-score (after Vehtari et al. (2017))
- `negative_log` : -1 * (log-score)
Returns
-------
pandas.Series with the following columns:
loo: approximated Leave-one-out cross-validation
loo_se: standard error of loo
p_loo: effective number of parameters
shape_warn: 1 if the estimated shape parameter of
Pareto distribution is greater than 0.7 for one or more samples
loo_i: array of pointwise predictive accuracy, only if pointwise True
pareto_k: array of Pareto shape values, only if pointwise True
loo_scale: scale of the loo results | ['Pareto', '-', 'smoothed', 'importance', 'sampling', 'leave', '-', 'one', '-', 'out', 'cross', '-', 'validation', '.'] | train | https://github.com/arviz-devs/arviz/blob/d04d8da07f029fd2931f48d2f7f324cf393e5277/arviz/stats/stats.py#L387-L490 |
1,339 | codelv/enaml-native | src/enamlnative/widgets/scroll_view.py | ScrollView._update_proxy | def _update_proxy(self, change):
""" An observer which sends the state change to the proxy.
"""
if change['type'] in ['event', 'update'] and self.proxy_is_active:
handler = getattr(self.proxy, 'set_' + change['name'], None)
if handler is not None:
handler(change['value']) | python | def _update_proxy(self, change):
""" An observer which sends the state change to the proxy.
"""
if change['type'] in ['event', 'update'] and self.proxy_is_active:
handler = getattr(self.proxy, 'set_' + change['name'], None)
if handler is not None:
handler(change['value']) | ['def', '_update_proxy', '(', 'self', ',', 'change', ')', ':', 'if', 'change', '[', "'type'", ']', 'in', '[', "'event'", ',', "'update'", ']', 'and', 'self', '.', 'proxy_is_active', ':', 'handler', '=', 'getattr', '(', 'self', '.', 'proxy', ',', "'set_'", '+', 'change', '[', "'name'", ']', ',', 'None', ')', 'if', 'handler', 'is', 'not', 'None', ':', 'handler', '(', 'change', '[', "'value'", ']', ')'] | An observer which sends the state change to the proxy. | ['An', 'observer', 'which', 'sends', 'the', 'state', 'change', 'to', 'the', 'proxy', '.'] | train | https://github.com/codelv/enaml-native/blob/c33986e9eda468c508806e0a3e73c771401e5718/src/enamlnative/widgets/scroll_view.py#L65-L72 |
1,340 | kislyuk/aegea | aegea/packages/github3/repos/hook.py | Hook.edit | def edit(self, config={}, events=[], add_events=[], rm_events=[],
active=True):
"""Edit this hook.
:param dict config: (optional), key-value pairs of settings for this
hook
:param list events: (optional), which events should this be triggered
for
:param list add_events: (optional), events to be added to the list of
events that this hook triggers for
:param list rm_events: (optional), events to be remvoed from the list
of events that this hook triggers for
:param bool active: (optional), should this event be active
:returns: bool
"""
data = {'config': config, 'active': active}
if events:
data['events'] = events
if add_events:
data['add_events'] = add_events
if rm_events:
data['remove_events'] = rm_events
json = self._json(self._patch(self._api, data=dumps(data)), 200)
if json:
self._update_(json)
return True
return False | python | def edit(self, config={}, events=[], add_events=[], rm_events=[],
active=True):
"""Edit this hook.
:param dict config: (optional), key-value pairs of settings for this
hook
:param list events: (optional), which events should this be triggered
for
:param list add_events: (optional), events to be added to the list of
events that this hook triggers for
:param list rm_events: (optional), events to be remvoed from the list
of events that this hook triggers for
:param bool active: (optional), should this event be active
:returns: bool
"""
data = {'config': config, 'active': active}
if events:
data['events'] = events
if add_events:
data['add_events'] = add_events
if rm_events:
data['remove_events'] = rm_events
json = self._json(self._patch(self._api, data=dumps(data)), 200)
if json:
self._update_(json)
return True
return False | ['def', 'edit', '(', 'self', ',', 'config', '=', '{', '}', ',', 'events', '=', '[', ']', ',', 'add_events', '=', '[', ']', ',', 'rm_events', '=', '[', ']', ',', 'active', '=', 'True', ')', ':', 'data', '=', '{', "'config'", ':', 'config', ',', "'active'", ':', 'active', '}', 'if', 'events', ':', 'data', '[', "'events'", ']', '=', 'events', 'if', 'add_events', ':', 'data', '[', "'add_events'", ']', '=', 'add_events', 'if', 'rm_events', ':', 'data', '[', "'remove_events'", ']', '=', 'rm_events', 'json', '=', 'self', '.', '_json', '(', 'self', '.', '_patch', '(', 'self', '.', '_api', ',', 'data', '=', 'dumps', '(', 'data', ')', ')', ',', '200', ')', 'if', 'json', ':', 'self', '.', '_update_', '(', 'json', ')', 'return', 'True', 'return', 'False'] | Edit this hook.
:param dict config: (optional), key-value pairs of settings for this
hook
:param list events: (optional), which events should this be triggered
for
:param list add_events: (optional), events to be added to the list of
events that this hook triggers for
:param list rm_events: (optional), events to be remvoed from the list
of events that this hook triggers for
:param bool active: (optional), should this event be active
:returns: bool | ['Edit', 'this', 'hook', '.'] | train | https://github.com/kislyuk/aegea/blob/94957e9dba036eae3052e2662c208b259c08399a/aegea/packages/github3/repos/hook.py#L65-L96 |
1,341 | coghost/izen | izen/chaos.py | RsaPub.rsa_base64_encrypt | def rsa_base64_encrypt(self, plain, b64=True):
"""
使用公钥加密 ``可见数据``
- 由于rsa公钥加密相对耗时, 多用来 ``加密数据量小`` 的数据
.. note::
1. 使用aes加密数据
2. 然后rsa用来加密aes加密数据时使用的key
:param plain:
:type plain:
:param b64:
:type b64:
:return:
:rtype:
"""
with open(self.key_file) as fp:
key_ = RSA.importKey(fp.read())
plain = helper.to_bytes(plain)
cipher = PKCS1_v1_5.new(key_).encrypt(plain)
cip = base64.b64encode(cipher) if b64 else cipher
return helper.to_str(cip) | python | def rsa_base64_encrypt(self, plain, b64=True):
"""
使用公钥加密 ``可见数据``
- 由于rsa公钥加密相对耗时, 多用来 ``加密数据量小`` 的数据
.. note::
1. 使用aes加密数据
2. 然后rsa用来加密aes加密数据时使用的key
:param plain:
:type plain:
:param b64:
:type b64:
:return:
:rtype:
"""
with open(self.key_file) as fp:
key_ = RSA.importKey(fp.read())
plain = helper.to_bytes(plain)
cipher = PKCS1_v1_5.new(key_).encrypt(plain)
cip = base64.b64encode(cipher) if b64 else cipher
return helper.to_str(cip) | ['def', 'rsa_base64_encrypt', '(', 'self', ',', 'plain', ',', 'b64', '=', 'True', ')', ':', 'with', 'open', '(', 'self', '.', 'key_file', ')', 'as', 'fp', ':', 'key_', '=', 'RSA', '.', 'importKey', '(', 'fp', '.', 'read', '(', ')', ')', 'plain', '=', 'helper', '.', 'to_bytes', '(', 'plain', ')', 'cipher', '=', 'PKCS1_v1_5', '.', 'new', '(', 'key_', ')', '.', 'encrypt', '(', 'plain', ')', 'cip', '=', 'base64', '.', 'b64encode', '(', 'cipher', ')', 'if', 'b64', 'else', 'cipher', 'return', 'helper', '.', 'to_str', '(', 'cip', ')'] | 使用公钥加密 ``可见数据``
- 由于rsa公钥加密相对耗时, 多用来 ``加密数据量小`` 的数据
.. note::
1. 使用aes加密数据
2. 然后rsa用来加密aes加密数据时使用的key
:param plain:
:type plain:
:param b64:
:type b64:
:return:
:rtype: | ['使用公钥加密', '可见数据'] | train | https://github.com/coghost/izen/blob/432db017f99dd2ba809e1ba1792145ab6510263d/izen/chaos.py#L143-L165 |
1,342 | doconix/django-mako-plus | django_mako_plus/tags.py | django_include | def django_include(context, template_name, **kwargs):
'''
Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2.1/topics/templates/.
The current context is sent to the included template, which makes all context
variables available to the Django template. Any additional kwargs are added
to the context.
'''
try:
djengine = engines['django']
except KeyError as e:
raise TemplateDoesNotExist("Django template engine not configured in settings, so template cannot be found: {}".format(template_name)) from e
djtemplate = djengine.get_template(template_name)
djcontext = {}
djcontext.update(context)
djcontext.update(kwargs)
return djtemplate.render(djcontext, context['request']) | python | def django_include(context, template_name, **kwargs):
'''
Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2.1/topics/templates/.
The current context is sent to the included template, which makes all context
variables available to the Django template. Any additional kwargs are added
to the context.
'''
try:
djengine = engines['django']
except KeyError as e:
raise TemplateDoesNotExist("Django template engine not configured in settings, so template cannot be found: {}".format(template_name)) from e
djtemplate = djengine.get_template(template_name)
djcontext = {}
djcontext.update(context)
djcontext.update(kwargs)
return djtemplate.render(djcontext, context['request']) | ['def', 'django_include', '(', 'context', ',', 'template_name', ',', '*', '*', 'kwargs', ')', ':', 'try', ':', 'djengine', '=', 'engines', '[', "'django'", ']', 'except', 'KeyError', 'as', 'e', ':', 'raise', 'TemplateDoesNotExist', '(', '"Django template engine not configured in settings, so template cannot be found: {}"', '.', 'format', '(', 'template_name', ')', ')', 'from', 'e', 'djtemplate', '=', 'djengine', '.', 'get_template', '(', 'template_name', ')', 'djcontext', '=', '{', '}', 'djcontext', '.', 'update', '(', 'context', ')', 'djcontext', '.', 'update', '(', 'kwargs', ')', 'return', 'djtemplate', '.', 'render', '(', 'djcontext', ',', 'context', '[', "'request'", ']', ')'] | Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2.1/topics/templates/.
The current context is sent to the included template, which makes all context
variables available to the Django template. Any additional kwargs are added
to the context. | ['Mako', 'tag', 'to', 'include', 'a', 'Django', 'template', 'withing', 'the', 'current', 'DMP', '(', 'Mako', ')', 'template', '.', 'Since', 'this', 'is', 'a', 'Django', 'template', 'it', 'is', 'search', 'for', 'using', 'the', 'Django', 'search', 'algorithm', '(', 'instead', 'of', 'the', 'DMP', 'app', '-', 'based', 'concept', ')', '.', 'See', 'https', ':', '//', 'docs', '.', 'djangoproject', '.', 'com', '/', 'en', '/', '2', '.', '1', '/', 'topics', '/', 'templates', '/', '.'] | train | https://github.com/doconix/django-mako-plus/blob/a90f9b4af19e5fa9f83452989cdcaed21569a181/django_mako_plus/tags.py#L14-L33 |
1,343 | ardydedase/pycouchbase | couchbase-python-cffi/couchbase_ffi/result.py | MultiResult._add_bad_rc | def _add_bad_rc(self, rc, result):
"""
Sets an error with a bad return code. Handles 'quiet' logic
:param rc: The error code
"""
if not rc:
return
self.all_ok = False
if rc == C.LCB_KEY_ENOENT and self._quiet:
return
try:
raise pycbc_exc_lcb(rc)
except PyCBC.default_exception as e:
e.all_results = self
e.key = result.key
e.result = result
self._add_err(sys.exc_info()) | python | def _add_bad_rc(self, rc, result):
"""
Sets an error with a bad return code. Handles 'quiet' logic
:param rc: The error code
"""
if not rc:
return
self.all_ok = False
if rc == C.LCB_KEY_ENOENT and self._quiet:
return
try:
raise pycbc_exc_lcb(rc)
except PyCBC.default_exception as e:
e.all_results = self
e.key = result.key
e.result = result
self._add_err(sys.exc_info()) | ['def', '_add_bad_rc', '(', 'self', ',', 'rc', ',', 'result', ')', ':', 'if', 'not', 'rc', ':', 'return', 'self', '.', 'all_ok', '=', 'False', 'if', 'rc', '==', 'C', '.', 'LCB_KEY_ENOENT', 'and', 'self', '.', '_quiet', ':', 'return', 'try', ':', 'raise', 'pycbc_exc_lcb', '(', 'rc', ')', 'except', 'PyCBC', '.', 'default_exception', 'as', 'e', ':', 'e', '.', 'all_results', '=', 'self', 'e', '.', 'key', '=', 'result', '.', 'key', 'e', '.', 'result', '=', 'result', 'self', '.', '_add_err', '(', 'sys', '.', 'exc_info', '(', ')', ')'] | Sets an error with a bad return code. Handles 'quiet' logic
:param rc: The error code | ['Sets', 'an', 'error', 'with', 'a', 'bad', 'return', 'code', '.', 'Handles', 'quiet', 'logic', ':', 'param', 'rc', ':', 'The', 'error', 'code'] | train | https://github.com/ardydedase/pycouchbase/blob/6f010b4d2ef41aead2366878d0cf0b1284c0db0e/couchbase-python-cffi/couchbase_ffi/result.py#L132-L150 |
1,344 | mabuchilab/QNET | src/qnet/algebra/pattern_matching/__init__.py | Pattern.finditer | def finditer(self, expr):
"""Return an iterator over all matches in `expr`
Iterate over all :class:`MatchDict` results of matches for any
matching (sub-)expressions in `expr`. The order of the matches conforms
to the equivalent matched expressions returned by :meth:`findall`.
"""
try:
for arg in expr.args:
for m in self.finditer(arg):
yield m
for arg in expr.kwargs.values():
for m in self.finditer(arg):
yield m
except AttributeError:
pass
m = self.match(expr)
if m:
yield m | python | def finditer(self, expr):
"""Return an iterator over all matches in `expr`
Iterate over all :class:`MatchDict` results of matches for any
matching (sub-)expressions in `expr`. The order of the matches conforms
to the equivalent matched expressions returned by :meth:`findall`.
"""
try:
for arg in expr.args:
for m in self.finditer(arg):
yield m
for arg in expr.kwargs.values():
for m in self.finditer(arg):
yield m
except AttributeError:
pass
m = self.match(expr)
if m:
yield m | ['def', 'finditer', '(', 'self', ',', 'expr', ')', ':', 'try', ':', 'for', 'arg', 'in', 'expr', '.', 'args', ':', 'for', 'm', 'in', 'self', '.', 'finditer', '(', 'arg', ')', ':', 'yield', 'm', 'for', 'arg', 'in', 'expr', '.', 'kwargs', '.', 'values', '(', ')', ':', 'for', 'm', 'in', 'self', '.', 'finditer', '(', 'arg', ')', ':', 'yield', 'm', 'except', 'AttributeError', ':', 'pass', 'm', '=', 'self', '.', 'match', '(', 'expr', ')', 'if', 'm', ':', 'yield', 'm'] | Return an iterator over all matches in `expr`
Iterate over all :class:`MatchDict` results of matches for any
matching (sub-)expressions in `expr`. The order of the matches conforms
to the equivalent matched expressions returned by :meth:`findall`. | ['Return', 'an', 'iterator', 'over', 'all', 'matches', 'in', 'expr'] | train | https://github.com/mabuchilab/QNET/blob/cc20d26dad78691d34c67173e5cd67dcac94208a/src/qnet/algebra/pattern_matching/__init__.py#L370-L388 |
1,345 | QUANTAXIS/QUANTAXIS | QUANTAXIS/QASetting/executor.py | execute | def execute(command, shell=None, working_dir=".", echo=False, echo_indent=0):
"""Execute a command on the command-line.
:param str,list command: The command to run
:param bool shell: Whether or not to use the shell. This is optional; if
``command`` is a basestring, shell will be set to True, otherwise it will
be false. You can override this behavior by setting this parameter
directly.
:param str working_dir: The directory in which to run the command.
:param bool echo: Whether or not to print the output from the command to
stdout.
:param int echo_indent: Any number of spaces to indent the echo for clarity
:returns: tuple: (return code, stdout)
Example
>>> from executor import execute
>>> return_code, text = execute("dir")
"""
if shell is None:
shell = True if isinstance(command, str) else False
p = Popen(command, stdin=PIPE, stdout=PIPE,
stderr=STDOUT, shell=shell, cwd=working_dir)
if echo:
stdout = ""
while p.poll() is None:
# This blocks until it receives a newline.
line = p.stdout.readline()
print(" " * echo_indent, line, end="")
stdout += line
# Read any last bits
line = p.stdout.read()
print(" " * echo_indent, line, end="")
print()
stdout += line
else:
stdout, _ = p.communicate()
return (p.returncode, stdout) | python | def execute(command, shell=None, working_dir=".", echo=False, echo_indent=0):
"""Execute a command on the command-line.
:param str,list command: The command to run
:param bool shell: Whether or not to use the shell. This is optional; if
``command`` is a basestring, shell will be set to True, otherwise it will
be false. You can override this behavior by setting this parameter
directly.
:param str working_dir: The directory in which to run the command.
:param bool echo: Whether or not to print the output from the command to
stdout.
:param int echo_indent: Any number of spaces to indent the echo for clarity
:returns: tuple: (return code, stdout)
Example
>>> from executor import execute
>>> return_code, text = execute("dir")
"""
if shell is None:
shell = True if isinstance(command, str) else False
p = Popen(command, stdin=PIPE, stdout=PIPE,
stderr=STDOUT, shell=shell, cwd=working_dir)
if echo:
stdout = ""
while p.poll() is None:
# This blocks until it receives a newline.
line = p.stdout.readline()
print(" " * echo_indent, line, end="")
stdout += line
# Read any last bits
line = p.stdout.read()
print(" " * echo_indent, line, end="")
print()
stdout += line
else:
stdout, _ = p.communicate()
return (p.returncode, stdout) | ['def', 'execute', '(', 'command', ',', 'shell', '=', 'None', ',', 'working_dir', '=', '"."', ',', 'echo', '=', 'False', ',', 'echo_indent', '=', '0', ')', ':', 'if', 'shell', 'is', 'None', ':', 'shell', '=', 'True', 'if', 'isinstance', '(', 'command', ',', 'str', ')', 'else', 'False', 'p', '=', 'Popen', '(', 'command', ',', 'stdin', '=', 'PIPE', ',', 'stdout', '=', 'PIPE', ',', 'stderr', '=', 'STDOUT', ',', 'shell', '=', 'shell', ',', 'cwd', '=', 'working_dir', ')', 'if', 'echo', ':', 'stdout', '=', '""', 'while', 'p', '.', 'poll', '(', ')', 'is', 'None', ':', '# This blocks until it receives a newline.', 'line', '=', 'p', '.', 'stdout', '.', 'readline', '(', ')', 'print', '(', '" "', '*', 'echo_indent', ',', 'line', ',', 'end', '=', '""', ')', 'stdout', '+=', 'line', '# Read any last bits', 'line', '=', 'p', '.', 'stdout', '.', 'read', '(', ')', 'print', '(', '" "', '*', 'echo_indent', ',', 'line', ',', 'end', '=', '""', ')', 'print', '(', ')', 'stdout', '+=', 'line', 'else', ':', 'stdout', ',', '_', '=', 'p', '.', 'communicate', '(', ')', 'return', '(', 'p', '.', 'returncode', ',', 'stdout', ')'] | Execute a command on the command-line.
:param str,list command: The command to run
:param bool shell: Whether or not to use the shell. This is optional; if
``command`` is a basestring, shell will be set to True, otherwise it will
be false. You can override this behavior by setting this parameter
directly.
:param str working_dir: The directory in which to run the command.
:param bool echo: Whether or not to print the output from the command to
stdout.
:param int echo_indent: Any number of spaces to indent the echo for clarity
:returns: tuple: (return code, stdout)
Example
>>> from executor import execute
>>> return_code, text = execute("dir") | ['Execute', 'a', 'command', 'on', 'the', 'command', '-', 'line', '.', ':', 'param', 'str', 'list', 'command', ':', 'The', 'command', 'to', 'run', ':', 'param', 'bool', 'shell', ':', 'Whether', 'or', 'not', 'to', 'use', 'the', 'shell', '.', 'This', 'is', 'optional', ';', 'if', 'command', 'is', 'a', 'basestring', 'shell', 'will', 'be', 'set', 'to', 'True', 'otherwise', 'it', 'will', 'be', 'false', '.', 'You', 'can', 'override', 'this', 'behavior', 'by', 'setting', 'this', 'parameter', 'directly', '.', ':', 'param', 'str', 'working_dir', ':', 'The', 'directory', 'in', 'which', 'to', 'run', 'the', 'command', '.', ':', 'param', 'bool', 'echo', ':', 'Whether', 'or', 'not', 'to', 'print', 'the', 'output', 'from', 'the', 'command', 'to', 'stdout', '.', ':', 'param', 'int', 'echo_indent', ':', 'Any', 'number', 'of', 'spaces', 'to', 'indent', 'the', 'echo', 'for', 'clarity', ':', 'returns', ':', 'tuple', ':', '(', 'return', 'code', 'stdout', ')', 'Example', '>>>', 'from', 'executor', 'import', 'execute', '>>>', 'return_code', 'text', '=', 'execute', '(', 'dir', ')'] | train | https://github.com/QUANTAXIS/QUANTAXIS/blob/bb1fe424e4108b62a1f712b81a05cf829297a5c0/QUANTAXIS/QASetting/executor.py#L33-L71 |
1,346 | aio-libs/aiodocker | aiodocker/docker.py | Docker._query_json | async def _query_json(
self, path, method="GET", *, params=None, data=None, headers=None, timeout=None
):
"""
A shorthand of _query() that treats the input as JSON.
"""
if headers is None:
headers = {}
headers["content-type"] = "application/json"
if not isinstance(data, (str, bytes)):
data = json.dumps(data)
response = await self._query(
path, method, params=params, data=data, headers=headers, timeout=timeout
)
data = await parse_result(response)
return data | python | async def _query_json(
self, path, method="GET", *, params=None, data=None, headers=None, timeout=None
):
"""
A shorthand of _query() that treats the input as JSON.
"""
if headers is None:
headers = {}
headers["content-type"] = "application/json"
if not isinstance(data, (str, bytes)):
data = json.dumps(data)
response = await self._query(
path, method, params=params, data=data, headers=headers, timeout=timeout
)
data = await parse_result(response)
return data | ['async', 'def', '_query_json', '(', 'self', ',', 'path', ',', 'method', '=', '"GET"', ',', '*', ',', 'params', '=', 'None', ',', 'data', '=', 'None', ',', 'headers', '=', 'None', ',', 'timeout', '=', 'None', ')', ':', 'if', 'headers', 'is', 'None', ':', 'headers', '=', '{', '}', 'headers', '[', '"content-type"', ']', '=', '"application/json"', 'if', 'not', 'isinstance', '(', 'data', ',', '(', 'str', ',', 'bytes', ')', ')', ':', 'data', '=', 'json', '.', 'dumps', '(', 'data', ')', 'response', '=', 'await', 'self', '.', '_query', '(', 'path', ',', 'method', ',', 'params', '=', 'params', ',', 'data', '=', 'data', ',', 'headers', '=', 'headers', ',', 'timeout', '=', 'timeout', ')', 'data', '=', 'await', 'parse_result', '(', 'response', ')', 'return', 'data'] | A shorthand of _query() that treats the input as JSON. | ['A', 'shorthand', 'of', '_query', '()', 'that', 'treats', 'the', 'input', 'as', 'JSON', '.'] | train | https://github.com/aio-libs/aiodocker/blob/88d0285ddba8e606ff684278e0a831347209189c/aiodocker/docker.py#L176-L191 |
1,347 | asmodehn/filefinder2 | filefinder2/util.py | module_for_loader | def module_for_loader(fxn):
"""Decorator to handle selecting the proper module for loaders.
The decorated function is passed the module to use instead of the module
name. The module passed in to the function is either from sys.modules if
it already exists or is a new module. If the module is new, then __name__
is set the first argument to the method, __loader__ is set to self, and
__package__ is set accordingly (if self.is_package() is defined) will be set
before it is passed to the decorated function (if self.is_package() does
not work for the module it will be set post-load).
If an exception is raised and the decorator created the module it is
subsequently removed from sys.modules.
The decorator assumes that the decorated function takes the module name as
the second argument.
"""
warnings.warn('The import system now takes care of this automatically.',
DeprecationWarning, stacklevel=2)
@functools.wraps(fxn)
def module_for_loader_wrapper(self, fullname, *args, **kwargs):
with _module_to_load(fullname) as module:
module.__loader__ = self
try:
is_package = self.is_package(fullname)
except (ImportError, AttributeError):
pass
else:
if is_package:
module.__package__ = fullname
else:
module.__package__ = fullname.rpartition('.')[0]
# If __package__ was not set above, __import__() will do it later.
return fxn(self, module, *args, **kwargs)
return module_for_loader_wrapper | python | def module_for_loader(fxn):
"""Decorator to handle selecting the proper module for loaders.
The decorated function is passed the module to use instead of the module
name. The module passed in to the function is either from sys.modules if
it already exists or is a new module. If the module is new, then __name__
is set the first argument to the method, __loader__ is set to self, and
__package__ is set accordingly (if self.is_package() is defined) will be set
before it is passed to the decorated function (if self.is_package() does
not work for the module it will be set post-load).
If an exception is raised and the decorator created the module it is
subsequently removed from sys.modules.
The decorator assumes that the decorated function takes the module name as
the second argument.
"""
warnings.warn('The import system now takes care of this automatically.',
DeprecationWarning, stacklevel=2)
@functools.wraps(fxn)
def module_for_loader_wrapper(self, fullname, *args, **kwargs):
with _module_to_load(fullname) as module:
module.__loader__ = self
try:
is_package = self.is_package(fullname)
except (ImportError, AttributeError):
pass
else:
if is_package:
module.__package__ = fullname
else:
module.__package__ = fullname.rpartition('.')[0]
# If __package__ was not set above, __import__() will do it later.
return fxn(self, module, *args, **kwargs)
return module_for_loader_wrapper | ['def', 'module_for_loader', '(', 'fxn', ')', ':', 'warnings', '.', 'warn', '(', "'The import system now takes care of this automatically.'", ',', 'DeprecationWarning', ',', 'stacklevel', '=', '2', ')', '@', 'functools', '.', 'wraps', '(', 'fxn', ')', 'def', 'module_for_loader_wrapper', '(', 'self', ',', 'fullname', ',', '*', 'args', ',', '*', '*', 'kwargs', ')', ':', 'with', '_module_to_load', '(', 'fullname', ')', 'as', 'module', ':', 'module', '.', '__loader__', '=', 'self', 'try', ':', 'is_package', '=', 'self', '.', 'is_package', '(', 'fullname', ')', 'except', '(', 'ImportError', ',', 'AttributeError', ')', ':', 'pass', 'else', ':', 'if', 'is_package', ':', 'module', '.', '__package__', '=', 'fullname', 'else', ':', 'module', '.', '__package__', '=', 'fullname', '.', 'rpartition', '(', "'.'", ')', '[', '0', ']', '# If __package__ was not set above, __import__() will do it later.', 'return', 'fxn', '(', 'self', ',', 'module', ',', '*', 'args', ',', '*', '*', 'kwargs', ')', 'return', 'module_for_loader_wrapper'] | Decorator to handle selecting the proper module for loaders.
The decorated function is passed the module to use instead of the module
name. The module passed in to the function is either from sys.modules if
it already exists or is a new module. If the module is new, then __name__
is set the first argument to the method, __loader__ is set to self, and
__package__ is set accordingly (if self.is_package() is defined) will be set
before it is passed to the decorated function (if self.is_package() does
not work for the module it will be set post-load).
If an exception is raised and the decorator created the module it is
subsequently removed from sys.modules.
The decorator assumes that the decorated function takes the module name as
the second argument. | ['Decorator', 'to', 'handle', 'selecting', 'the', 'proper', 'module', 'for', 'loaders', '.', 'The', 'decorated', 'function', 'is', 'passed', 'the', 'module', 'to', 'use', 'instead', 'of', 'the', 'module', 'name', '.', 'The', 'module', 'passed', 'in', 'to', 'the', 'function', 'is', 'either', 'from', 'sys', '.', 'modules', 'if', 'it', 'already', 'exists', 'or', 'is', 'a', 'new', 'module', '.', 'If', 'the', 'module', 'is', 'new', 'then', '__name__', 'is', 'set', 'the', 'first', 'argument', 'to', 'the', 'method', '__loader__', 'is', 'set', 'to', 'self', 'and', '__package__', 'is', 'set', 'accordingly', '(', 'if', 'self', '.', 'is_package', '()', 'is', 'defined', ')', 'will', 'be', 'set', 'before', 'it', 'is', 'passed', 'to', 'the', 'decorated', 'function', '(', 'if', 'self', '.', 'is_package', '()', 'does', 'not', 'work', 'for', 'the', 'module', 'it', 'will', 'be', 'set', 'post', '-', 'load', ')', '.', 'If', 'an', 'exception', 'is', 'raised', 'and', 'the', 'decorator', 'created', 'the', 'module', 'it', 'is', 'subsequently', 'removed', 'from', 'sys', '.', 'modules', '.', 'The', 'decorator', 'assumes', 'that', 'the', 'decorated', 'function', 'takes', 'the', 'module', 'name', 'as', 'the', 'second', 'argument', '.'] | train | https://github.com/asmodehn/filefinder2/blob/3f0b211ce11a34562e2a2160e039ae5290b68d6b/filefinder2/util.py#L169-L201 |
1,348 | kgori/treeCl | treeCl/bootstrap.py | optimise_levenberg_marquardt | def optimise_levenberg_marquardt(x, a, c, damping=0.001, tolerance=0.001):
"""
Optimise value of x using levenberg-marquardt
"""
x_new = x
x_old = x-1 # dummy value
f_old = f(x_new, a, c)
while np.abs(x_new - x_old).sum() > tolerance:
x_old = x_new
x_tmp = levenberg_marquardt_update(x_old, a, c, damping)
f_new = f(x_tmp, a, c)
if f_new < f_old:
damping = np.max(damping/10., 1e-20)
x_new = x_tmp
f_old = f_new
else:
damping *= 10.
return x_new | python | def optimise_levenberg_marquardt(x, a, c, damping=0.001, tolerance=0.001):
"""
Optimise value of x using levenberg-marquardt
"""
x_new = x
x_old = x-1 # dummy value
f_old = f(x_new, a, c)
while np.abs(x_new - x_old).sum() > tolerance:
x_old = x_new
x_tmp = levenberg_marquardt_update(x_old, a, c, damping)
f_new = f(x_tmp, a, c)
if f_new < f_old:
damping = np.max(damping/10., 1e-20)
x_new = x_tmp
f_old = f_new
else:
damping *= 10.
return x_new | ['def', 'optimise_levenberg_marquardt', '(', 'x', ',', 'a', ',', 'c', ',', 'damping', '=', '0.001', ',', 'tolerance', '=', '0.001', ')', ':', 'x_new', '=', 'x', 'x_old', '=', 'x', '-', '1', '# dummy value', 'f_old', '=', 'f', '(', 'x_new', ',', 'a', ',', 'c', ')', 'while', 'np', '.', 'abs', '(', 'x_new', '-', 'x_old', ')', '.', 'sum', '(', ')', '>', 'tolerance', ':', 'x_old', '=', 'x_new', 'x_tmp', '=', 'levenberg_marquardt_update', '(', 'x_old', ',', 'a', ',', 'c', ',', 'damping', ')', 'f_new', '=', 'f', '(', 'x_tmp', ',', 'a', ',', 'c', ')', 'if', 'f_new', '<', 'f_old', ':', 'damping', '=', 'np', '.', 'max', '(', 'damping', '/', '10.', ',', '1e-20', ')', 'x_new', '=', 'x_tmp', 'f_old', '=', 'f_new', 'else', ':', 'damping', '*=', '10.', 'return', 'x_new'] | Optimise value of x using levenberg-marquardt | ['Optimise', 'value', 'of', 'x', 'using', 'levenberg', '-', 'marquardt'] | train | https://github.com/kgori/treeCl/blob/fed624b3db1c19cc07175ca04e3eda6905a8d305/treeCl/bootstrap.py#L143-L160 |
1,349 | pypa/pipenv | pipenv/vendor/tomlkit/parser.py | Parser._parse_table | def _parse_table(
self, parent_name=None
): # type: (Optional[str]) -> Tuple[Key, Union[Table, AoT]]
"""
Parses a table element.
"""
if self._current != "[":
raise self.parse_error(
InternalParserError, "_parse_table() called on non-bracket character."
)
indent = self.extract()
self.inc() # Skip opening bracket
if self.end():
raise self.parse_error(UnexpectedEofError)
is_aot = False
if self._current == "[":
if not self.inc():
raise self.parse_error(UnexpectedEofError)
is_aot = True
# Key
self.mark()
while self._current != "]" and self.inc():
if self.end():
raise self.parse_error(UnexpectedEofError)
pass
name = self.extract()
if not name.strip():
raise self.parse_error(EmptyTableNameError)
key = Key(name, sep="")
name_parts = tuple(self._split_table_name(name))
missing_table = False
if parent_name:
parent_name_parts = tuple(self._split_table_name(parent_name))
else:
parent_name_parts = tuple()
if len(name_parts) > len(parent_name_parts) + 1:
missing_table = True
name_parts = name_parts[len(parent_name_parts) :]
values = Container(True)
self.inc() # Skip closing bracket
if is_aot:
# TODO: Verify close bracket
self.inc()
cws, comment, trail = self._parse_comment_trail()
result = Null()
if len(name_parts) > 1:
if missing_table:
# Missing super table
# i.e. a table initialized like this: [foo.bar]
# without initializing [foo]
#
# So we have to create the parent tables
table = Table(
Container(True),
Trivia(indent, cws, comment, trail),
is_aot and name_parts[0].key in self._aot_stack,
is_super_table=True,
name=name_parts[0].key,
)
result = table
key = name_parts[0]
for i, _name in enumerate(name_parts[1:]):
if _name in table:
child = table[_name]
else:
child = Table(
Container(True),
Trivia(indent, cws, comment, trail),
is_aot and i == len(name_parts[1:]) - 1,
is_super_table=i < len(name_parts[1:]) - 1,
name=_name.key,
display_name=name if i == len(name_parts[1:]) - 1 else None,
)
if is_aot and i == len(name_parts[1:]) - 1:
table.append(_name, AoT([child], name=table.name, parsed=True))
else:
table.append(_name, child)
table = child
values = table.value
else:
if name_parts:
key = name_parts[0]
while not self.end():
item = self._parse_item()
if item:
_key, item = item
if not self._merge_ws(item, values):
if _key is not None and _key.is_dotted():
self._handle_dotted_key(values, _key, item)
else:
values.append(_key, item)
else:
if self._current == "[":
is_aot_next, name_next = self._peek_table()
if self._is_child(name, name_next):
key_next, table_next = self._parse_table(name)
values.append(key_next, table_next)
# Picking up any sibling
while not self.end():
_, name_next = self._peek_table()
if not self._is_child(name, name_next):
break
key_next, table_next = self._parse_table(name)
values.append(key_next, table_next)
break
else:
raise self.parse_error(
InternalParserError,
"_parse_item() returned None on a non-bracket character.",
)
if isinstance(result, Null):
result = Table(
values,
Trivia(indent, cws, comment, trail),
is_aot,
name=name,
display_name=name,
)
if is_aot and (not self._aot_stack or name != self._aot_stack[-1]):
result = self._parse_aot(result, name)
return key, result | python | def _parse_table(
self, parent_name=None
): # type: (Optional[str]) -> Tuple[Key, Union[Table, AoT]]
"""
Parses a table element.
"""
if self._current != "[":
raise self.parse_error(
InternalParserError, "_parse_table() called on non-bracket character."
)
indent = self.extract()
self.inc() # Skip opening bracket
if self.end():
raise self.parse_error(UnexpectedEofError)
is_aot = False
if self._current == "[":
if not self.inc():
raise self.parse_error(UnexpectedEofError)
is_aot = True
# Key
self.mark()
while self._current != "]" and self.inc():
if self.end():
raise self.parse_error(UnexpectedEofError)
pass
name = self.extract()
if not name.strip():
raise self.parse_error(EmptyTableNameError)
key = Key(name, sep="")
name_parts = tuple(self._split_table_name(name))
missing_table = False
if parent_name:
parent_name_parts = tuple(self._split_table_name(parent_name))
else:
parent_name_parts = tuple()
if len(name_parts) > len(parent_name_parts) + 1:
missing_table = True
name_parts = name_parts[len(parent_name_parts) :]
values = Container(True)
self.inc() # Skip closing bracket
if is_aot:
# TODO: Verify close bracket
self.inc()
cws, comment, trail = self._parse_comment_trail()
result = Null()
if len(name_parts) > 1:
if missing_table:
# Missing super table
# i.e. a table initialized like this: [foo.bar]
# without initializing [foo]
#
# So we have to create the parent tables
table = Table(
Container(True),
Trivia(indent, cws, comment, trail),
is_aot and name_parts[0].key in self._aot_stack,
is_super_table=True,
name=name_parts[0].key,
)
result = table
key = name_parts[0]
for i, _name in enumerate(name_parts[1:]):
if _name in table:
child = table[_name]
else:
child = Table(
Container(True),
Trivia(indent, cws, comment, trail),
is_aot and i == len(name_parts[1:]) - 1,
is_super_table=i < len(name_parts[1:]) - 1,
name=_name.key,
display_name=name if i == len(name_parts[1:]) - 1 else None,
)
if is_aot and i == len(name_parts[1:]) - 1:
table.append(_name, AoT([child], name=table.name, parsed=True))
else:
table.append(_name, child)
table = child
values = table.value
else:
if name_parts:
key = name_parts[0]
while not self.end():
item = self._parse_item()
if item:
_key, item = item
if not self._merge_ws(item, values):
if _key is not None and _key.is_dotted():
self._handle_dotted_key(values, _key, item)
else:
values.append(_key, item)
else:
if self._current == "[":
is_aot_next, name_next = self._peek_table()
if self._is_child(name, name_next):
key_next, table_next = self._parse_table(name)
values.append(key_next, table_next)
# Picking up any sibling
while not self.end():
_, name_next = self._peek_table()
if not self._is_child(name, name_next):
break
key_next, table_next = self._parse_table(name)
values.append(key_next, table_next)
break
else:
raise self.parse_error(
InternalParserError,
"_parse_item() returned None on a non-bracket character.",
)
if isinstance(result, Null):
result = Table(
values,
Trivia(indent, cws, comment, trail),
is_aot,
name=name,
display_name=name,
)
if is_aot and (not self._aot_stack or name != self._aot_stack[-1]):
result = self._parse_aot(result, name)
return key, result | ['def', '_parse_table', '(', 'self', ',', 'parent_name', '=', 'None', ')', ':', '# type: (Optional[str]) -> Tuple[Key, Union[Table, AoT]]', 'if', 'self', '.', '_current', '!=', '"["', ':', 'raise', 'self', '.', 'parse_error', '(', 'InternalParserError', ',', '"_parse_table() called on non-bracket character."', ')', 'indent', '=', 'self', '.', 'extract', '(', ')', 'self', '.', 'inc', '(', ')', '# Skip opening bracket', 'if', 'self', '.', 'end', '(', ')', ':', 'raise', 'self', '.', 'parse_error', '(', 'UnexpectedEofError', ')', 'is_aot', '=', 'False', 'if', 'self', '.', '_current', '==', '"["', ':', 'if', 'not', 'self', '.', 'inc', '(', ')', ':', 'raise', 'self', '.', 'parse_error', '(', 'UnexpectedEofError', ')', 'is_aot', '=', 'True', '# Key', 'self', '.', 'mark', '(', ')', 'while', 'self', '.', '_current', '!=', '"]"', 'and', 'self', '.', 'inc', '(', ')', ':', 'if', 'self', '.', 'end', '(', ')', ':', 'raise', 'self', '.', 'parse_error', '(', 'UnexpectedEofError', ')', 'pass', 'name', '=', 'self', '.', 'extract', '(', ')', 'if', 'not', 'name', '.', 'strip', '(', ')', ':', 'raise', 'self', '.', 'parse_error', '(', 'EmptyTableNameError', ')', 'key', '=', 'Key', '(', 'name', ',', 'sep', '=', '""', ')', 'name_parts', '=', 'tuple', '(', 'self', '.', '_split_table_name', '(', 'name', ')', ')', 'missing_table', '=', 'False', 'if', 'parent_name', ':', 'parent_name_parts', '=', 'tuple', '(', 'self', '.', '_split_table_name', '(', 'parent_name', ')', ')', 'else', ':', 'parent_name_parts', '=', 'tuple', '(', ')', 'if', 'len', '(', 'name_parts', ')', '>', 'len', '(', 'parent_name_parts', ')', '+', '1', ':', 'missing_table', '=', 'True', 'name_parts', '=', 'name_parts', '[', 'len', '(', 'parent_name_parts', ')', ':', ']', 'values', '=', 'Container', '(', 'True', ')', 'self', '.', 'inc', '(', ')', '# Skip closing bracket', 'if', 'is_aot', ':', '# TODO: Verify close bracket', 'self', '.', 'inc', '(', ')', 'cws', ',', 'comment', ',', 'trail', '=', 'self', '.', '_parse_comment_trail', '(', ')', 'result', '=', 'Null', '(', ')', 'if', 'len', '(', 'name_parts', ')', '>', '1', ':', 'if', 'missing_table', ':', '# Missing super table', '# i.e. a table initialized like this: [foo.bar]', '# without initializing [foo]', '#', '# So we have to create the parent tables', 'table', '=', 'Table', '(', 'Container', '(', 'True', ')', ',', 'Trivia', '(', 'indent', ',', 'cws', ',', 'comment', ',', 'trail', ')', ',', 'is_aot', 'and', 'name_parts', '[', '0', ']', '.', 'key', 'in', 'self', '.', '_aot_stack', ',', 'is_super_table', '=', 'True', ',', 'name', '=', 'name_parts', '[', '0', ']', '.', 'key', ',', ')', 'result', '=', 'table', 'key', '=', 'name_parts', '[', '0', ']', 'for', 'i', ',', '_name', 'in', 'enumerate', '(', 'name_parts', '[', '1', ':', ']', ')', ':', 'if', '_name', 'in', 'table', ':', 'child', '=', 'table', '[', '_name', ']', 'else', ':', 'child', '=', 'Table', '(', 'Container', '(', 'True', ')', ',', 'Trivia', '(', 'indent', ',', 'cws', ',', 'comment', ',', 'trail', ')', ',', 'is_aot', 'and', 'i', '==', 'len', '(', 'name_parts', '[', '1', ':', ']', ')', '-', '1', ',', 'is_super_table', '=', 'i', '<', 'len', '(', 'name_parts', '[', '1', ':', ']', ')', '-', '1', ',', 'name', '=', '_name', '.', 'key', ',', 'display_name', '=', 'name', 'if', 'i', '==', 'len', '(', 'name_parts', '[', '1', ':', ']', ')', '-', '1', 'else', 'None', ',', ')', 'if', 'is_aot', 'and', 'i', '==', 'len', '(', 'name_parts', '[', '1', ':', ']', ')', '-', '1', ':', 'table', '.', 'append', '(', '_name', ',', 'AoT', '(', '[', 'child', ']', ',', 'name', '=', 'table', '.', 'name', ',', 'parsed', '=', 'True', ')', ')', 'else', ':', 'table', '.', 'append', '(', '_name', ',', 'child', ')', 'table', '=', 'child', 'values', '=', 'table', '.', 'value', 'else', ':', 'if', 'name_parts', ':', 'key', '=', 'name_parts', '[', '0', ']', 'while', 'not', 'self', '.', 'end', '(', ')', ':', 'item', '=', 'self', '.', '_parse_item', '(', ')', 'if', 'item', ':', '_key', ',', 'item', '=', 'item', 'if', 'not', 'self', '.', '_merge_ws', '(', 'item', ',', 'values', ')', ':', 'if', '_key', 'is', 'not', 'None', 'and', '_key', '.', 'is_dotted', '(', ')', ':', 'self', '.', '_handle_dotted_key', '(', 'values', ',', '_key', ',', 'item', ')', 'else', ':', 'values', '.', 'append', '(', '_key', ',', 'item', ')', 'else', ':', 'if', 'self', '.', '_current', '==', '"["', ':', 'is_aot_next', ',', 'name_next', '=', 'self', '.', '_peek_table', '(', ')', 'if', 'self', '.', '_is_child', '(', 'name', ',', 'name_next', ')', ':', 'key_next', ',', 'table_next', '=', 'self', '.', '_parse_table', '(', 'name', ')', 'values', '.', 'append', '(', 'key_next', ',', 'table_next', ')', '# Picking up any sibling', 'while', 'not', 'self', '.', 'end', '(', ')', ':', '_', ',', 'name_next', '=', 'self', '.', '_peek_table', '(', ')', 'if', 'not', 'self', '.', '_is_child', '(', 'name', ',', 'name_next', ')', ':', 'break', 'key_next', ',', 'table_next', '=', 'self', '.', '_parse_table', '(', 'name', ')', 'values', '.', 'append', '(', 'key_next', ',', 'table_next', ')', 'break', 'else', ':', 'raise', 'self', '.', 'parse_error', '(', 'InternalParserError', ',', '"_parse_item() returned None on a non-bracket character."', ',', ')', 'if', 'isinstance', '(', 'result', ',', 'Null', ')', ':', 'result', '=', 'Table', '(', 'values', ',', 'Trivia', '(', 'indent', ',', 'cws', ',', 'comment', ',', 'trail', ')', ',', 'is_aot', ',', 'name', '=', 'name', ',', 'display_name', '=', 'name', ',', ')', 'if', 'is_aot', 'and', '(', 'not', 'self', '.', '_aot_stack', 'or', 'name', '!=', 'self', '.', '_aot_stack', '[', '-', '1', ']', ')', ':', 'result', '=', 'self', '.', '_parse_aot', '(', 'result', ',', 'name', ')', 'return', 'key', ',', 'result'] | Parses a table element. | ['Parses', 'a', 'table', 'element', '.'] | train | https://github.com/pypa/pipenv/blob/cae8d76c210b9777e90aab76e9c4b0e53bb19cde/pipenv/vendor/tomlkit/parser.py#L855-L1005 |
1,350 | bigchaindb/bigchaindb-driver | bigchaindb_driver/common/transaction.py | Transaction.inputs_valid | def inputs_valid(self, outputs=None):
"""Validates the Inputs in the Transaction against given
Outputs.
Note:
Given a `CREATE` Transaction is passed,
dummy values for Outputs are submitted for validation that
evaluate parts of the validation-checks to `True`.
Args:
outputs (:obj:`list` of :class:`~bigchaindb.common.
transaction.Output`): A list of Outputs to check the
Inputs against.
Returns:
bool: If all Inputs are valid.
"""
if self.operation == Transaction.CREATE:
# NOTE: Since in the case of a `CREATE`-transaction we do not have
# to check for outputs, we're just submitting dummy
# values to the actual method. This simplifies it's logic
# greatly, as we do not have to check against `None` values.
return self._inputs_valid(['dummyvalue'
for _ in self.inputs])
elif self.operation == Transaction.TRANSFER:
return self._inputs_valid([output.fulfillment.condition_uri
for output in outputs])
else:
allowed_ops = ', '.join(self.__class__.ALLOWED_OPERATIONS)
raise TypeError('`operation` must be one of {}'
.format(allowed_ops)) | python | def inputs_valid(self, outputs=None):
"""Validates the Inputs in the Transaction against given
Outputs.
Note:
Given a `CREATE` Transaction is passed,
dummy values for Outputs are submitted for validation that
evaluate parts of the validation-checks to `True`.
Args:
outputs (:obj:`list` of :class:`~bigchaindb.common.
transaction.Output`): A list of Outputs to check the
Inputs against.
Returns:
bool: If all Inputs are valid.
"""
if self.operation == Transaction.CREATE:
# NOTE: Since in the case of a `CREATE`-transaction we do not have
# to check for outputs, we're just submitting dummy
# values to the actual method. This simplifies it's logic
# greatly, as we do not have to check against `None` values.
return self._inputs_valid(['dummyvalue'
for _ in self.inputs])
elif self.operation == Transaction.TRANSFER:
return self._inputs_valid([output.fulfillment.condition_uri
for output in outputs])
else:
allowed_ops = ', '.join(self.__class__.ALLOWED_OPERATIONS)
raise TypeError('`operation` must be one of {}'
.format(allowed_ops)) | ['def', 'inputs_valid', '(', 'self', ',', 'outputs', '=', 'None', ')', ':', 'if', 'self', '.', 'operation', '==', 'Transaction', '.', 'CREATE', ':', '# NOTE: Since in the case of a `CREATE`-transaction we do not have', "# to check for outputs, we're just submitting dummy", "# values to the actual method. This simplifies it's logic", '# greatly, as we do not have to check against `None` values.', 'return', 'self', '.', '_inputs_valid', '(', '[', "'dummyvalue'", 'for', '_', 'in', 'self', '.', 'inputs', ']', ')', 'elif', 'self', '.', 'operation', '==', 'Transaction', '.', 'TRANSFER', ':', 'return', 'self', '.', '_inputs_valid', '(', '[', 'output', '.', 'fulfillment', '.', 'condition_uri', 'for', 'output', 'in', 'outputs', ']', ')', 'else', ':', 'allowed_ops', '=', "', '", '.', 'join', '(', 'self', '.', '__class__', '.', 'ALLOWED_OPERATIONS', ')', 'raise', 'TypeError', '(', "'`operation` must be one of {}'", '.', 'format', '(', 'allowed_ops', ')', ')'] | Validates the Inputs in the Transaction against given
Outputs.
Note:
Given a `CREATE` Transaction is passed,
dummy values for Outputs are submitted for validation that
evaluate parts of the validation-checks to `True`.
Args:
outputs (:obj:`list` of :class:`~bigchaindb.common.
transaction.Output`): A list of Outputs to check the
Inputs against.
Returns:
bool: If all Inputs are valid. | ['Validates', 'the', 'Inputs', 'in', 'the', 'Transaction', 'against', 'given', 'Outputs', '.'] | train | https://github.com/bigchaindb/bigchaindb-driver/blob/c294a535f0696bd19483ae11a4882b74e6fc061e/bigchaindb_driver/common/transaction.py#L945-L975 |
1,351 | tensorflow/cleverhans | examples/multigpu_advtrain/make_model.py | make_basic_ngpu | def make_basic_ngpu(nb_classes=10, input_shape=(None, 28, 28, 1), **kwargs):
"""
Create a multi-GPU model similar to the basic cnn in the tutorials.
"""
model = make_basic_cnn()
layers = model.layers
model = MLPnGPU(nb_classes, layers, input_shape)
return model | python | def make_basic_ngpu(nb_classes=10, input_shape=(None, 28, 28, 1), **kwargs):
"""
Create a multi-GPU model similar to the basic cnn in the tutorials.
"""
model = make_basic_cnn()
layers = model.layers
model = MLPnGPU(nb_classes, layers, input_shape)
return model | ['def', 'make_basic_ngpu', '(', 'nb_classes', '=', '10', ',', 'input_shape', '=', '(', 'None', ',', '28', ',', '28', ',', '1', ')', ',', '*', '*', 'kwargs', ')', ':', 'model', '=', 'make_basic_cnn', '(', ')', 'layers', '=', 'model', '.', 'layers', 'model', '=', 'MLPnGPU', '(', 'nb_classes', ',', 'layers', ',', 'input_shape', ')', 'return', 'model'] | Create a multi-GPU model similar to the basic cnn in the tutorials. | ['Create', 'a', 'multi', '-', 'GPU', 'model', 'similar', 'to', 'the', 'basic', 'cnn', 'in', 'the', 'tutorials', '.'] | train | https://github.com/tensorflow/cleverhans/blob/97488e215760547b81afc53f5e5de8ba7da5bd98/examples/multigpu_advtrain/make_model.py#L27-L35 |
1,352 | evhub/coconut | coconut/compiler/compiler.py | Compiler.case_stmt_handle | def case_stmt_handle(self, loc, tokens):
"""Process case blocks."""
if len(tokens) == 2:
item, cases = tokens
default = None
elif len(tokens) == 3:
item, cases, default = tokens
else:
raise CoconutInternalException("invalid case tokens", tokens)
check_var = case_check_var + "_" + str(self.case_check_count)
self.case_check_count += 1
out = (
match_to_var + " = " + item + "\n"
+ match_case_tokens(loc, cases[0], check_var, True)
)
for case in cases[1:]:
out += (
"if not " + check_var + ":\n" + openindent
+ match_case_tokens(loc, case, check_var, False) + closeindent
)
if default is not None:
out += "if not " + check_var + default
return out | python | def case_stmt_handle(self, loc, tokens):
"""Process case blocks."""
if len(tokens) == 2:
item, cases = tokens
default = None
elif len(tokens) == 3:
item, cases, default = tokens
else:
raise CoconutInternalException("invalid case tokens", tokens)
check_var = case_check_var + "_" + str(self.case_check_count)
self.case_check_count += 1
out = (
match_to_var + " = " + item + "\n"
+ match_case_tokens(loc, cases[0], check_var, True)
)
for case in cases[1:]:
out += (
"if not " + check_var + ":\n" + openindent
+ match_case_tokens(loc, case, check_var, False) + closeindent
)
if default is not None:
out += "if not " + check_var + default
return out | ['def', 'case_stmt_handle', '(', 'self', ',', 'loc', ',', 'tokens', ')', ':', 'if', 'len', '(', 'tokens', ')', '==', '2', ':', 'item', ',', 'cases', '=', 'tokens', 'default', '=', 'None', 'elif', 'len', '(', 'tokens', ')', '==', '3', ':', 'item', ',', 'cases', ',', 'default', '=', 'tokens', 'else', ':', 'raise', 'CoconutInternalException', '(', '"invalid case tokens"', ',', 'tokens', ')', 'check_var', '=', 'case_check_var', '+', '"_"', '+', 'str', '(', 'self', '.', 'case_check_count', ')', 'self', '.', 'case_check_count', '+=', '1', 'out', '=', '(', 'match_to_var', '+', '" = "', '+', 'item', '+', '"\\n"', '+', 'match_case_tokens', '(', 'loc', ',', 'cases', '[', '0', ']', ',', 'check_var', ',', 'True', ')', ')', 'for', 'case', 'in', 'cases', '[', '1', ':', ']', ':', 'out', '+=', '(', '"if not "', '+', 'check_var', '+', '":\\n"', '+', 'openindent', '+', 'match_case_tokens', '(', 'loc', ',', 'case', ',', 'check_var', ',', 'False', ')', '+', 'closeindent', ')', 'if', 'default', 'is', 'not', 'None', ':', 'out', '+=', '"if not "', '+', 'check_var', '+', 'default', 'return', 'out'] | Process case blocks. | ['Process', 'case', 'blocks', '.'] | train | https://github.com/evhub/coconut/blob/ff97177344e7604e89a0a98a977a87ed2a56fc6d/coconut/compiler/compiler.py#L1851-L1873 |
1,353 | tanghaibao/jcvi | jcvi/formats/posmap.py | bed | def bed(args):
"""
%prog bed frgscffile
Convert the frgscf posmap file to bed format.
"""
p = OptionParser(bed.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
frgscffile, = args
bedfile = frgscffile.rsplit(".", 1)[0] + ".bed"
fw = open(bedfile, "w")
fp = open(frgscffile)
for row in fp:
f = FrgScfLine(row)
print(f.bedline, file=fw)
logging.debug("File written to `{0}`.".format(bedfile))
return bedfile | python | def bed(args):
"""
%prog bed frgscffile
Convert the frgscf posmap file to bed format.
"""
p = OptionParser(bed.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
frgscffile, = args
bedfile = frgscffile.rsplit(".", 1)[0] + ".bed"
fw = open(bedfile, "w")
fp = open(frgscffile)
for row in fp:
f = FrgScfLine(row)
print(f.bedline, file=fw)
logging.debug("File written to `{0}`.".format(bedfile))
return bedfile | ['def', 'bed', '(', 'args', ')', ':', 'p', '=', 'OptionParser', '(', 'bed', '.', '__doc__', ')', 'opts', ',', 'args', '=', 'p', '.', 'parse_args', '(', 'args', ')', 'if', 'len', '(', 'args', ')', '!=', '1', ':', 'sys', '.', 'exit', '(', 'not', 'p', '.', 'print_help', '(', ')', ')', 'frgscffile', ',', '=', 'args', 'bedfile', '=', 'frgscffile', '.', 'rsplit', '(', '"."', ',', '1', ')', '[', '0', ']', '+', '".bed"', 'fw', '=', 'open', '(', 'bedfile', ',', '"w"', ')', 'fp', '=', 'open', '(', 'frgscffile', ')', 'for', 'row', 'in', 'fp', ':', 'f', '=', 'FrgScfLine', '(', 'row', ')', 'print', '(', 'f', '.', 'bedline', ',', 'file', '=', 'fw', ')', 'logging', '.', 'debug', '(', '"File written to `{0}`."', '.', 'format', '(', 'bedfile', ')', ')', 'return', 'bedfile'] | %prog bed frgscffile
Convert the frgscf posmap file to bed format. | ['%prog', 'bed', 'frgscffile'] | train | https://github.com/tanghaibao/jcvi/blob/d2e31a77b6ade7f41f3b321febc2b4744d1cdeca/jcvi/formats/posmap.py#L241-L264 |
1,354 | B2W-BIT/aiologger | aiologger/logger.py | Logger.exception | def exception( # type: ignore
self, msg, *args, exc_info=True, **kwargs
) -> Task:
"""
Convenience method for logging an ERROR with exception information.
"""
return self.error(msg, *args, exc_info=exc_info, **kwargs) | python | def exception( # type: ignore
self, msg, *args, exc_info=True, **kwargs
) -> Task:
"""
Convenience method for logging an ERROR with exception information.
"""
return self.error(msg, *args, exc_info=exc_info, **kwargs) | ['def', 'exception', '(', '# type: ignore', 'self', ',', 'msg', ',', '*', 'args', ',', 'exc_info', '=', 'True', ',', '*', '*', 'kwargs', ')', '->', 'Task', ':', 'return', 'self', '.', 'error', '(', 'msg', ',', '*', 'args', ',', 'exc_info', '=', 'exc_info', ',', '*', '*', 'kwargs', ')'] | Convenience method for logging an ERROR with exception information. | ['Convenience', 'method', 'for', 'logging', 'an', 'ERROR', 'with', 'exception', 'information', '.'] | train | https://github.com/B2W-BIT/aiologger/blob/0b366597a8305d5577a267305e81d5e4784cd398/aiologger/logger.py#L218-L224 |
1,355 | DataDog/integrations-core | tokumx/datadog_checks/tokumx/vendor/pymongo/common.py | validate_read_preference_tags | def validate_read_preference_tags(name, value):
"""Parse readPreferenceTags if passed as a client kwarg.
"""
if not isinstance(value, list):
value = [value]
tag_sets = []
for tag_set in value:
if tag_set == '':
tag_sets.append({})
continue
try:
tag_sets.append(dict([tag.split(":")
for tag in tag_set.split(",")]))
except Exception:
raise ValueError("%r not a valid "
"value for %s" % (tag_set, name))
return tag_sets | python | def validate_read_preference_tags(name, value):
"""Parse readPreferenceTags if passed as a client kwarg.
"""
if not isinstance(value, list):
value = [value]
tag_sets = []
for tag_set in value:
if tag_set == '':
tag_sets.append({})
continue
try:
tag_sets.append(dict([tag.split(":")
for tag in tag_set.split(",")]))
except Exception:
raise ValueError("%r not a valid "
"value for %s" % (tag_set, name))
return tag_sets | ['def', 'validate_read_preference_tags', '(', 'name', ',', 'value', ')', ':', 'if', 'not', 'isinstance', '(', 'value', ',', 'list', ')', ':', 'value', '=', '[', 'value', ']', 'tag_sets', '=', '[', ']', 'for', 'tag_set', 'in', 'value', ':', 'if', 'tag_set', '==', "''", ':', 'tag_sets', '.', 'append', '(', '{', '}', ')', 'continue', 'try', ':', 'tag_sets', '.', 'append', '(', 'dict', '(', '[', 'tag', '.', 'split', '(', '":"', ')', 'for', 'tag', 'in', 'tag_set', '.', 'split', '(', '","', ')', ']', ')', ')', 'except', 'Exception', ':', 'raise', 'ValueError', '(', '"%r not a valid "', '"value for %s"', '%', '(', 'tag_set', ',', 'name', ')', ')', 'return', 'tag_sets'] | Parse readPreferenceTags if passed as a client kwarg. | ['Parse', 'readPreferenceTags', 'if', 'passed', 'as', 'a', 'client', 'kwarg', '.'] | train | https://github.com/DataDog/integrations-core/blob/ebd41c873cf9f97a8c51bf9459bc6a7536af8acd/tokumx/datadog_checks/tokumx/vendor/pymongo/common.py#L338-L355 |
1,356 | dsoprea/NsqSpinner | nsq/identify.py | Identify.output_buffer_size | def output_buffer_size(self, output_buffer_size_b):
"""output_buffer_size (nsqd 0.2.21+) the size in bytes of the buffer
nsqd will use when writing to this client.
Valid range: 64 <= output_buffer_size <= configured_max (-1 disables
output buffering)
--max-output-buffer-size (nsqd flag) controls the max
Defaults to 16kb
"""
assert issubclass(output_buffer_size_b.__class__, int)
return self.__push('output_buffer_size', output_buffer_size_b) | python | def output_buffer_size(self, output_buffer_size_b):
"""output_buffer_size (nsqd 0.2.21+) the size in bytes of the buffer
nsqd will use when writing to this client.
Valid range: 64 <= output_buffer_size <= configured_max (-1 disables
output buffering)
--max-output-buffer-size (nsqd flag) controls the max
Defaults to 16kb
"""
assert issubclass(output_buffer_size_b.__class__, int)
return self.__push('output_buffer_size', output_buffer_size_b) | ['def', 'output_buffer_size', '(', 'self', ',', 'output_buffer_size_b', ')', ':', 'assert', 'issubclass', '(', 'output_buffer_size_b', '.', '__class__', ',', 'int', ')', 'return', 'self', '.', '__push', '(', "'output_buffer_size'", ',', 'output_buffer_size_b', ')'] | output_buffer_size (nsqd 0.2.21+) the size in bytes of the buffer
nsqd will use when writing to this client.
Valid range: 64 <= output_buffer_size <= configured_max (-1 disables
output buffering)
--max-output-buffer-size (nsqd flag) controls the max
Defaults to 16kb | ['output_buffer_size', '(', 'nsqd', '0', '.', '2', '.', '21', '+', ')', 'the', 'size', 'in', 'bytes', 'of', 'the', 'buffer', 'nsqd', 'will', 'use', 'when', 'writing', 'to', 'this', 'client', '.'] | train | https://github.com/dsoprea/NsqSpinner/blob/972237b8ddce737983bfed001fde52e5236be695/nsq/identify.py#L118-L132 |
1,357 | HewlettPackard/python-hpOneView | hpOneView/resources/resource.py | ResourceClient.patch | def patch(self, id_or_uri, operation, path, value, timeout=-1, custom_headers=None):
"""
Uses the PATCH to update a resource.
Only one operation can be performed in each PATCH call.
Args:
id_or_uri: Can be either the resource ID or the resource URI.
operation: Patch operation
path: Path
value: Value
timeout: Timeout in seconds. Wait for task completion by default. The timeout does not abort the operation
in OneView; it just stops waiting for its completion.
Returns:
Updated resource.
"""
patch_request_body = [{'op': operation, 'path': path, 'value': value}]
return self.patch_request(id_or_uri=id_or_uri,
body=patch_request_body,
timeout=timeout,
custom_headers=custom_headers) | python | def patch(self, id_or_uri, operation, path, value, timeout=-1, custom_headers=None):
"""
Uses the PATCH to update a resource.
Only one operation can be performed in each PATCH call.
Args:
id_or_uri: Can be either the resource ID or the resource URI.
operation: Patch operation
path: Path
value: Value
timeout: Timeout in seconds. Wait for task completion by default. The timeout does not abort the operation
in OneView; it just stops waiting for its completion.
Returns:
Updated resource.
"""
patch_request_body = [{'op': operation, 'path': path, 'value': value}]
return self.patch_request(id_or_uri=id_or_uri,
body=patch_request_body,
timeout=timeout,
custom_headers=custom_headers) | ['def', 'patch', '(', 'self', ',', 'id_or_uri', ',', 'operation', ',', 'path', ',', 'value', ',', 'timeout', '=', '-', '1', ',', 'custom_headers', '=', 'None', ')', ':', 'patch_request_body', '=', '[', '{', "'op'", ':', 'operation', ',', "'path'", ':', 'path', ',', "'value'", ':', 'value', '}', ']', 'return', 'self', '.', 'patch_request', '(', 'id_or_uri', '=', 'id_or_uri', ',', 'body', '=', 'patch_request_body', ',', 'timeout', '=', 'timeout', ',', 'custom_headers', '=', 'custom_headers', ')'] | Uses the PATCH to update a resource.
Only one operation can be performed in each PATCH call.
Args:
id_or_uri: Can be either the resource ID or the resource URI.
operation: Patch operation
path: Path
value: Value
timeout: Timeout in seconds. Wait for task completion by default. The timeout does not abort the operation
in OneView; it just stops waiting for its completion.
Returns:
Updated resource. | ['Uses', 'the', 'PATCH', 'to', 'update', 'a', 'resource', '.'] | train | https://github.com/HewlettPackard/python-hpOneView/blob/3c6219723ef25e6e0c83d44a89007f89bc325b89/hpOneView/resources/resource.py#L1403-L1425 |
1,358 | wroberts/fsed | fsed/fsed.py | detect_pattern_format | def detect_pattern_format(pattern_filename, encoding, on_word_boundaries):
'''
Automatically detects the pattern file format, and determines
whether the Aho-Corasick string matching should pay attention to
word boundaries or not.
Arguments:
- `pattern_filename`:
- `encoding`:
- `on_word_boundaries`:
'''
tsv = True
boundaries = on_word_boundaries
with open_file(pattern_filename) as input_file:
for line in input_file:
line = line.decode(encoding)
if line.count('\t') != 1:
tsv = False
if '\\b' in line:
boundaries = True
if boundaries and not tsv:
break
return tsv, boundaries | python | def detect_pattern_format(pattern_filename, encoding, on_word_boundaries):
'''
Automatically detects the pattern file format, and determines
whether the Aho-Corasick string matching should pay attention to
word boundaries or not.
Arguments:
- `pattern_filename`:
- `encoding`:
- `on_word_boundaries`:
'''
tsv = True
boundaries = on_word_boundaries
with open_file(pattern_filename) as input_file:
for line in input_file:
line = line.decode(encoding)
if line.count('\t') != 1:
tsv = False
if '\\b' in line:
boundaries = True
if boundaries and not tsv:
break
return tsv, boundaries | ['def', 'detect_pattern_format', '(', 'pattern_filename', ',', 'encoding', ',', 'on_word_boundaries', ')', ':', 'tsv', '=', 'True', 'boundaries', '=', 'on_word_boundaries', 'with', 'open_file', '(', 'pattern_filename', ')', 'as', 'input_file', ':', 'for', 'line', 'in', 'input_file', ':', 'line', '=', 'line', '.', 'decode', '(', 'encoding', ')', 'if', 'line', '.', 'count', '(', "'\\t'", ')', '!=', '1', ':', 'tsv', '=', 'False', 'if', "'\\\\b'", 'in', 'line', ':', 'boundaries', '=', 'True', 'if', 'boundaries', 'and', 'not', 'tsv', ':', 'break', 'return', 'tsv', ',', 'boundaries'] | Automatically detects the pattern file format, and determines
whether the Aho-Corasick string matching should pay attention to
word boundaries or not.
Arguments:
- `pattern_filename`:
- `encoding`:
- `on_word_boundaries`: | ['Automatically', 'detects', 'the', 'pattern', 'file', 'format', 'and', 'determines', 'whether', 'the', 'Aho', '-', 'Corasick', 'string', 'matching', 'should', 'pay', 'attention', 'to', 'word', 'boundaries', 'or', 'not', '.'] | train | https://github.com/wroberts/fsed/blob/c0c1c5e0ea3a413ef679fdf71635f7f2e5d79ca2/fsed/fsed.py#L43-L65 |
1,359 | GNS3/gns3-server | gns3server/compute/dynamips/nodes/ethernet_hub.py | EthernetHub.start_capture | def start_capture(self, port_number, output_file, data_link_type="DLT_EN10MB"):
"""
Starts a packet capture.
:param port_number: allocated port number
:param output_file: PCAP destination file for the capture
:param data_link_type: PCAP data link type (DLT_*), default is DLT_EN10MB
"""
if port_number not in self._mappings:
raise DynamipsError("Port {} is not allocated".format(port_number))
nio = self._mappings[port_number]
data_link_type = data_link_type.lower()
if data_link_type.startswith("dlt_"):
data_link_type = data_link_type[4:]
if nio.input_filter[0] is not None and nio.output_filter[0] is not None:
raise DynamipsError("Port {} has already a filter applied".format(port_number))
yield from nio.bind_filter("both", "capture")
yield from nio.setup_filter("both", '{} "{}"'.format(data_link_type, output_file))
log.info('Ethernet hub "{name}" [{id}]: starting packet capture on port {port}'.format(name=self._name,
id=self._id,
port=port_number)) | python | def start_capture(self, port_number, output_file, data_link_type="DLT_EN10MB"):
"""
Starts a packet capture.
:param port_number: allocated port number
:param output_file: PCAP destination file for the capture
:param data_link_type: PCAP data link type (DLT_*), default is DLT_EN10MB
"""
if port_number not in self._mappings:
raise DynamipsError("Port {} is not allocated".format(port_number))
nio = self._mappings[port_number]
data_link_type = data_link_type.lower()
if data_link_type.startswith("dlt_"):
data_link_type = data_link_type[4:]
if nio.input_filter[0] is not None and nio.output_filter[0] is not None:
raise DynamipsError("Port {} has already a filter applied".format(port_number))
yield from nio.bind_filter("both", "capture")
yield from nio.setup_filter("both", '{} "{}"'.format(data_link_type, output_file))
log.info('Ethernet hub "{name}" [{id}]: starting packet capture on port {port}'.format(name=self._name,
id=self._id,
port=port_number)) | ['def', 'start_capture', '(', 'self', ',', 'port_number', ',', 'output_file', ',', 'data_link_type', '=', '"DLT_EN10MB"', ')', ':', 'if', 'port_number', 'not', 'in', 'self', '.', '_mappings', ':', 'raise', 'DynamipsError', '(', '"Port {} is not allocated"', '.', 'format', '(', 'port_number', ')', ')', 'nio', '=', 'self', '.', '_mappings', '[', 'port_number', ']', 'data_link_type', '=', 'data_link_type', '.', 'lower', '(', ')', 'if', 'data_link_type', '.', 'startswith', '(', '"dlt_"', ')', ':', 'data_link_type', '=', 'data_link_type', '[', '4', ':', ']', 'if', 'nio', '.', 'input_filter', '[', '0', ']', 'is', 'not', 'None', 'and', 'nio', '.', 'output_filter', '[', '0', ']', 'is', 'not', 'None', ':', 'raise', 'DynamipsError', '(', '"Port {} has already a filter applied"', '.', 'format', '(', 'port_number', ')', ')', 'yield', 'from', 'nio', '.', 'bind_filter', '(', '"both"', ',', '"capture"', ')', 'yield', 'from', 'nio', '.', 'setup_filter', '(', '"both"', ',', '\'{} "{}"\'', '.', 'format', '(', 'data_link_type', ',', 'output_file', ')', ')', 'log', '.', 'info', '(', '\'Ethernet hub "{name}" [{id}]: starting packet capture on port {port}\'', '.', 'format', '(', 'name', '=', 'self', '.', '_name', ',', 'id', '=', 'self', '.', '_id', ',', 'port', '=', 'port_number', ')', ')'] | Starts a packet capture.
:param port_number: allocated port number
:param output_file: PCAP destination file for the capture
:param data_link_type: PCAP data link type (DLT_*), default is DLT_EN10MB | ['Starts', 'a', 'packet', 'capture', '.'] | train | https://github.com/GNS3/gns3-server/blob/a221678448fb5d24e977ef562f81d56aacc89ab1/gns3server/compute/dynamips/nodes/ethernet_hub.py#L186-L212 |
1,360 | StorjOld/heartbeat | heartbeat/util.py | KeyedPRF.eval | def eval(self, x):
"""This method returns the evaluation of the function with input x
:param x: this is the input as a Long
"""
aes = AES.new(self.key, AES.MODE_CFB, "\0" * AES.block_size)
while True:
nonce = 0
data = KeyedPRF.pad(SHA256.new(str(x + nonce).encode()).digest(),
(number.size(self.range) + 7) // 8)
num = self.mask & number.bytes_to_long(aes.encrypt(data))
if (num < self.range):
return num
nonce += 1 | python | def eval(self, x):
"""This method returns the evaluation of the function with input x
:param x: this is the input as a Long
"""
aes = AES.new(self.key, AES.MODE_CFB, "\0" * AES.block_size)
while True:
nonce = 0
data = KeyedPRF.pad(SHA256.new(str(x + nonce).encode()).digest(),
(number.size(self.range) + 7) // 8)
num = self.mask & number.bytes_to_long(aes.encrypt(data))
if (num < self.range):
return num
nonce += 1 | ['def', 'eval', '(', 'self', ',', 'x', ')', ':', 'aes', '=', 'AES', '.', 'new', '(', 'self', '.', 'key', ',', 'AES', '.', 'MODE_CFB', ',', '"\\0"', '*', 'AES', '.', 'block_size', ')', 'while', 'True', ':', 'nonce', '=', '0', 'data', '=', 'KeyedPRF', '.', 'pad', '(', 'SHA256', '.', 'new', '(', 'str', '(', 'x', '+', 'nonce', ')', '.', 'encode', '(', ')', ')', '.', 'digest', '(', ')', ',', '(', 'number', '.', 'size', '(', 'self', '.', 'range', ')', '+', '7', ')', '//', '8', ')', 'num', '=', 'self', '.', 'mask', '&', 'number', '.', 'bytes_to_long', '(', 'aes', '.', 'encrypt', '(', 'data', ')', ')', 'if', '(', 'num', '<', 'self', '.', 'range', ')', ':', 'return', 'num', 'nonce', '+=', '1'] | This method returns the evaluation of the function with input x
:param x: this is the input as a Long | ['This', 'method', 'returns', 'the', 'evaluation', 'of', 'the', 'function', 'with', 'input', 'x'] | train | https://github.com/StorjOld/heartbeat/blob/4d54f2011f1e9f688073d4347bc51bb7bd682718/heartbeat/util.py#L83-L96 |
1,361 | openid/python-openid | openid/extensions/draft/pape2.py | Response.parseExtensionArgs | def parseExtensionArgs(self, args, strict=False):
"""Parse the provider authentication policy arguments into the
internal state of this object
@param args: unqualified provider authentication policy
arguments
@param strict: Whether to raise an exception when bad data is
encountered
@returns: None. The data is parsed into the internal fields of
this object.
"""
policies_str = args.get('auth_policies')
if policies_str and policies_str != 'none':
self.auth_policies = policies_str.split(' ')
nist_level_str = args.get('nist_auth_level')
if nist_level_str:
try:
nist_level = int(nist_level_str)
except ValueError:
if strict:
raise ValueError('nist_auth_level must be an integer between '
'zero and four, inclusive')
else:
self.nist_auth_level = None
else:
if 0 <= nist_level < 5:
self.nist_auth_level = nist_level
auth_time = args.get('auth_time')
if auth_time:
if TIME_VALIDATOR.match(auth_time):
self.auth_time = auth_time
elif strict:
raise ValueError("auth_time must be in RFC3339 format") | python | def parseExtensionArgs(self, args, strict=False):
"""Parse the provider authentication policy arguments into the
internal state of this object
@param args: unqualified provider authentication policy
arguments
@param strict: Whether to raise an exception when bad data is
encountered
@returns: None. The data is parsed into the internal fields of
this object.
"""
policies_str = args.get('auth_policies')
if policies_str and policies_str != 'none':
self.auth_policies = policies_str.split(' ')
nist_level_str = args.get('nist_auth_level')
if nist_level_str:
try:
nist_level = int(nist_level_str)
except ValueError:
if strict:
raise ValueError('nist_auth_level must be an integer between '
'zero and four, inclusive')
else:
self.nist_auth_level = None
else:
if 0 <= nist_level < 5:
self.nist_auth_level = nist_level
auth_time = args.get('auth_time')
if auth_time:
if TIME_VALIDATOR.match(auth_time):
self.auth_time = auth_time
elif strict:
raise ValueError("auth_time must be in RFC3339 format") | ['def', 'parseExtensionArgs', '(', 'self', ',', 'args', ',', 'strict', '=', 'False', ')', ':', 'policies_str', '=', 'args', '.', 'get', '(', "'auth_policies'", ')', 'if', 'policies_str', 'and', 'policies_str', '!=', "'none'", ':', 'self', '.', 'auth_policies', '=', 'policies_str', '.', 'split', '(', "' '", ')', 'nist_level_str', '=', 'args', '.', 'get', '(', "'nist_auth_level'", ')', 'if', 'nist_level_str', ':', 'try', ':', 'nist_level', '=', 'int', '(', 'nist_level_str', ')', 'except', 'ValueError', ':', 'if', 'strict', ':', 'raise', 'ValueError', '(', "'nist_auth_level must be an integer between '", "'zero and four, inclusive'", ')', 'else', ':', 'self', '.', 'nist_auth_level', '=', 'None', 'else', ':', 'if', '0', '<=', 'nist_level', '<', '5', ':', 'self', '.', 'nist_auth_level', '=', 'nist_level', 'auth_time', '=', 'args', '.', 'get', '(', "'auth_time'", ')', 'if', 'auth_time', ':', 'if', 'TIME_VALIDATOR', '.', 'match', '(', 'auth_time', ')', ':', 'self', '.', 'auth_time', '=', 'auth_time', 'elif', 'strict', ':', 'raise', 'ValueError', '(', '"auth_time must be in RFC3339 format"', ')'] | Parse the provider authentication policy arguments into the
internal state of this object
@param args: unqualified provider authentication policy
arguments
@param strict: Whether to raise an exception when bad data is
encountered
@returns: None. The data is parsed into the internal fields of
this object. | ['Parse', 'the', 'provider', 'authentication', 'policy', 'arguments', 'into', 'the', 'internal', 'state', 'of', 'this', 'object'] | train | https://github.com/openid/python-openid/blob/f7e13536f0d1828d3cef5ae7a7b55cabadff37fc/openid/extensions/draft/pape2.py#L211-L247 |
1,362 | PGower/PyCanvas | pycanvas/apis/content_migrations.py | list_migration_issues_courses | def list_migration_issues_courses(self, course_id, content_migration_id):
"""
List migration issues.
Returns paginated migration issues
"""
path = {}
data = {}
params = {}
# REQUIRED - PATH - course_id
"""ID"""
path["course_id"] = course_id
# REQUIRED - PATH - content_migration_id
"""ID"""
path["content_migration_id"] = content_migration_id
self.logger.debug("GET /api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues with query params: {params} and form data: {data}".format(params=params, data=data, **path))
return self.generic_request("GET", "/api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues".format(**path), data=data, params=params, all_pages=True) | python | def list_migration_issues_courses(self, course_id, content_migration_id):
"""
List migration issues.
Returns paginated migration issues
"""
path = {}
data = {}
params = {}
# REQUIRED - PATH - course_id
"""ID"""
path["course_id"] = course_id
# REQUIRED - PATH - content_migration_id
"""ID"""
path["content_migration_id"] = content_migration_id
self.logger.debug("GET /api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues with query params: {params} and form data: {data}".format(params=params, data=data, **path))
return self.generic_request("GET", "/api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues".format(**path), data=data, params=params, all_pages=True) | ['def', 'list_migration_issues_courses', '(', 'self', ',', 'course_id', ',', 'content_migration_id', ')', ':', 'path', '=', '{', '}', 'data', '=', '{', '}', 'params', '=', '{', '}', '# REQUIRED - PATH - course_id\r', '"""ID"""', 'path', '[', '"course_id"', ']', '=', 'course_id', '# REQUIRED - PATH - content_migration_id\r', '"""ID"""', 'path', '[', '"content_migration_id"', ']', '=', 'content_migration_id', 'self', '.', 'logger', '.', 'debug', '(', '"GET /api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues with query params: {params} and form data: {data}"', '.', 'format', '(', 'params', '=', 'params', ',', 'data', '=', 'data', ',', '*', '*', 'path', ')', ')', 'return', 'self', '.', 'generic_request', '(', '"GET"', ',', '"/api/v1/courses/{course_id}/content_migrations/{content_migration_id}/migration_issues"', '.', 'format', '(', '*', '*', 'path', ')', ',', 'data', '=', 'data', ',', 'params', '=', 'params', ',', 'all_pages', '=', 'True', ')'] | List migration issues.
Returns paginated migration issues | ['List', 'migration', 'issues', '.', 'Returns', 'paginated', 'migration', 'issues'] | train | https://github.com/PGower/PyCanvas/blob/68520005382b440a1e462f9df369f54d364e21e8/pycanvas/apis/content_migrations.py#L40-L59 |
1,363 | pyQode/pyqode.cobol | pyqode/cobol/modes/indenter.py | IndenterMode.unindent | def unindent(self):
"""
Un-indents text at cursor position.
"""
_logger().debug('unindent')
cursor = self.editor.textCursor()
_logger().debug('cursor has selection %r', cursor.hasSelection())
if cursor.hasSelection():
cursor.beginEditBlock()
self.unindent_selection(cursor)
cursor.endEditBlock()
self.editor.setTextCursor(cursor)
else:
tab_len = self.editor.tab_length
indentation = cursor.positionInBlock()
indentation -= self.min_column
if indentation == 0:
return
max_spaces = indentation % tab_len
if max_spaces == 0:
max_spaces = tab_len
spaces = self.count_deletable_spaces(cursor, max_spaces)
_logger().info('deleting %d space before cursor' % spaces)
cursor.beginEditBlock()
for _ in range(spaces):
cursor.deletePreviousChar()
cursor.endEditBlock()
self.editor.setTextCursor(cursor)
_logger().debug(cursor.block().text()) | python | def unindent(self):
"""
Un-indents text at cursor position.
"""
_logger().debug('unindent')
cursor = self.editor.textCursor()
_logger().debug('cursor has selection %r', cursor.hasSelection())
if cursor.hasSelection():
cursor.beginEditBlock()
self.unindent_selection(cursor)
cursor.endEditBlock()
self.editor.setTextCursor(cursor)
else:
tab_len = self.editor.tab_length
indentation = cursor.positionInBlock()
indentation -= self.min_column
if indentation == 0:
return
max_spaces = indentation % tab_len
if max_spaces == 0:
max_spaces = tab_len
spaces = self.count_deletable_spaces(cursor, max_spaces)
_logger().info('deleting %d space before cursor' % spaces)
cursor.beginEditBlock()
for _ in range(spaces):
cursor.deletePreviousChar()
cursor.endEditBlock()
self.editor.setTextCursor(cursor)
_logger().debug(cursor.block().text()) | ['def', 'unindent', '(', 'self', ')', ':', '_logger', '(', ')', '.', 'debug', '(', "'unindent'", ')', 'cursor', '=', 'self', '.', 'editor', '.', 'textCursor', '(', ')', '_logger', '(', ')', '.', 'debug', '(', "'cursor has selection %r'", ',', 'cursor', '.', 'hasSelection', '(', ')', ')', 'if', 'cursor', '.', 'hasSelection', '(', ')', ':', 'cursor', '.', 'beginEditBlock', '(', ')', 'self', '.', 'unindent_selection', '(', 'cursor', ')', 'cursor', '.', 'endEditBlock', '(', ')', 'self', '.', 'editor', '.', 'setTextCursor', '(', 'cursor', ')', 'else', ':', 'tab_len', '=', 'self', '.', 'editor', '.', 'tab_length', 'indentation', '=', 'cursor', '.', 'positionInBlock', '(', ')', 'indentation', '-=', 'self', '.', 'min_column', 'if', 'indentation', '==', '0', ':', 'return', 'max_spaces', '=', 'indentation', '%', 'tab_len', 'if', 'max_spaces', '==', '0', ':', 'max_spaces', '=', 'tab_len', 'spaces', '=', 'self', '.', 'count_deletable_spaces', '(', 'cursor', ',', 'max_spaces', ')', '_logger', '(', ')', '.', 'info', '(', "'deleting %d space before cursor'", '%', 'spaces', ')', 'cursor', '.', 'beginEditBlock', '(', ')', 'for', '_', 'in', 'range', '(', 'spaces', ')', ':', 'cursor', '.', 'deletePreviousChar', '(', ')', 'cursor', '.', 'endEditBlock', '(', ')', 'self', '.', 'editor', '.', 'setTextCursor', '(', 'cursor', ')', '_logger', '(', ')', '.', 'debug', '(', 'cursor', '.', 'block', '(', ')', '.', 'text', '(', ')', ')'] | Un-indents text at cursor position. | ['Un', '-', 'indents', 'text', 'at', 'cursor', 'position', '.'] | train | https://github.com/pyQode/pyqode.cobol/blob/eedae4e320a4b2d0c44abb2c3061091321648fb7/pyqode/cobol/modes/indenter.py#L149-L178 |
1,364 | cyrus-/cypy | cypy/__init__.py | fn_kwargs | def fn_kwargs(callable):
"""Returns a dict with the kwargs from the provided function.
Example
>>> def x(a, b=0, *args, **kwargs): pass
>>> func_kwargs(x) == { 'b': 0 }
"""
fn = get_fn(callable)
(args, _, _, defaults) = _inspect.getargspec(fn)
if defaults is None: return { }
return dict(list(zip(reversed(args), reversed(defaults)))) | python | def fn_kwargs(callable):
"""Returns a dict with the kwargs from the provided function.
Example
>>> def x(a, b=0, *args, **kwargs): pass
>>> func_kwargs(x) == { 'b': 0 }
"""
fn = get_fn(callable)
(args, _, _, defaults) = _inspect.getargspec(fn)
if defaults is None: return { }
return dict(list(zip(reversed(args), reversed(defaults)))) | ['def', 'fn_kwargs', '(', 'callable', ')', ':', 'fn', '=', 'get_fn', '(', 'callable', ')', '(', 'args', ',', '_', ',', '_', ',', 'defaults', ')', '=', '_inspect', '.', 'getargspec', '(', 'fn', ')', 'if', 'defaults', 'is', 'None', ':', 'return', '{', '}', 'return', 'dict', '(', 'list', '(', 'zip', '(', 'reversed', '(', 'args', ')', ',', 'reversed', '(', 'defaults', ')', ')', ')', ')'] | Returns a dict with the kwargs from the provided function.
Example
>>> def x(a, b=0, *args, **kwargs): pass
>>> func_kwargs(x) == { 'b': 0 } | ['Returns', 'a', 'dict', 'with', 'the', 'kwargs', 'from', 'the', 'provided', 'function', '.'] | train | https://github.com/cyrus-/cypy/blob/04bb59e91fa314e8cf987743189c77a9b6bc371d/cypy/__init__.py#L742-L754 |
1,365 | gabstopper/smc-python | smc/elements/network.py | IPList.update_or_create | def update_or_create(cls, append_lists=True, with_status=False, **kwargs):
"""
Update or create an IPList.
:param bool append_lists: append to existing IP List
:param dict kwargs: provide at minimum the name attribute
and optionally match the create constructor values
:raises FetchElementFailed: Reason for retrieval failure
"""
was_created, was_modified = False, False
element = None
try:
element = cls.get(kwargs.get('name'))
if append_lists:
iplist = element.iplist
diff = [i for i in kwargs.get('iplist', []) if i not in iplist]
if diff:
iplist.extend(diff)
else:
iplist = []
else:
iplist = kwargs.get('iplist', [])
if iplist:
element.upload(json={'ip': iplist}, as_type='json')
was_modified = True
except ElementNotFound:
element = cls.create(
kwargs.get('name'),
iplist = kwargs.get('iplist', []))
was_created = True
if with_status:
return element, was_modified, was_created
return element | python | def update_or_create(cls, append_lists=True, with_status=False, **kwargs):
"""
Update or create an IPList.
:param bool append_lists: append to existing IP List
:param dict kwargs: provide at minimum the name attribute
and optionally match the create constructor values
:raises FetchElementFailed: Reason for retrieval failure
"""
was_created, was_modified = False, False
element = None
try:
element = cls.get(kwargs.get('name'))
if append_lists:
iplist = element.iplist
diff = [i for i in kwargs.get('iplist', []) if i not in iplist]
if diff:
iplist.extend(diff)
else:
iplist = []
else:
iplist = kwargs.get('iplist', [])
if iplist:
element.upload(json={'ip': iplist}, as_type='json')
was_modified = True
except ElementNotFound:
element = cls.create(
kwargs.get('name'),
iplist = kwargs.get('iplist', []))
was_created = True
if with_status:
return element, was_modified, was_created
return element | ['def', 'update_or_create', '(', 'cls', ',', 'append_lists', '=', 'True', ',', 'with_status', '=', 'False', ',', '*', '*', 'kwargs', ')', ':', 'was_created', ',', 'was_modified', '=', 'False', ',', 'False', 'element', '=', 'None', 'try', ':', 'element', '=', 'cls', '.', 'get', '(', 'kwargs', '.', 'get', '(', "'name'", ')', ')', 'if', 'append_lists', ':', 'iplist', '=', 'element', '.', 'iplist', 'diff', '=', '[', 'i', 'for', 'i', 'in', 'kwargs', '.', 'get', '(', "'iplist'", ',', '[', ']', ')', 'if', 'i', 'not', 'in', 'iplist', ']', 'if', 'diff', ':', 'iplist', '.', 'extend', '(', 'diff', ')', 'else', ':', 'iplist', '=', '[', ']', 'else', ':', 'iplist', '=', 'kwargs', '.', 'get', '(', "'iplist'", ',', '[', ']', ')', 'if', 'iplist', ':', 'element', '.', 'upload', '(', 'json', '=', '{', "'ip'", ':', 'iplist', '}', ',', 'as_type', '=', "'json'", ')', 'was_modified', '=', 'True', 'except', 'ElementNotFound', ':', 'element', '=', 'cls', '.', 'create', '(', 'kwargs', '.', 'get', '(', "'name'", ')', ',', 'iplist', '=', 'kwargs', '.', 'get', '(', "'iplist'", ',', '[', ']', ')', ')', 'was_created', '=', 'True', 'if', 'with_status', ':', 'return', 'element', ',', 'was_modified', ',', 'was_created', 'return', 'element'] | Update or create an IPList.
:param bool append_lists: append to existing IP List
:param dict kwargs: provide at minimum the name attribute
and optionally match the create constructor values
:raises FetchElementFailed: Reason for retrieval failure | ['Update', 'or', 'create', 'an', 'IPList', '.', ':', 'param', 'bool', 'append_lists', ':', 'append', 'to', 'existing', 'IP', 'List', ':', 'param', 'dict', 'kwargs', ':', 'provide', 'at', 'minimum', 'the', 'name', 'attribute', 'and', 'optionally', 'match', 'the', 'create', 'constructor', 'values', ':', 'raises', 'FetchElementFailed', ':', 'Reason', 'for', 'retrieval', 'failure'] | train | https://github.com/gabstopper/smc-python/blob/e027b8a5dcfaf884eada32d113d41c1e56b32457/smc/elements/network.py#L458-L493 |
1,366 | pytorch/text | torchtext/data/field.py | SubwordField.segment | def segment(self, *args):
"""Segment one or more datasets with this subword field.
Arguments:
Positional arguments: Dataset objects or other indexable
mutable sequences to segment. If a Dataset object is provided,
all columns corresponding to this field are used; individual
columns can also be provided directly.
"""
sources = []
for arg in args:
if isinstance(arg, Dataset):
sources += [getattr(arg, name) for name, field in
arg.fields.items() if field is self]
else:
sources.append(arg)
for data in sources:
for x in tqdm(data, 'segmenting'):
x[:] = self.vocab.segment(x) | python | def segment(self, *args):
"""Segment one or more datasets with this subword field.
Arguments:
Positional arguments: Dataset objects or other indexable
mutable sequences to segment. If a Dataset object is provided,
all columns corresponding to this field are used; individual
columns can also be provided directly.
"""
sources = []
for arg in args:
if isinstance(arg, Dataset):
sources += [getattr(arg, name) for name, field in
arg.fields.items() if field is self]
else:
sources.append(arg)
for data in sources:
for x in tqdm(data, 'segmenting'):
x[:] = self.vocab.segment(x) | ['def', 'segment', '(', 'self', ',', '*', 'args', ')', ':', 'sources', '=', '[', ']', 'for', 'arg', 'in', 'args', ':', 'if', 'isinstance', '(', 'arg', ',', 'Dataset', ')', ':', 'sources', '+=', '[', 'getattr', '(', 'arg', ',', 'name', ')', 'for', 'name', ',', 'field', 'in', 'arg', '.', 'fields', '.', 'items', '(', ')', 'if', 'field', 'is', 'self', ']', 'else', ':', 'sources', '.', 'append', '(', 'arg', ')', 'for', 'data', 'in', 'sources', ':', 'for', 'x', 'in', 'tqdm', '(', 'data', ',', "'segmenting'", ')', ':', 'x', '[', ':', ']', '=', 'self', '.', 'vocab', '.', 'segment', '(', 'x', ')'] | Segment one or more datasets with this subword field.
Arguments:
Positional arguments: Dataset objects or other indexable
mutable sequences to segment. If a Dataset object is provided,
all columns corresponding to this field are used; individual
columns can also be provided directly. | ['Segment', 'one', 'or', 'more', 'datasets', 'with', 'this', 'subword', 'field', '.'] | train | https://github.com/pytorch/text/blob/26bfce6869dc704f1d86792f9a681d453d7e7bb8/torchtext/data/field.py#L424-L442 |
1,367 | DLR-RM/RAFCON | source/rafcon/core/states/state.py | State.get_uppermost_library_root_state | def get_uppermost_library_root_state(self):
"""Find state_copy of uppermost LibraryState
Method checks if there is a parent library root state and assigns it to be the current library root state till
there is no further parent library root state.
"""
library_root_state = self.get_next_upper_library_root_state()
parent_library_root_state = library_root_state
# initial a library root state has to be found and if there is no further parent root state
# parent_library_root_state and library_root_state are no more identical
while parent_library_root_state and library_root_state is parent_library_root_state:
if library_root_state:
parent_library_root_state = library_root_state.parent.get_next_upper_library_root_state()
if parent_library_root_state:
library_root_state = parent_library_root_state
return library_root_state | python | def get_uppermost_library_root_state(self):
"""Find state_copy of uppermost LibraryState
Method checks if there is a parent library root state and assigns it to be the current library root state till
there is no further parent library root state.
"""
library_root_state = self.get_next_upper_library_root_state()
parent_library_root_state = library_root_state
# initial a library root state has to be found and if there is no further parent root state
# parent_library_root_state and library_root_state are no more identical
while parent_library_root_state and library_root_state is parent_library_root_state:
if library_root_state:
parent_library_root_state = library_root_state.parent.get_next_upper_library_root_state()
if parent_library_root_state:
library_root_state = parent_library_root_state
return library_root_state | ['def', 'get_uppermost_library_root_state', '(', 'self', ')', ':', 'library_root_state', '=', 'self', '.', 'get_next_upper_library_root_state', '(', ')', 'parent_library_root_state', '=', 'library_root_state', '# initial a library root state has to be found and if there is no further parent root state', '# parent_library_root_state and library_root_state are no more identical', 'while', 'parent_library_root_state', 'and', 'library_root_state', 'is', 'parent_library_root_state', ':', 'if', 'library_root_state', ':', 'parent_library_root_state', '=', 'library_root_state', '.', 'parent', '.', 'get_next_upper_library_root_state', '(', ')', 'if', 'parent_library_root_state', ':', 'library_root_state', '=', 'parent_library_root_state', 'return', 'library_root_state'] | Find state_copy of uppermost LibraryState
Method checks if there is a parent library root state and assigns it to be the current library root state till
there is no further parent library root state. | ['Find', 'state_copy', 'of', 'uppermost', 'LibraryState'] | train | https://github.com/DLR-RM/RAFCON/blob/24942ef1a904531f49ab8830a1dbb604441be498/source/rafcon/core/states/state.py#L1441-L1459 |
1,368 | StackStorm/pybind | pybind/slxos/v17s_1_02/__init__.py | brocade_mc_hms_operational._set_igmp_snooping_state | def _set_igmp_snooping_state(self, v, load=False):
"""
Setter method for igmp_snooping_state, mapped from YANG variable /igmp_snooping_state (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_igmp_snooping_state is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_igmp_snooping_state() directly.
YANG Description: IGMP Snooping Root MO
"""
if hasattr(v, "_utype"):
v = v._utype(v)
try:
t = YANGDynClass(v,base=igmp_snooping_state.igmp_snooping_state, is_container='container', presence=False, yang_name="igmp-snooping-state", rest_name="igmp-snooping-state", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mc-hms-igmp-snooping', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mc-hms-operational', defining_module='brocade-mc-hms-operational', yang_type='container', is_config=True)
except (TypeError, ValueError):
raise ValueError({
'error-string': """igmp_snooping_state must be of a type compatible with container""",
'defined-type': "container",
'generated-type': """YANGDynClass(base=igmp_snooping_state.igmp_snooping_state, is_container='container', presence=False, yang_name="igmp-snooping-state", rest_name="igmp-snooping-state", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mc-hms-igmp-snooping', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mc-hms-operational', defining_module='brocade-mc-hms-operational', yang_type='container', is_config=True)""",
})
self.__igmp_snooping_state = t
if hasattr(self, '_set'):
self._set() | python | def _set_igmp_snooping_state(self, v, load=False):
"""
Setter method for igmp_snooping_state, mapped from YANG variable /igmp_snooping_state (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_igmp_snooping_state is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_igmp_snooping_state() directly.
YANG Description: IGMP Snooping Root MO
"""
if hasattr(v, "_utype"):
v = v._utype(v)
try:
t = YANGDynClass(v,base=igmp_snooping_state.igmp_snooping_state, is_container='container', presence=False, yang_name="igmp-snooping-state", rest_name="igmp-snooping-state", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mc-hms-igmp-snooping', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mc-hms-operational', defining_module='brocade-mc-hms-operational', yang_type='container', is_config=True)
except (TypeError, ValueError):
raise ValueError({
'error-string': """igmp_snooping_state must be of a type compatible with container""",
'defined-type': "container",
'generated-type': """YANGDynClass(base=igmp_snooping_state.igmp_snooping_state, is_container='container', presence=False, yang_name="igmp-snooping-state", rest_name="igmp-snooping-state", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mc-hms-igmp-snooping', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mc-hms-operational', defining_module='brocade-mc-hms-operational', yang_type='container', is_config=True)""",
})
self.__igmp_snooping_state = t
if hasattr(self, '_set'):
self._set() | ['def', '_set_igmp_snooping_state', '(', 'self', ',', 'v', ',', 'load', '=', 'False', ')', ':', 'if', 'hasattr', '(', 'v', ',', '"_utype"', ')', ':', 'v', '=', 'v', '.', '_utype', '(', 'v', ')', 'try', ':', 't', '=', 'YANGDynClass', '(', 'v', ',', 'base', '=', 'igmp_snooping_state', '.', 'igmp_snooping_state', ',', 'is_container', '=', "'container'", ',', 'presence', '=', 'False', ',', 'yang_name', '=', '"igmp-snooping-state"', ',', 'rest_name', '=', '"igmp-snooping-state"', ',', 'parent', '=', 'self', ',', 'path_helper', '=', 'self', '.', '_path_helper', ',', 'extmethods', '=', 'self', '.', '_extmethods', ',', 'register_paths', '=', 'True', ',', 'extensions', '=', '{', "u'tailf-common'", ':', '{', "u'callpoint'", ':', "u'mc-hms-igmp-snooping'", ',', "u'cli-suppress-show-path'", ':', 'None', '}', '}', ',', 'namespace', '=', "'urn:brocade.com:mgmt:brocade-mc-hms-operational'", ',', 'defining_module', '=', "'brocade-mc-hms-operational'", ',', 'yang_type', '=', "'container'", ',', 'is_config', '=', 'True', ')', 'except', '(', 'TypeError', ',', 'ValueError', ')', ':', 'raise', 'ValueError', '(', '{', "'error-string'", ':', '"""igmp_snooping_state must be of a type compatible with container"""', ',', "'defined-type'", ':', '"container"', ',', "'generated-type'", ':', '"""YANGDynClass(base=igmp_snooping_state.igmp_snooping_state, is_container=\'container\', presence=False, yang_name="igmp-snooping-state", rest_name="igmp-snooping-state", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u\'tailf-common\': {u\'callpoint\': u\'mc-hms-igmp-snooping\', u\'cli-suppress-show-path\': None}}, namespace=\'urn:brocade.com:mgmt:brocade-mc-hms-operational\', defining_module=\'brocade-mc-hms-operational\', yang_type=\'container\', is_config=True)"""', ',', '}', ')', 'self', '.', '__igmp_snooping_state', '=', 't', 'if', 'hasattr', '(', 'self', ',', "'_set'", ')', ':', 'self', '.', '_set', '(', ')'] | Setter method for igmp_snooping_state, mapped from YANG variable /igmp_snooping_state (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_igmp_snooping_state is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_igmp_snooping_state() directly.
YANG Description: IGMP Snooping Root MO | ['Setter', 'method', 'for', 'igmp_snooping_state', 'mapped', 'from', 'YANG', 'variable', '/', 'igmp_snooping_state', '(', 'container', ')', 'If', 'this', 'variable', 'is', 'read', '-', 'only', '(', 'config', ':', 'false', ')', 'in', 'the', 'source', 'YANG', 'file', 'then', '_set_igmp_snooping_state', 'is', 'considered', 'as', 'a', 'private', 'method', '.', 'Backends', 'looking', 'to', 'populate', 'this', 'variable', 'should', 'do', 'so', 'via', 'calling', 'thisObj', '.', '_set_igmp_snooping_state', '()', 'directly', '.'] | train | https://github.com/StackStorm/pybind/blob/44c467e71b2b425be63867aba6e6fa28b2cfe7fb/pybind/slxos/v17s_1_02/__init__.py#L1023-L1046 |
1,369 | ARMmbed/icetea | icetea_lib/build/build.py | BuildHttp.get_file | def get_file(self):
"""
Load data into a file and return file path.
:return: path to file as string
"""
content = self._load()
if not content:
return None
filename = "temporary_file.bin"
with open(filename, "wb") as file_name:
file_name.write(content)
return filename | python | def get_file(self):
"""
Load data into a file and return file path.
:return: path to file as string
"""
content = self._load()
if not content:
return None
filename = "temporary_file.bin"
with open(filename, "wb") as file_name:
file_name.write(content)
return filename | ['def', 'get_file', '(', 'self', ')', ':', 'content', '=', 'self', '.', '_load', '(', ')', 'if', 'not', 'content', ':', 'return', 'None', 'filename', '=', '"temporary_file.bin"', 'with', 'open', '(', 'filename', ',', '"wb"', ')', 'as', 'file_name', ':', 'file_name', '.', 'write', '(', 'content', ')', 'return', 'filename'] | Load data into a file and return file path.
:return: path to file as string | ['Load', 'data', 'into', 'a', 'file', 'and', 'return', 'file', 'path', '.'] | train | https://github.com/ARMmbed/icetea/blob/b2b97ac607429830cf7d62dae2e3903692c7c778/icetea_lib/build/build.py#L200-L212 |
1,370 | tensorpack/tensorpack | tensorpack/models/_old_batch_norm.py | BatchNorm | def BatchNorm(inputs, training=None, momentum=0.9, epsilon=1e-5,
center=True, scale=True,
gamma_initializer=tf.ones_initializer(),
data_format='channels_last',
internal_update=False):
"""
Mostly equivalent to `tf.layers.batch_normalization`, but difference in
the following:
1. Accepts `data_format` rather than `axis`. For 2D input, this argument will be ignored.
2. Default value for `momentum` and `epsilon` is different.
3. Default value for `training` is automatically obtained from `TowerContext`.
4. Support the `internal_update` option.
Args:
internal_update (bool): if False, add EMA update ops to
`tf.GraphKeys.UPDATE_OPS`. If True, update EMA inside the layer
by control dependencies.
Variable Names:
* ``beta``: the bias term. Will be zero-inited by default.
* ``gamma``: the scale term. Will be one-inited by default. Input will be transformed by ``x * gamma + beta``.
* ``mean/EMA``: the moving average of mean.
* ``variance/EMA``: the moving average of variance.
Note:
1. About multi-GPU training: moving averages across GPUs are not aggregated.
Batch statistics are computed independently. This is consistent with most frameworks.
2. Combinations of ``training`` and ``ctx.is_training``:
* ``training == ctx.is_training``: standard BN, EMA are
maintained during training and used during inference. This is
the default.
* ``training and not ctx.is_training``: still use batch statistics in inference.
* ``not training and ctx.is_training``: use EMA to normalize in
training. This is useful when you load a pre-trained BN and
don't want to fine tune the EMA. EMA will not be updated in
this case.
"""
data_format = get_data_format(data_format, keras_mode=False)
shape = inputs.get_shape().as_list()
ndims = len(shape)
assert ndims in [2, 4]
if ndims == 2:
data_format = 'NHWC'
if data_format == 'NCHW':
n_out = shape[1]
else:
n_out = shape[-1] # channel
assert n_out is not None, "Input to BatchNorm cannot have unknown channels!"
beta, gamma, moving_mean, moving_var = get_bn_variables(n_out, scale, center, gamma_initializer)
ctx = get_current_tower_context()
use_local_stat = training
if use_local_stat is None:
use_local_stat = ctx.is_training
use_local_stat = bool(use_local_stat)
if use_local_stat:
if ndims == 2:
inputs = tf.reshape(inputs, [-1, 1, 1, n_out]) # fused_bn only takes 4D input
# fused_bn has error using NCHW? (see #190)
xn, batch_mean, batch_var = tf.nn.fused_batch_norm(
inputs, gamma, beta, epsilon=epsilon,
is_training=True, data_format=data_format)
if ndims == 2:
xn = tf.squeeze(xn, [1, 2])
else:
if ctx.is_training:
assert get_tf_version_tuple() >= (1, 4), \
"Fine tuning a BatchNorm model with fixed statistics is only " \
"supported after https://github.com/tensorflow/tensorflow/pull/12580 "
if ctx.is_main_training_tower: # only warn in first tower
logger.warn("[BatchNorm] Using moving_mean/moving_variance in training.")
# Using moving_mean/moving_variance in training, which means we
# loaded a pre-trained BN and only fine-tuning the affine part.
xn, _, _ = tf.nn.fused_batch_norm(
inputs, gamma, beta,
mean=moving_mean, variance=moving_var, epsilon=epsilon,
data_format=data_format, is_training=False)
else:
if ndims == 4:
xn, _, _ = tf.nn.fused_batch_norm(
inputs, gamma, beta,
mean=moving_mean, variance=moving_var, epsilon=epsilon,
data_format=data_format, is_training=False)
else:
xn = tf.nn.batch_normalization(
inputs, moving_mean, moving_var, beta, gamma, epsilon)
# maintain EMA only on one GPU is OK, even in replicated mode.
# because training time doesn't use EMA
if ctx.is_main_training_tower:
add_model_variable(moving_mean)
add_model_variable(moving_var)
if ctx.is_main_training_tower and use_local_stat:
ret = update_bn_ema(xn, batch_mean, batch_var, moving_mean, moving_var, momentum, internal_update)
else:
ret = tf.identity(xn, name='output')
vh = ret.variables = VariableHolder(mean=moving_mean, variance=moving_var)
if scale:
vh.gamma = gamma
if center:
vh.beta = beta
return ret | python | def BatchNorm(inputs, training=None, momentum=0.9, epsilon=1e-5,
center=True, scale=True,
gamma_initializer=tf.ones_initializer(),
data_format='channels_last',
internal_update=False):
"""
Mostly equivalent to `tf.layers.batch_normalization`, but difference in
the following:
1. Accepts `data_format` rather than `axis`. For 2D input, this argument will be ignored.
2. Default value for `momentum` and `epsilon` is different.
3. Default value for `training` is automatically obtained from `TowerContext`.
4. Support the `internal_update` option.
Args:
internal_update (bool): if False, add EMA update ops to
`tf.GraphKeys.UPDATE_OPS`. If True, update EMA inside the layer
by control dependencies.
Variable Names:
* ``beta``: the bias term. Will be zero-inited by default.
* ``gamma``: the scale term. Will be one-inited by default. Input will be transformed by ``x * gamma + beta``.
* ``mean/EMA``: the moving average of mean.
* ``variance/EMA``: the moving average of variance.
Note:
1. About multi-GPU training: moving averages across GPUs are not aggregated.
Batch statistics are computed independently. This is consistent with most frameworks.
2. Combinations of ``training`` and ``ctx.is_training``:
* ``training == ctx.is_training``: standard BN, EMA are
maintained during training and used during inference. This is
the default.
* ``training and not ctx.is_training``: still use batch statistics in inference.
* ``not training and ctx.is_training``: use EMA to normalize in
training. This is useful when you load a pre-trained BN and
don't want to fine tune the EMA. EMA will not be updated in
this case.
"""
data_format = get_data_format(data_format, keras_mode=False)
shape = inputs.get_shape().as_list()
ndims = len(shape)
assert ndims in [2, 4]
if ndims == 2:
data_format = 'NHWC'
if data_format == 'NCHW':
n_out = shape[1]
else:
n_out = shape[-1] # channel
assert n_out is not None, "Input to BatchNorm cannot have unknown channels!"
beta, gamma, moving_mean, moving_var = get_bn_variables(n_out, scale, center, gamma_initializer)
ctx = get_current_tower_context()
use_local_stat = training
if use_local_stat is None:
use_local_stat = ctx.is_training
use_local_stat = bool(use_local_stat)
if use_local_stat:
if ndims == 2:
inputs = tf.reshape(inputs, [-1, 1, 1, n_out]) # fused_bn only takes 4D input
# fused_bn has error using NCHW? (see #190)
xn, batch_mean, batch_var = tf.nn.fused_batch_norm(
inputs, gamma, beta, epsilon=epsilon,
is_training=True, data_format=data_format)
if ndims == 2:
xn = tf.squeeze(xn, [1, 2])
else:
if ctx.is_training:
assert get_tf_version_tuple() >= (1, 4), \
"Fine tuning a BatchNorm model with fixed statistics is only " \
"supported after https://github.com/tensorflow/tensorflow/pull/12580 "
if ctx.is_main_training_tower: # only warn in first tower
logger.warn("[BatchNorm] Using moving_mean/moving_variance in training.")
# Using moving_mean/moving_variance in training, which means we
# loaded a pre-trained BN and only fine-tuning the affine part.
xn, _, _ = tf.nn.fused_batch_norm(
inputs, gamma, beta,
mean=moving_mean, variance=moving_var, epsilon=epsilon,
data_format=data_format, is_training=False)
else:
if ndims == 4:
xn, _, _ = tf.nn.fused_batch_norm(
inputs, gamma, beta,
mean=moving_mean, variance=moving_var, epsilon=epsilon,
data_format=data_format, is_training=False)
else:
xn = tf.nn.batch_normalization(
inputs, moving_mean, moving_var, beta, gamma, epsilon)
# maintain EMA only on one GPU is OK, even in replicated mode.
# because training time doesn't use EMA
if ctx.is_main_training_tower:
add_model_variable(moving_mean)
add_model_variable(moving_var)
if ctx.is_main_training_tower and use_local_stat:
ret = update_bn_ema(xn, batch_mean, batch_var, moving_mean, moving_var, momentum, internal_update)
else:
ret = tf.identity(xn, name='output')
vh = ret.variables = VariableHolder(mean=moving_mean, variance=moving_var)
if scale:
vh.gamma = gamma
if center:
vh.beta = beta
return ret | ['def', 'BatchNorm', '(', 'inputs', ',', 'training', '=', 'None', ',', 'momentum', '=', '0.9', ',', 'epsilon', '=', '1e-5', ',', 'center', '=', 'True', ',', 'scale', '=', 'True', ',', 'gamma_initializer', '=', 'tf', '.', 'ones_initializer', '(', ')', ',', 'data_format', '=', "'channels_last'", ',', 'internal_update', '=', 'False', ')', ':', 'data_format', '=', 'get_data_format', '(', 'data_format', ',', 'keras_mode', '=', 'False', ')', 'shape', '=', 'inputs', '.', 'get_shape', '(', ')', '.', 'as_list', '(', ')', 'ndims', '=', 'len', '(', 'shape', ')', 'assert', 'ndims', 'in', '[', '2', ',', '4', ']', 'if', 'ndims', '==', '2', ':', 'data_format', '=', "'NHWC'", 'if', 'data_format', '==', "'NCHW'", ':', 'n_out', '=', 'shape', '[', '1', ']', 'else', ':', 'n_out', '=', 'shape', '[', '-', '1', ']', '# channel', 'assert', 'n_out', 'is', 'not', 'None', ',', '"Input to BatchNorm cannot have unknown channels!"', 'beta', ',', 'gamma', ',', 'moving_mean', ',', 'moving_var', '=', 'get_bn_variables', '(', 'n_out', ',', 'scale', ',', 'center', ',', 'gamma_initializer', ')', 'ctx', '=', 'get_current_tower_context', '(', ')', 'use_local_stat', '=', 'training', 'if', 'use_local_stat', 'is', 'None', ':', 'use_local_stat', '=', 'ctx', '.', 'is_training', 'use_local_stat', '=', 'bool', '(', 'use_local_stat', ')', 'if', 'use_local_stat', ':', 'if', 'ndims', '==', '2', ':', 'inputs', '=', 'tf', '.', 'reshape', '(', 'inputs', ',', '[', '-', '1', ',', '1', ',', '1', ',', 'n_out', ']', ')', '# fused_bn only takes 4D input', '# fused_bn has error using NCHW? (see #190)', 'xn', ',', 'batch_mean', ',', 'batch_var', '=', 'tf', '.', 'nn', '.', 'fused_batch_norm', '(', 'inputs', ',', 'gamma', ',', 'beta', ',', 'epsilon', '=', 'epsilon', ',', 'is_training', '=', 'True', ',', 'data_format', '=', 'data_format', ')', 'if', 'ndims', '==', '2', ':', 'xn', '=', 'tf', '.', 'squeeze', '(', 'xn', ',', '[', '1', ',', '2', ']', ')', 'else', ':', 'if', 'ctx', '.', 'is_training', ':', 'assert', 'get_tf_version_tuple', '(', ')', '>=', '(', '1', ',', '4', ')', ',', '"Fine tuning a BatchNorm model with fixed statistics is only "', '"supported after https://github.com/tensorflow/tensorflow/pull/12580 "', 'if', 'ctx', '.', 'is_main_training_tower', ':', '# only warn in first tower', 'logger', '.', 'warn', '(', '"[BatchNorm] Using moving_mean/moving_variance in training."', ')', '# Using moving_mean/moving_variance in training, which means we', '# loaded a pre-trained BN and only fine-tuning the affine part.', 'xn', ',', '_', ',', '_', '=', 'tf', '.', 'nn', '.', 'fused_batch_norm', '(', 'inputs', ',', 'gamma', ',', 'beta', ',', 'mean', '=', 'moving_mean', ',', 'variance', '=', 'moving_var', ',', 'epsilon', '=', 'epsilon', ',', 'data_format', '=', 'data_format', ',', 'is_training', '=', 'False', ')', 'else', ':', 'if', 'ndims', '==', '4', ':', 'xn', ',', '_', ',', '_', '=', 'tf', '.', 'nn', '.', 'fused_batch_norm', '(', 'inputs', ',', 'gamma', ',', 'beta', ',', 'mean', '=', 'moving_mean', ',', 'variance', '=', 'moving_var', ',', 'epsilon', '=', 'epsilon', ',', 'data_format', '=', 'data_format', ',', 'is_training', '=', 'False', ')', 'else', ':', 'xn', '=', 'tf', '.', 'nn', '.', 'batch_normalization', '(', 'inputs', ',', 'moving_mean', ',', 'moving_var', ',', 'beta', ',', 'gamma', ',', 'epsilon', ')', '# maintain EMA only on one GPU is OK, even in replicated mode.', "# because training time doesn't use EMA", 'if', 'ctx', '.', 'is_main_training_tower', ':', 'add_model_variable', '(', 'moving_mean', ')', 'add_model_variable', '(', 'moving_var', ')', 'if', 'ctx', '.', 'is_main_training_tower', 'and', 'use_local_stat', ':', 'ret', '=', 'update_bn_ema', '(', 'xn', ',', 'batch_mean', ',', 'batch_var', ',', 'moving_mean', ',', 'moving_var', ',', 'momentum', ',', 'internal_update', ')', 'else', ':', 'ret', '=', 'tf', '.', 'identity', '(', 'xn', ',', 'name', '=', "'output'", ')', 'vh', '=', 'ret', '.', 'variables', '=', 'VariableHolder', '(', 'mean', '=', 'moving_mean', ',', 'variance', '=', 'moving_var', ')', 'if', 'scale', ':', 'vh', '.', 'gamma', '=', 'gamma', 'if', 'center', ':', 'vh', '.', 'beta', '=', 'beta', 'return', 'ret'] | Mostly equivalent to `tf.layers.batch_normalization`, but difference in
the following:
1. Accepts `data_format` rather than `axis`. For 2D input, this argument will be ignored.
2. Default value for `momentum` and `epsilon` is different.
3. Default value for `training` is automatically obtained from `TowerContext`.
4. Support the `internal_update` option.
Args:
internal_update (bool): if False, add EMA update ops to
`tf.GraphKeys.UPDATE_OPS`. If True, update EMA inside the layer
by control dependencies.
Variable Names:
* ``beta``: the bias term. Will be zero-inited by default.
* ``gamma``: the scale term. Will be one-inited by default. Input will be transformed by ``x * gamma + beta``.
* ``mean/EMA``: the moving average of mean.
* ``variance/EMA``: the moving average of variance.
Note:
1. About multi-GPU training: moving averages across GPUs are not aggregated.
Batch statistics are computed independently. This is consistent with most frameworks.
2. Combinations of ``training`` and ``ctx.is_training``:
* ``training == ctx.is_training``: standard BN, EMA are
maintained during training and used during inference. This is
the default.
* ``training and not ctx.is_training``: still use batch statistics in inference.
* ``not training and ctx.is_training``: use EMA to normalize in
training. This is useful when you load a pre-trained BN and
don't want to fine tune the EMA. EMA will not be updated in
this case. | ['Mostly', 'equivalent', 'to', 'tf', '.', 'layers', '.', 'batch_normalization', 'but', 'difference', 'in', 'the', 'following', ':', '1', '.', 'Accepts', 'data_format', 'rather', 'than', 'axis', '.', 'For', '2D', 'input', 'this', 'argument', 'will', 'be', 'ignored', '.', '2', '.', 'Default', 'value', 'for', 'momentum', 'and', 'epsilon', 'is', 'different', '.', '3', '.', 'Default', 'value', 'for', 'training', 'is', 'automatically', 'obtained', 'from', 'TowerContext', '.', '4', '.', 'Support', 'the', 'internal_update', 'option', '.', 'Args', ':', 'internal_update', '(', 'bool', ')', ':', 'if', 'False', 'add', 'EMA', 'update', 'ops', 'to', 'tf', '.', 'GraphKeys', '.', 'UPDATE_OPS', '.', 'If', 'True', 'update', 'EMA', 'inside', 'the', 'layer', 'by', 'control', 'dependencies', '.', 'Variable', 'Names', ':', '*', 'beta', ':', 'the', 'bias', 'term', '.', 'Will', 'be', 'zero', '-', 'inited', 'by', 'default', '.', '*', 'gamma', ':', 'the', 'scale', 'term', '.', 'Will', 'be', 'one', '-', 'inited', 'by', 'default', '.', 'Input', 'will', 'be', 'transformed', 'by', 'x', '*', 'gamma', '+', 'beta', '.', '*', 'mean', '/', 'EMA', ':', 'the', 'moving', 'average', 'of', 'mean', '.', '*', 'variance', '/', 'EMA', ':', 'the', 'moving', 'average', 'of', 'variance', '.', 'Note', ':', '1', '.', 'About', 'multi', '-', 'GPU', 'training', ':', 'moving', 'averages', 'across', 'GPUs', 'are', 'not', 'aggregated', '.', 'Batch', 'statistics', 'are', 'computed', 'independently', '.', 'This', 'is', 'consistent', 'with', 'most', 'frameworks', '.', '2', '.', 'Combinations', 'of', 'training', 'and', 'ctx', '.', 'is_training', ':', '*', 'training', '==', 'ctx', '.', 'is_training', ':', 'standard', 'BN', 'EMA', 'are', 'maintained', 'during', 'training', 'and', 'used', 'during', 'inference', '.', 'This', 'is', 'the', 'default', '.', '*', 'training', 'and', 'not', 'ctx', '.', 'is_training', ':', 'still', 'use', 'batch', 'statistics', 'in', 'inference', '.', '*', 'not', 'training', 'and', 'ctx', '.', 'is_training', ':', 'use', 'EMA', 'to', 'normalize', 'in', 'training', '.', 'This', 'is', 'useful', 'when', 'you', 'load', 'a', 'pre', '-', 'trained', 'BN', 'and', 'don', 't', 'want', 'to', 'fine', 'tune', 'the', 'EMA', '.', 'EMA', 'will', 'not', 'be', 'updated', 'in', 'this', 'case', '.'] | train | https://github.com/tensorpack/tensorpack/blob/d7a13cb74c9066bc791d7aafc3b744b60ee79a9f/tensorpack/models/_old_batch_norm.py#L67-L169 |
1,371 | NORDUnet/python-norduniclient | norduniclient/core.py | create_location_relationship | def create_location_relationship(manager, location_handle_id, other_handle_id, rel_type):
"""
Makes relationship between the two nodes and returns the relationship.
If a relationship is not possible NoRelationshipPossible exception is
raised.
"""
other_meta_type = get_node_meta_type(manager, other_handle_id)
if other_meta_type == 'Location' and rel_type == 'Has':
return _create_relationship(manager, location_handle_id, other_handle_id, rel_type)
raise exceptions.NoRelationshipPossible(location_handle_id, 'Location', other_handle_id, other_meta_type, rel_type) | python | def create_location_relationship(manager, location_handle_id, other_handle_id, rel_type):
"""
Makes relationship between the two nodes and returns the relationship.
If a relationship is not possible NoRelationshipPossible exception is
raised.
"""
other_meta_type = get_node_meta_type(manager, other_handle_id)
if other_meta_type == 'Location' and rel_type == 'Has':
return _create_relationship(manager, location_handle_id, other_handle_id, rel_type)
raise exceptions.NoRelationshipPossible(location_handle_id, 'Location', other_handle_id, other_meta_type, rel_type) | ['def', 'create_location_relationship', '(', 'manager', ',', 'location_handle_id', ',', 'other_handle_id', ',', 'rel_type', ')', ':', 'other_meta_type', '=', 'get_node_meta_type', '(', 'manager', ',', 'other_handle_id', ')', 'if', 'other_meta_type', '==', "'Location'", 'and', 'rel_type', '==', "'Has'", ':', 'return', '_create_relationship', '(', 'manager', ',', 'location_handle_id', ',', 'other_handle_id', ',', 'rel_type', ')', 'raise', 'exceptions', '.', 'NoRelationshipPossible', '(', 'location_handle_id', ',', "'Location'", ',', 'other_handle_id', ',', 'other_meta_type', ',', 'rel_type', ')'] | Makes relationship between the two nodes and returns the relationship.
If a relationship is not possible NoRelationshipPossible exception is
raised. | ['Makes', 'relationship', 'between', 'the', 'two', 'nodes', 'and', 'returns', 'the', 'relationship', '.', 'If', 'a', 'relationship', 'is', 'not', 'possible', 'NoRelationshipPossible', 'exception', 'is', 'raised', '.'] | train | https://github.com/NORDUnet/python-norduniclient/blob/ee5084a6f45caac614b4fda4a023749ca52f786c/norduniclient/core.py#L594-L603 |
1,372 | talkincode/toughlib | toughlib/btforms/net.py | validip | def validip(ip, defaultaddr="0.0.0.0", defaultport=8080):
"""Returns `(ip_address, port)` from string `ip_addr_port`"""
addr = defaultaddr
port = defaultport
ip = ip.split(":", 1)
if len(ip) == 1:
if not ip[0]:
pass
elif validipaddr(ip[0]):
addr = ip[0]
elif validipport(ip[0]):
port = int(ip[0])
else:
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
elif len(ip) == 2:
addr, port = ip
if not validipaddr(addr) and validipport(port):
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
port = int(port)
else:
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
return (addr, port) | python | def validip(ip, defaultaddr="0.0.0.0", defaultport=8080):
"""Returns `(ip_address, port)` from string `ip_addr_port`"""
addr = defaultaddr
port = defaultport
ip = ip.split(":", 1)
if len(ip) == 1:
if not ip[0]:
pass
elif validipaddr(ip[0]):
addr = ip[0]
elif validipport(ip[0]):
port = int(ip[0])
else:
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
elif len(ip) == 2:
addr, port = ip
if not validipaddr(addr) and validipport(port):
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
port = int(port)
else:
raise ValueError, ':'.join(ip) + ' is not a valid IP address/port'
return (addr, port) | ['def', 'validip', '(', 'ip', ',', 'defaultaddr', '=', '"0.0.0.0"', ',', 'defaultport', '=', '8080', ')', ':', 'addr', '=', 'defaultaddr', 'port', '=', 'defaultport', 'ip', '=', 'ip', '.', 'split', '(', '":"', ',', '1', ')', 'if', 'len', '(', 'ip', ')', '==', '1', ':', 'if', 'not', 'ip', '[', '0', ']', ':', 'pass', 'elif', 'validipaddr', '(', 'ip', '[', '0', ']', ')', ':', 'addr', '=', 'ip', '[', '0', ']', 'elif', 'validipport', '(', 'ip', '[', '0', ']', ')', ':', 'port', '=', 'int', '(', 'ip', '[', '0', ']', ')', 'else', ':', 'raise', 'ValueError', ',', "':'", '.', 'join', '(', 'ip', ')', '+', "' is not a valid IP address/port'", 'elif', 'len', '(', 'ip', ')', '==', '2', ':', 'addr', ',', 'port', '=', 'ip', 'if', 'not', 'validipaddr', '(', 'addr', ')', 'and', 'validipport', '(', 'port', ')', ':', 'raise', 'ValueError', ',', "':'", '.', 'join', '(', 'ip', ')', '+', "' is not a valid IP address/port'", 'port', '=', 'int', '(', 'port', ')', 'else', ':', 'raise', 'ValueError', ',', "':'", '.', 'join', '(', 'ip', ')', '+', "' is not a valid IP address/port'", 'return', '(', 'addr', ',', 'port', ')'] | Returns `(ip_address, port)` from string `ip_addr_port` | ['Returns', '(', 'ip_address', 'port', ')', 'from', 'string', 'ip_addr_port'] | train | https://github.com/talkincode/toughlib/blob/1c2f7dde3a7f101248f1b5f5d428cc85466995cf/toughlib/btforms/net.py#L54-L76 |
1,373 | ARMmbed/mbed-cloud-sdk-python | src/mbed_cloud/update/update.py | UpdateAPI.get_firmware_manifest | def get_firmware_manifest(self, manifest_id):
"""Get manifest with provided manifest_id.
:param str manifest_id: ID of manifest to retrieve (Required)
:return: FirmwareManifest
"""
api = self._get_api(update_service.DefaultApi)
return FirmwareManifest(api.firmware_manifest_retrieve(manifest_id=manifest_id)) | python | def get_firmware_manifest(self, manifest_id):
"""Get manifest with provided manifest_id.
:param str manifest_id: ID of manifest to retrieve (Required)
:return: FirmwareManifest
"""
api = self._get_api(update_service.DefaultApi)
return FirmwareManifest(api.firmware_manifest_retrieve(manifest_id=manifest_id)) | ['def', 'get_firmware_manifest', '(', 'self', ',', 'manifest_id', ')', ':', 'api', '=', 'self', '.', '_get_api', '(', 'update_service', '.', 'DefaultApi', ')', 'return', 'FirmwareManifest', '(', 'api', '.', 'firmware_manifest_retrieve', '(', 'manifest_id', '=', 'manifest_id', ')', ')'] | Get manifest with provided manifest_id.
:param str manifest_id: ID of manifest to retrieve (Required)
:return: FirmwareManifest | ['Get', 'manifest', 'with', 'provided', 'manifest_id', '.'] | train | https://github.com/ARMmbed/mbed-cloud-sdk-python/blob/c0af86fb2cdd4dc7ed26f236139241067d293509/src/mbed_cloud/update/update.py#L248-L255 |
1,374 | locationlabs/mockredis | mockredis/script.py | Script._python_to_lua | def _python_to_lua(pval):
"""
Convert Python object(s) into Lua object(s), as at times Python object(s)
are not compatible with Lua functions
"""
import lua
if pval is None:
# Python None --> Lua None
return lua.eval("")
if isinstance(pval, (list, tuple, set)):
# Python list --> Lua table
# e.g.: in lrange
# in Python returns: [v1, v2, v3]
# in Lua returns: {v1, v2, v3}
lua_list = lua.eval("{}")
lua_table = lua.eval("table")
for item in pval:
lua_table.insert(lua_list, Script._python_to_lua(item))
return lua_list
elif isinstance(pval, dict):
# Python dict --> Lua dict
# e.g.: in hgetall
# in Python returns: {k1:v1, k2:v2, k3:v3}
# in Lua returns: {k1, v1, k2, v2, k3, v3}
lua_dict = lua.eval("{}")
lua_table = lua.eval("table")
for k, v in pval.iteritems():
lua_table.insert(lua_dict, Script._python_to_lua(k))
lua_table.insert(lua_dict, Script._python_to_lua(v))
return lua_dict
elif isinstance(pval, str):
# Python string --> Lua userdata
return pval
elif isinstance(pval, bool):
# Python bool--> Lua boolean
return lua.eval(str(pval).lower())
elif isinstance(pval, (int, long, float)):
# Python int --> Lua number
lua_globals = lua.globals()
return lua_globals.tonumber(str(pval))
raise RuntimeError("Invalid Python type: " + str(type(pval))) | python | def _python_to_lua(pval):
"""
Convert Python object(s) into Lua object(s), as at times Python object(s)
are not compatible with Lua functions
"""
import lua
if pval is None:
# Python None --> Lua None
return lua.eval("")
if isinstance(pval, (list, tuple, set)):
# Python list --> Lua table
# e.g.: in lrange
# in Python returns: [v1, v2, v3]
# in Lua returns: {v1, v2, v3}
lua_list = lua.eval("{}")
lua_table = lua.eval("table")
for item in pval:
lua_table.insert(lua_list, Script._python_to_lua(item))
return lua_list
elif isinstance(pval, dict):
# Python dict --> Lua dict
# e.g.: in hgetall
# in Python returns: {k1:v1, k2:v2, k3:v3}
# in Lua returns: {k1, v1, k2, v2, k3, v3}
lua_dict = lua.eval("{}")
lua_table = lua.eval("table")
for k, v in pval.iteritems():
lua_table.insert(lua_dict, Script._python_to_lua(k))
lua_table.insert(lua_dict, Script._python_to_lua(v))
return lua_dict
elif isinstance(pval, str):
# Python string --> Lua userdata
return pval
elif isinstance(pval, bool):
# Python bool--> Lua boolean
return lua.eval(str(pval).lower())
elif isinstance(pval, (int, long, float)):
# Python int --> Lua number
lua_globals = lua.globals()
return lua_globals.tonumber(str(pval))
raise RuntimeError("Invalid Python type: " + str(type(pval))) | ['def', '_python_to_lua', '(', 'pval', ')', ':', 'import', 'lua', 'if', 'pval', 'is', 'None', ':', '# Python None --> Lua None', 'return', 'lua', '.', 'eval', '(', '""', ')', 'if', 'isinstance', '(', 'pval', ',', '(', 'list', ',', 'tuple', ',', 'set', ')', ')', ':', '# Python list --> Lua table', '# e.g.: in lrange', '# in Python returns: [v1, v2, v3]', '# in Lua returns: {v1, v2, v3}', 'lua_list', '=', 'lua', '.', 'eval', '(', '"{}"', ')', 'lua_table', '=', 'lua', '.', 'eval', '(', '"table"', ')', 'for', 'item', 'in', 'pval', ':', 'lua_table', '.', 'insert', '(', 'lua_list', ',', 'Script', '.', '_python_to_lua', '(', 'item', ')', ')', 'return', 'lua_list', 'elif', 'isinstance', '(', 'pval', ',', 'dict', ')', ':', '# Python dict --> Lua dict', '# e.g.: in hgetall', '# in Python returns: {k1:v1, k2:v2, k3:v3}', '# in Lua returns: {k1, v1, k2, v2, k3, v3}', 'lua_dict', '=', 'lua', '.', 'eval', '(', '"{}"', ')', 'lua_table', '=', 'lua', '.', 'eval', '(', '"table"', ')', 'for', 'k', ',', 'v', 'in', 'pval', '.', 'iteritems', '(', ')', ':', 'lua_table', '.', 'insert', '(', 'lua_dict', ',', 'Script', '.', '_python_to_lua', '(', 'k', ')', ')', 'lua_table', '.', 'insert', '(', 'lua_dict', ',', 'Script', '.', '_python_to_lua', '(', 'v', ')', ')', 'return', 'lua_dict', 'elif', 'isinstance', '(', 'pval', ',', 'str', ')', ':', '# Python string --> Lua userdata', 'return', 'pval', 'elif', 'isinstance', '(', 'pval', ',', 'bool', ')', ':', '# Python bool--> Lua boolean', 'return', 'lua', '.', 'eval', '(', 'str', '(', 'pval', ')', '.', 'lower', '(', ')', ')', 'elif', 'isinstance', '(', 'pval', ',', '(', 'int', ',', 'long', ',', 'float', ')', ')', ':', '# Python int --> Lua number', 'lua_globals', '=', 'lua', '.', 'globals', '(', ')', 'return', 'lua_globals', '.', 'tonumber', '(', 'str', '(', 'pval', ')', ')', 'raise', 'RuntimeError', '(', '"Invalid Python type: "', '+', 'str', '(', 'type', '(', 'pval', ')', ')', ')'] | Convert Python object(s) into Lua object(s), as at times Python object(s)
are not compatible with Lua functions | ['Convert', 'Python', 'object', '(', 's', ')', 'into', 'Lua', 'object', '(', 's', ')', 'as', 'at', 'times', 'Python', 'object', '(', 's', ')', 'are', 'not', 'compatible', 'with', 'Lua', 'functions'] | train | https://github.com/locationlabs/mockredis/blob/fd4e3117066ff0c24e86ebca007853a8092e3254/mockredis/script.py#L138-L179 |
1,375 | secdev/scapy | scapy/modules/krack/automaton.py | KrackAP.build_GTK_KDE | def build_GTK_KDE(self):
"""Build the Key Data Encapsulation for GTK
KeyID: 0
Ref: 802.11i p81
"""
return b''.join([
b'\xdd', # Type KDE
chb(len(self.gtk_full) + 6),
b'\x00\x0f\xac', # OUI
b'\x01', # GTK KDE
b'\x00\x00', # KeyID - Tx - Reserved x2
self.gtk_full,
]) | python | def build_GTK_KDE(self):
"""Build the Key Data Encapsulation for GTK
KeyID: 0
Ref: 802.11i p81
"""
return b''.join([
b'\xdd', # Type KDE
chb(len(self.gtk_full) + 6),
b'\x00\x0f\xac', # OUI
b'\x01', # GTK KDE
b'\x00\x00', # KeyID - Tx - Reserved x2
self.gtk_full,
]) | ['def', 'build_GTK_KDE', '(', 'self', ')', ':', 'return', "b''", '.', 'join', '(', '[', "b'\\xdd'", ',', '# Type KDE', 'chb', '(', 'len', '(', 'self', '.', 'gtk_full', ')', '+', '6', ')', ',', "b'\\x00\\x0f\\xac'", ',', '# OUI', "b'\\x01'", ',', '# GTK KDE', "b'\\x00\\x00'", ',', '# KeyID - Tx - Reserved x2', 'self', '.', 'gtk_full', ',', ']', ')'] | Build the Key Data Encapsulation for GTK
KeyID: 0
Ref: 802.11i p81 | ['Build', 'the', 'Key', 'Data', 'Encapsulation', 'for', 'GTK', 'KeyID', ':', '0', 'Ref', ':', '802', '.', '11i', 'p81'] | train | https://github.com/secdev/scapy/blob/3ffe757c184017dd46464593a8f80f85abc1e79a/scapy/modules/krack/automaton.py#L301-L313 |
1,376 | hsolbrig/PyShEx | pyshex/shape_expressions_language/p5_context.py | Context._visit_shape_te | def _visit_shape_te(self, te: ShExJ.tripleExpr, visit_center: _VisitorCenter) -> None:
"""
Visit a triple expression that was reached through a shape. This, in turn, is used to visit additional shapes
that are referenced by a TripleConstraint
:param te: Triple expression reached through a Shape.expression
:param visit_center: context used in shape visitor
"""
if isinstance(te, ShExJ.TripleConstraint) and te.valueExpr is not None:
visit_center.f(visit_center.arg_cntxt, te.valueExpr, self) | python | def _visit_shape_te(self, te: ShExJ.tripleExpr, visit_center: _VisitorCenter) -> None:
"""
Visit a triple expression that was reached through a shape. This, in turn, is used to visit additional shapes
that are referenced by a TripleConstraint
:param te: Triple expression reached through a Shape.expression
:param visit_center: context used in shape visitor
"""
if isinstance(te, ShExJ.TripleConstraint) and te.valueExpr is not None:
visit_center.f(visit_center.arg_cntxt, te.valueExpr, self) | ['def', '_visit_shape_te', '(', 'self', ',', 'te', ':', 'ShExJ', '.', 'tripleExpr', ',', 'visit_center', ':', '_VisitorCenter', ')', '->', 'None', ':', 'if', 'isinstance', '(', 'te', ',', 'ShExJ', '.', 'TripleConstraint', ')', 'and', 'te', '.', 'valueExpr', 'is', 'not', 'None', ':', 'visit_center', '.', 'f', '(', 'visit_center', '.', 'arg_cntxt', ',', 'te', '.', 'valueExpr', ',', 'self', ')'] | Visit a triple expression that was reached through a shape. This, in turn, is used to visit additional shapes
that are referenced by a TripleConstraint
:param te: Triple expression reached through a Shape.expression
:param visit_center: context used in shape visitor | ['Visit', 'a', 'triple', 'expression', 'that', 'was', 'reached', 'through', 'a', 'shape', '.', 'This', 'in', 'turn', 'is', 'used', 'to', 'visit', 'additional', 'shapes', 'that', 'are', 'referenced', 'by', 'a', 'TripleConstraint', ':', 'param', 'te', ':', 'Triple', 'expression', 'reached', 'through', 'a', 'Shape', '.', 'expression', ':', 'param', 'visit_center', ':', 'context', 'used', 'in', 'shape', 'visitor'] | train | https://github.com/hsolbrig/PyShEx/blob/9d659cc36e808afd66d4a6d60e8ea21cb12eb744/pyshex/shape_expressions_language/p5_context.py#L335-L343 |
1,377 | merll/docker-map | dockermap/build/context.py | get_exclusions | def get_exclusions(path):
"""
Generates exclusion patterns from a ``.dockerignore`` file located in the given path. Returns ``None`` if the
file does not exist.
:param path: Path to look up the ``.dockerignore`` in.
:type path: unicode | str
:return: List of patterns, that can be passed into :func:`get_filter_func`.
:rtype: list[(__RegEx, bool)]
"""
if not os.path.isdir(path):
return None
dockerignore_file = os.path.join(path, '.dockerignore')
if not os.path.isfile(dockerignore_file):
return None
with open(dockerignore_file, 'rb') as dif:
return list(preprocess_matches(dif.readlines())) | python | def get_exclusions(path):
"""
Generates exclusion patterns from a ``.dockerignore`` file located in the given path. Returns ``None`` if the
file does not exist.
:param path: Path to look up the ``.dockerignore`` in.
:type path: unicode | str
:return: List of patterns, that can be passed into :func:`get_filter_func`.
:rtype: list[(__RegEx, bool)]
"""
if not os.path.isdir(path):
return None
dockerignore_file = os.path.join(path, '.dockerignore')
if not os.path.isfile(dockerignore_file):
return None
with open(dockerignore_file, 'rb') as dif:
return list(preprocess_matches(dif.readlines())) | ['def', 'get_exclusions', '(', 'path', ')', ':', 'if', 'not', 'os', '.', 'path', '.', 'isdir', '(', 'path', ')', ':', 'return', 'None', 'dockerignore_file', '=', 'os', '.', 'path', '.', 'join', '(', 'path', ',', "'.dockerignore'", ')', 'if', 'not', 'os', '.', 'path', '.', 'isfile', '(', 'dockerignore_file', ')', ':', 'return', 'None', 'with', 'open', '(', 'dockerignore_file', ',', "'rb'", ')', 'as', 'dif', ':', 'return', 'list', '(', 'preprocess_matches', '(', 'dif', '.', 'readlines', '(', ')', ')', ')'] | Generates exclusion patterns from a ``.dockerignore`` file located in the given path. Returns ``None`` if the
file does not exist.
:param path: Path to look up the ``.dockerignore`` in.
:type path: unicode | str
:return: List of patterns, that can be passed into :func:`get_filter_func`.
:rtype: list[(__RegEx, bool)] | ['Generates', 'exclusion', 'patterns', 'from', 'a', '.', 'dockerignore', 'file', 'located', 'in', 'the', 'given', 'path', '.', 'Returns', 'None', 'if', 'the', 'file', 'does', 'not', 'exist', '.'] | train | https://github.com/merll/docker-map/blob/e14fe86a6ff5c33d121eb2f9157e9359cb80dd02/dockermap/build/context.py#L45-L61 |
1,378 | productml/blurr | blurr/core/field_complex.py | Map.set | def set(self, key: Any, value: Any) -> None:
""" Sets the value of a key to a supplied value """
if key is not None:
self[key] = value | python | def set(self, key: Any, value: Any) -> None:
""" Sets the value of a key to a supplied value """
if key is not None:
self[key] = value | ['def', 'set', '(', 'self', ',', 'key', ':', 'Any', ',', 'value', ':', 'Any', ')', '->', 'None', ':', 'if', 'key', 'is', 'not', 'None', ':', 'self', '[', 'key', ']', '=', 'value'] | Sets the value of a key to a supplied value | ['Sets', 'the', 'value', 'of', 'a', 'key', 'to', 'a', 'supplied', 'value'] | train | https://github.com/productml/blurr/blob/1b688b2c4a9bbbb2139c58bf0682ddc05a6c24fa/blurr/core/field_complex.py#L11-L14 |
1,379 | Robpol86/terminaltables | terminaltables/base_table.py | BaseTable.gen_row_lines | def gen_row_lines(self, row, style, inner_widths, height):
r"""Combine cells in row and group them into lines with vertical borders.
Caller is expected to pass yielded lines to ''.join() to combine them into a printable line. Caller must append
newline character to the end of joined line.
In:
['Row One Column One', 'Two', 'Three']
Out:
[
('|', ' Row One Column One ', '|', ' Two ', '|', ' Three ', '|'),
]
In:
['Row One\nColumn One', 'Two', 'Three'],
Out:
[
('|', ' Row One ', '|', ' Two ', '|', ' Three ', '|'),
('|', ' Column One ', '|', ' ', '|', ' ', '|'),
]
:param iter row: One row in the table. List of cells.
:param str style: Type of border characters to use.
:param iter inner_widths: List of widths (no padding) for each column.
:param int height: Inner height (no padding) (number of lines) to expand row to.
:return: Yields lines split into components in a list. Caller must ''.join() line.
"""
cells_in_row = list()
# Resize row if it doesn't have enough cells.
if len(row) != len(inner_widths):
row = row + [''] * (len(inner_widths) - len(row))
# Pad and align each cell. Split each cell into lines to support multi-line cells.
for i, cell in enumerate(row):
align = (self.justify_columns.get(i),)
inner_dimensions = (inner_widths[i], height)
padding = (self.padding_left, self.padding_right, 0, 0)
cells_in_row.append(align_and_pad_cell(cell, align, inner_dimensions, padding))
# Determine border characters.
if style == 'heading':
left = self.CHAR_H_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_H_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_H_OUTER_RIGHT_VERTICAL if self.outer_border else ''
elif style == 'footing':
left = self.CHAR_F_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_F_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_F_OUTER_RIGHT_VERTICAL if self.outer_border else ''
else:
left = self.CHAR_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_OUTER_RIGHT_VERTICAL if self.outer_border else ''
# Yield each line.
for line in build_row(cells_in_row, left, center, right):
yield line | python | def gen_row_lines(self, row, style, inner_widths, height):
r"""Combine cells in row and group them into lines with vertical borders.
Caller is expected to pass yielded lines to ''.join() to combine them into a printable line. Caller must append
newline character to the end of joined line.
In:
['Row One Column One', 'Two', 'Three']
Out:
[
('|', ' Row One Column One ', '|', ' Two ', '|', ' Three ', '|'),
]
In:
['Row One\nColumn One', 'Two', 'Three'],
Out:
[
('|', ' Row One ', '|', ' Two ', '|', ' Three ', '|'),
('|', ' Column One ', '|', ' ', '|', ' ', '|'),
]
:param iter row: One row in the table. List of cells.
:param str style: Type of border characters to use.
:param iter inner_widths: List of widths (no padding) for each column.
:param int height: Inner height (no padding) (number of lines) to expand row to.
:return: Yields lines split into components in a list. Caller must ''.join() line.
"""
cells_in_row = list()
# Resize row if it doesn't have enough cells.
if len(row) != len(inner_widths):
row = row + [''] * (len(inner_widths) - len(row))
# Pad and align each cell. Split each cell into lines to support multi-line cells.
for i, cell in enumerate(row):
align = (self.justify_columns.get(i),)
inner_dimensions = (inner_widths[i], height)
padding = (self.padding_left, self.padding_right, 0, 0)
cells_in_row.append(align_and_pad_cell(cell, align, inner_dimensions, padding))
# Determine border characters.
if style == 'heading':
left = self.CHAR_H_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_H_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_H_OUTER_RIGHT_VERTICAL if self.outer_border else ''
elif style == 'footing':
left = self.CHAR_F_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_F_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_F_OUTER_RIGHT_VERTICAL if self.outer_border else ''
else:
left = self.CHAR_OUTER_LEFT_VERTICAL if self.outer_border else ''
center = self.CHAR_INNER_VERTICAL if self.inner_column_border else ''
right = self.CHAR_OUTER_RIGHT_VERTICAL if self.outer_border else ''
# Yield each line.
for line in build_row(cells_in_row, left, center, right):
yield line | ['def', 'gen_row_lines', '(', 'self', ',', 'row', ',', 'style', ',', 'inner_widths', ',', 'height', ')', ':', 'cells_in_row', '=', 'list', '(', ')', "# Resize row if it doesn't have enough cells.", 'if', 'len', '(', 'row', ')', '!=', 'len', '(', 'inner_widths', ')', ':', 'row', '=', 'row', '+', '[', "''", ']', '*', '(', 'len', '(', 'inner_widths', ')', '-', 'len', '(', 'row', ')', ')', '# Pad and align each cell. Split each cell into lines to support multi-line cells.', 'for', 'i', ',', 'cell', 'in', 'enumerate', '(', 'row', ')', ':', 'align', '=', '(', 'self', '.', 'justify_columns', '.', 'get', '(', 'i', ')', ',', ')', 'inner_dimensions', '=', '(', 'inner_widths', '[', 'i', ']', ',', 'height', ')', 'padding', '=', '(', 'self', '.', 'padding_left', ',', 'self', '.', 'padding_right', ',', '0', ',', '0', ')', 'cells_in_row', '.', 'append', '(', 'align_and_pad_cell', '(', 'cell', ',', 'align', ',', 'inner_dimensions', ',', 'padding', ')', ')', '# Determine border characters.', 'if', 'style', '==', "'heading'", ':', 'left', '=', 'self', '.', 'CHAR_H_OUTER_LEFT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", 'center', '=', 'self', '.', 'CHAR_H_INNER_VERTICAL', 'if', 'self', '.', 'inner_column_border', 'else', "''", 'right', '=', 'self', '.', 'CHAR_H_OUTER_RIGHT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", 'elif', 'style', '==', "'footing'", ':', 'left', '=', 'self', '.', 'CHAR_F_OUTER_LEFT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", 'center', '=', 'self', '.', 'CHAR_F_INNER_VERTICAL', 'if', 'self', '.', 'inner_column_border', 'else', "''", 'right', '=', 'self', '.', 'CHAR_F_OUTER_RIGHT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", 'else', ':', 'left', '=', 'self', '.', 'CHAR_OUTER_LEFT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", 'center', '=', 'self', '.', 'CHAR_INNER_VERTICAL', 'if', 'self', '.', 'inner_column_border', 'else', "''", 'right', '=', 'self', '.', 'CHAR_OUTER_RIGHT_VERTICAL', 'if', 'self', '.', 'outer_border', 'else', "''", '# Yield each line.', 'for', 'line', 'in', 'build_row', '(', 'cells_in_row', ',', 'left', ',', 'center', ',', 'right', ')', ':', 'yield', 'line'] | r"""Combine cells in row and group them into lines with vertical borders.
Caller is expected to pass yielded lines to ''.join() to combine them into a printable line. Caller must append
newline character to the end of joined line.
In:
['Row One Column One', 'Two', 'Three']
Out:
[
('|', ' Row One Column One ', '|', ' Two ', '|', ' Three ', '|'),
]
In:
['Row One\nColumn One', 'Two', 'Three'],
Out:
[
('|', ' Row One ', '|', ' Two ', '|', ' Three ', '|'),
('|', ' Column One ', '|', ' ', '|', ' ', '|'),
]
:param iter row: One row in the table. List of cells.
:param str style: Type of border characters to use.
:param iter inner_widths: List of widths (no padding) for each column.
:param int height: Inner height (no padding) (number of lines) to expand row to.
:return: Yields lines split into components in a list. Caller must ''.join() line. | ['r', 'Combine', 'cells', 'in', 'row', 'and', 'group', 'them', 'into', 'lines', 'with', 'vertical', 'borders', '.'] | train | https://github.com/Robpol86/terminaltables/blob/ad8f46e50afdbaea377fc1f713bc0e7a31c4fccc/terminaltables/base_table.py#L112-L169 |
1,380 | pypa/pipenv | pipenv/vendor/distlib/locators.py | SimpleScrapingLocator._process_download | def _process_download(self, url):
"""
See if an URL is a suitable download for a project.
If it is, register information in the result dictionary (for
_get_project) about the specific version it's for.
Note that the return value isn't actually used other than as a boolean
value.
"""
if self.platform_check and self._is_platform_dependent(url):
info = None
else:
info = self.convert_url_to_download_info(url, self.project_name)
logger.debug('process_download: %s -> %s', url, info)
if info:
with self._lock: # needed because self.result is shared
self._update_version_data(self.result, info)
return info | python | def _process_download(self, url):
"""
See if an URL is a suitable download for a project.
If it is, register information in the result dictionary (for
_get_project) about the specific version it's for.
Note that the return value isn't actually used other than as a boolean
value.
"""
if self.platform_check and self._is_platform_dependent(url):
info = None
else:
info = self.convert_url_to_download_info(url, self.project_name)
logger.debug('process_download: %s -> %s', url, info)
if info:
with self._lock: # needed because self.result is shared
self._update_version_data(self.result, info)
return info | ['def', '_process_download', '(', 'self', ',', 'url', ')', ':', 'if', 'self', '.', 'platform_check', 'and', 'self', '.', '_is_platform_dependent', '(', 'url', ')', ':', 'info', '=', 'None', 'else', ':', 'info', '=', 'self', '.', 'convert_url_to_download_info', '(', 'url', ',', 'self', '.', 'project_name', ')', 'logger', '.', 'debug', '(', "'process_download: %s -> %s'", ',', 'url', ',', 'info', ')', 'if', 'info', ':', 'with', 'self', '.', '_lock', ':', '# needed because self.result is shared', 'self', '.', '_update_version_data', '(', 'self', '.', 'result', ',', 'info', ')', 'return', 'info'] | See if an URL is a suitable download for a project.
If it is, register information in the result dictionary (for
_get_project) about the specific version it's for.
Note that the return value isn't actually used other than as a boolean
value. | ['See', 'if', 'an', 'URL', 'is', 'a', 'suitable', 'download', 'for', 'a', 'project', '.'] | train | https://github.com/pypa/pipenv/blob/cae8d76c210b9777e90aab76e9c4b0e53bb19cde/pipenv/vendor/distlib/locators.py#L673-L691 |
1,381 | ansible/ansible-container | container/openshift/deploy.py | Deploy.get_route_templates | def get_route_templates(self):
"""
Generate Openshift route templates or playbook tasks. Each port on a service definition found in container.yml
represents an externally exposed port.
"""
def _get_published_ports(service_config):
result = []
for port in service_config.get('ports', []):
protocol = 'TCP'
if isinstance(port, string_types) and '/' in port:
port, protocol = port.split('/')
if isinstance(port, string_types) and ':' in port:
host, container = port.split(':')
else:
host = port
result.append({'port': host, 'protocol': protocol.lower()})
return result
templates = []
for name, service_config in self._services.items():
state = service_config.get(self.CONFIG_KEY, {}).get('state', 'present')
force = service_config.get(self.CONFIG_KEY, {}).get('force', False)
published_ports = _get_published_ports(service_config)
if state != 'present':
continue
for port in published_ports:
route_name = "%s-%s" % (name, port['port'])
labels = dict(
app=self._namespace_name,
service=name
)
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = 'Route'
template['force'] = force
template['metadata'] = CommentedMap([
('name', route_name),
('namespace', self._namespace_name),
('labels', labels.copy())
])
template['spec'] = CommentedMap([
('to', CommentedMap([
('kind', 'Service'),
('name', name)
])),
('port', CommentedMap([
('targetPort', 'port-{}-{}'.format(port['port'], port['protocol']))
]))
])
if service_config.get(self.CONFIG_KEY, {}).get('routes'):
for route in service_config[self.CONFIG_KEY]['routes']:
if str(route.get('port')) == str(port['port']):
for key, value in route.items():
if key not in ('force', 'port'):
self.copy_attribute(template['spec'], key, value)
templates.append(template)
return templates | python | def get_route_templates(self):
"""
Generate Openshift route templates or playbook tasks. Each port on a service definition found in container.yml
represents an externally exposed port.
"""
def _get_published_ports(service_config):
result = []
for port in service_config.get('ports', []):
protocol = 'TCP'
if isinstance(port, string_types) and '/' in port:
port, protocol = port.split('/')
if isinstance(port, string_types) and ':' in port:
host, container = port.split(':')
else:
host = port
result.append({'port': host, 'protocol': protocol.lower()})
return result
templates = []
for name, service_config in self._services.items():
state = service_config.get(self.CONFIG_KEY, {}).get('state', 'present')
force = service_config.get(self.CONFIG_KEY, {}).get('force', False)
published_ports = _get_published_ports(service_config)
if state != 'present':
continue
for port in published_ports:
route_name = "%s-%s" % (name, port['port'])
labels = dict(
app=self._namespace_name,
service=name
)
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = 'Route'
template['force'] = force
template['metadata'] = CommentedMap([
('name', route_name),
('namespace', self._namespace_name),
('labels', labels.copy())
])
template['spec'] = CommentedMap([
('to', CommentedMap([
('kind', 'Service'),
('name', name)
])),
('port', CommentedMap([
('targetPort', 'port-{}-{}'.format(port['port'], port['protocol']))
]))
])
if service_config.get(self.CONFIG_KEY, {}).get('routes'):
for route in service_config[self.CONFIG_KEY]['routes']:
if str(route.get('port')) == str(port['port']):
for key, value in route.items():
if key not in ('force', 'port'):
self.copy_attribute(template['spec'], key, value)
templates.append(template)
return templates | ['def', 'get_route_templates', '(', 'self', ')', ':', 'def', '_get_published_ports', '(', 'service_config', ')', ':', 'result', '=', '[', ']', 'for', 'port', 'in', 'service_config', '.', 'get', '(', "'ports'", ',', '[', ']', ')', ':', 'protocol', '=', "'TCP'", 'if', 'isinstance', '(', 'port', ',', 'string_types', ')', 'and', "'/'", 'in', 'port', ':', 'port', ',', 'protocol', '=', 'port', '.', 'split', '(', "'/'", ')', 'if', 'isinstance', '(', 'port', ',', 'string_types', ')', 'and', "':'", 'in', 'port', ':', 'host', ',', 'container', '=', 'port', '.', 'split', '(', "':'", ')', 'else', ':', 'host', '=', 'port', 'result', '.', 'append', '(', '{', "'port'", ':', 'host', ',', "'protocol'", ':', 'protocol', '.', 'lower', '(', ')', '}', ')', 'return', 'result', 'templates', '=', '[', ']', 'for', 'name', ',', 'service_config', 'in', 'self', '.', '_services', '.', 'items', '(', ')', ':', 'state', '=', 'service_config', '.', 'get', '(', 'self', '.', 'CONFIG_KEY', ',', '{', '}', ')', '.', 'get', '(', "'state'", ',', "'present'", ')', 'force', '=', 'service_config', '.', 'get', '(', 'self', '.', 'CONFIG_KEY', ',', '{', '}', ')', '.', 'get', '(', "'force'", ',', 'False', ')', 'published_ports', '=', '_get_published_ports', '(', 'service_config', ')', 'if', 'state', '!=', "'present'", ':', 'continue', 'for', 'port', 'in', 'published_ports', ':', 'route_name', '=', '"%s-%s"', '%', '(', 'name', ',', 'port', '[', "'port'", ']', ')', 'labels', '=', 'dict', '(', 'app', '=', 'self', '.', '_namespace_name', ',', 'service', '=', 'name', ')', 'template', '=', 'CommentedMap', '(', ')', 'template', '[', "'apiVersion'", ']', '=', 'self', '.', 'DEFAULT_API_VERSION', 'template', '[', "'kind'", ']', '=', "'Route'", 'template', '[', "'force'", ']', '=', 'force', 'template', '[', "'metadata'", ']', '=', 'CommentedMap', '(', '[', '(', "'name'", ',', 'route_name', ')', ',', '(', "'namespace'", ',', 'self', '.', '_namespace_name', ')', ',', '(', "'labels'", ',', 'labels', '.', 'copy', '(', ')', ')', ']', ')', 'template', '[', "'spec'", ']', '=', 'CommentedMap', '(', '[', '(', "'to'", ',', 'CommentedMap', '(', '[', '(', "'kind'", ',', "'Service'", ')', ',', '(', "'name'", ',', 'name', ')', ']', ')', ')', ',', '(', "'port'", ',', 'CommentedMap', '(', '[', '(', "'targetPort'", ',', "'port-{}-{}'", '.', 'format', '(', 'port', '[', "'port'", ']', ',', 'port', '[', "'protocol'", ']', ')', ')', ']', ')', ')', ']', ')', 'if', 'service_config', '.', 'get', '(', 'self', '.', 'CONFIG_KEY', ',', '{', '}', ')', '.', 'get', '(', "'routes'", ')', ':', 'for', 'route', 'in', 'service_config', '[', 'self', '.', 'CONFIG_KEY', ']', '[', "'routes'", ']', ':', 'if', 'str', '(', 'route', '.', 'get', '(', "'port'", ')', ')', '==', 'str', '(', 'port', '[', "'port'", ']', ')', ':', 'for', 'key', ',', 'value', 'in', 'route', '.', 'items', '(', ')', ':', 'if', 'key', 'not', 'in', '(', "'force'", ',', "'port'", ')', ':', 'self', '.', 'copy_attribute', '(', 'template', '[', "'spec'", ']', ',', 'key', ',', 'value', ')', 'templates', '.', 'append', '(', 'template', ')', 'return', 'templates'] | Generate Openshift route templates or playbook tasks. Each port on a service definition found in container.yml
represents an externally exposed port. | ['Generate', 'Openshift', 'route', 'templates', 'or', 'playbook', 'tasks', '.', 'Each', 'port', 'on', 'a', 'service', 'definition', 'found', 'in', 'container', '.', 'yml', 'represents', 'an', 'externally', 'exposed', 'port', '.'] | train | https://github.com/ansible/ansible-container/blob/d031c1a6133d5482a5d054fcbdbecafb923f8b4b/container/openshift/deploy.py#L56-L117 |
1,382 | studionow/pybrightcove | pybrightcove/video.py | Video.add_custom_metadata | def add_custom_metadata(self, key, value, meta_type=None):
"""
Add custom metadata to the Video. meta_type is required for XML API.
"""
self.metadata.append({'key': key, 'value': value, 'type': meta_type}) | python | def add_custom_metadata(self, key, value, meta_type=None):
"""
Add custom metadata to the Video. meta_type is required for XML API.
"""
self.metadata.append({'key': key, 'value': value, 'type': meta_type}) | ['def', 'add_custom_metadata', '(', 'self', ',', 'key', ',', 'value', ',', 'meta_type', '=', 'None', ')', ':', 'self', '.', 'metadata', '.', 'append', '(', '{', "'key'", ':', 'key', ',', "'value'", ':', 'value', ',', "'type'", ':', 'meta_type', '}', ')'] | Add custom metadata to the Video. meta_type is required for XML API. | ['Add', 'custom', 'metadata', 'to', 'the', 'Video', '.', 'meta_type', 'is', 'required', 'for', 'XML', 'API', '.'] | train | https://github.com/studionow/pybrightcove/blob/19c946b689a80156e070fe9bc35589c4b768e614/pybrightcove/video.py#L487-L491 |
1,383 | shidenggui/easytrader | easytrader/yh_clienttrader.py | YHClientTrader.login | def login(self, user, password, exe_path, comm_password=None, **kwargs):
"""
登陆客户端
:param user: 账号
:param password: 明文密码
:param exe_path: 客户端路径类似 'C:\\中国银河证券双子星3.2\\Binarystar.exe',
默认 'C:\\中国银河证券双子星3.2\\Binarystar.exe'
:param comm_password: 通讯密码, 华泰需要，可不设
:return:
"""
try:
self._app = pywinauto.Application().connect(
path=self._run_exe_path(exe_path), timeout=1
)
# pylint: disable=broad-except
except Exception:
self._app = pywinauto.Application().start(exe_path)
is_xiadan = True if "xiadan.exe" in exe_path else False
# wait login window ready
while True:
try:
self._app.top_window().Edit1.wait("ready")
break
except RuntimeError:
pass
self._app.top_window().Edit1.type_keys(user)
self._app.top_window().Edit2.type_keys(password)
while True:
self._app.top_window().Edit3.type_keys(
self._handle_verify_code(is_xiadan)
)
self._app.top_window()["确定" if is_xiadan else "登录"].click()
# detect login is success or not
try:
self._app.top_window().wait_not("exists visible", 10)
break
# pylint: disable=broad-except
except Exception:
if is_xiadan:
self._app.top_window()["确定"].click()
self._app = pywinauto.Application().connect(
path=self._run_exe_path(exe_path), timeout=10
)
self._close_prompt_windows()
self._main = self._app.window(title="网上股票交易系统5.0")
try:
self._main.child_window(
control_id=129, class_name="SysTreeView32"
).wait("ready", 2)
# pylint: disable=broad-except
except Exception:
self.wait(2)
self._switch_window_to_normal_mode() | python | def login(self, user, password, exe_path, comm_password=None, **kwargs):
"""
登陆客户端
:param user: 账号
:param password: 明文密码
:param exe_path: 客户端路径类似 'C:\\中国银河证券双子星3.2\\Binarystar.exe',
默认 'C:\\中国银河证券双子星3.2\\Binarystar.exe'
:param comm_password: 通讯密码, 华泰需要，可不设
:return:
"""
try:
self._app = pywinauto.Application().connect(
path=self._run_exe_path(exe_path), timeout=1
)
# pylint: disable=broad-except
except Exception:
self._app = pywinauto.Application().start(exe_path)
is_xiadan = True if "xiadan.exe" in exe_path else False
# wait login window ready
while True:
try:
self._app.top_window().Edit1.wait("ready")
break
except RuntimeError:
pass
self._app.top_window().Edit1.type_keys(user)
self._app.top_window().Edit2.type_keys(password)
while True:
self._app.top_window().Edit3.type_keys(
self._handle_verify_code(is_xiadan)
)
self._app.top_window()["确定" if is_xiadan else "登录"].click()
# detect login is success or not
try:
self._app.top_window().wait_not("exists visible", 10)
break
# pylint: disable=broad-except
except Exception:
if is_xiadan:
self._app.top_window()["确定"].click()
self._app = pywinauto.Application().connect(
path=self._run_exe_path(exe_path), timeout=10
)
self._close_prompt_windows()
self._main = self._app.window(title="网上股票交易系统5.0")
try:
self._main.child_window(
control_id=129, class_name="SysTreeView32"
).wait("ready", 2)
# pylint: disable=broad-except
except Exception:
self.wait(2)
self._switch_window_to_normal_mode() | ['def', 'login', '(', 'self', ',', 'user', ',', 'password', ',', 'exe_path', ',', 'comm_password', '=', 'None', ',', '*', '*', 'kwargs', ')', ':', 'try', ':', 'self', '.', '_app', '=', 'pywinauto', '.', 'Application', '(', ')', '.', 'connect', '(', 'path', '=', 'self', '.', '_run_exe_path', '(', 'exe_path', ')', ',', 'timeout', '=', '1', ')', '# pylint: disable=broad-except', 'except', 'Exception', ':', 'self', '.', '_app', '=', 'pywinauto', '.', 'Application', '(', ')', '.', 'start', '(', 'exe_path', ')', 'is_xiadan', '=', 'True', 'if', '"xiadan.exe"', 'in', 'exe_path', 'else', 'False', '# wait login window ready', 'while', 'True', ':', 'try', ':', 'self', '.', '_app', '.', 'top_window', '(', ')', '.', 'Edit1', '.', 'wait', '(', '"ready"', ')', 'break', 'except', 'RuntimeError', ':', 'pass', 'self', '.', '_app', '.', 'top_window', '(', ')', '.', 'Edit1', '.', 'type_keys', '(', 'user', ')', 'self', '.', '_app', '.', 'top_window', '(', ')', '.', 'Edit2', '.', 'type_keys', '(', 'password', ')', 'while', 'True', ':', 'self', '.', '_app', '.', 'top_window', '(', ')', '.', 'Edit3', '.', 'type_keys', '(', 'self', '.', '_handle_verify_code', '(', 'is_xiadan', ')', ')', 'self', '.', '_app', '.', 'top_window', '(', ')', '[', '"确定" if ', 's_', 'iadan els', ' "登录', '].click(', ')', '', '', '', '', '# detect login is success or not', 'try', ':', 'self', '.', '_app', '.', 'top_window', '(', ')', '.', 'wait_not', '(', '"exists visible"', ',', '10', ')', 'break', '# pylint: disable=broad-except', 'except', 'Exception', ':', 'if', 'is_xiadan', ':', 'self', '.', '_app', '.', 'top_window', '(', ')', '[', '"确定"].cl', 'i', 'c', 'k()', '', '', 'self', '.', '_app', '=', 'pywinauto', '.', 'Application', '(', ')', '.', 'connect', '(', 'path', '=', 'self', '.', '_run_exe_path', '(', 'exe_path', ')', ',', 'timeout', '=', '10', ')', 'self', '.', '_close_prompt_windows', '(', ')', 'self', '.', '_main', '=', 'self', '.', '_app', '.', 'window', '(', 'title', '=', '"网上股票交易系统5.0")', '', 'try', ':', 'self', '.', '_main', '.', 'child_window', '(', 'control_id', '=', '129', ',', 'class_name', '=', '"SysTreeView32"', ')', '.', 'wait', '(', '"ready"', ',', '2', ')', '# pylint: disable=broad-except', 'except', 'Exception', ':', 'self', '.', 'wait', '(', '2', ')', 'self', '.', '_switch_window_to_normal_mode', '(', ')'] | 登陆客户端
:param user: 账号
:param password: 明文密码
:param exe_path: 客户端路径类似 'C:\\中国银河证券双子星3.2\\Binarystar.exe',
默认 'C:\\中国银河证券双子星3.2\\Binarystar.exe'
:param comm_password: 通讯密码, 华泰需要，可不设
:return: | ['登陆客户端', ':', 'param', 'user', ':', '账号', ':', 'param', 'password', ':', '明文密码', ':', 'param', 'exe_path', ':', '客户端路径类似', 'C', ':', '\\\\', '中国银河证券双子星3', '.', '2', '\\\\', 'Binarystar', '.', 'exe', '默认', 'C', ':', '\\\\', '中国银河证券双子星3', '.', '2', '\\\\', 'Binarystar', '.', 'exe', ':', 'param', 'comm_password', ':', '通讯密码', '华泰需要，可不设', ':', 'return', ':'] | train | https://github.com/shidenggui/easytrader/blob/e5ae4daeda4ea125763a95b280dd694c7f68257d/easytrader/yh_clienttrader.py#L25-L80 |
1,384 | Vito2015/pyextend | pyextend/formula/lbstools.py | calc_distance | def calc_distance(lng1, lat1, lng2, lat2):
"""Calc distance (km) by geo-coordinates.
@:param lng1: first coordinate.lng
@:param lat1: first coordinate.lat
@:param lng2: second coordinate.lng
@:param lat2: second coordinate.lat
@:return distance: km
"""
ra = 6378.140 # 赤道半径 (km)
rb = 6356.755 # 极半径 (km)
flatten = (ra - rb) / ra # 地球扁率
rad_lat_1 = math.radians(lat1)
rad_lng_1 = math.radians(lng1)
rad_lat_2 = math.radians(lat2)
rad_lng_2 = math.radians(lng2)
p1 = math.atan(rb / ra * math.tan(rad_lat_1))
p2 = math.atan(rb / ra * math.tan(rad_lat_2))
xx = math.acos(math.sin(p1) * math.sin(p2) + math.cos(p1) * math.cos(p2) * math.cos(rad_lng_1 - rad_lng_2))
c1 = (math.sin(xx) - xx) * (math.sin(p1) + math.sin(p2)) ** 2 / math.cos(xx / 2) ** 2
c2 = (math.sin(xx) + xx) * (math.sin(p1) - math.sin(p2)) ** 2 / math.sin(xx / 2) ** 2
dr = flatten / 8 * (c1 - c2)
distance = ra * (xx + dr)
return distance | python | def calc_distance(lng1, lat1, lng2, lat2):
"""Calc distance (km) by geo-coordinates.
@:param lng1: first coordinate.lng
@:param lat1: first coordinate.lat
@:param lng2: second coordinate.lng
@:param lat2: second coordinate.lat
@:return distance: km
"""
ra = 6378.140 # 赤道半径 (km)
rb = 6356.755 # 极半径 (km)
flatten = (ra - rb) / ra # 地球扁率
rad_lat_1 = math.radians(lat1)
rad_lng_1 = math.radians(lng1)
rad_lat_2 = math.radians(lat2)
rad_lng_2 = math.radians(lng2)
p1 = math.atan(rb / ra * math.tan(rad_lat_1))
p2 = math.atan(rb / ra * math.tan(rad_lat_2))
xx = math.acos(math.sin(p1) * math.sin(p2) + math.cos(p1) * math.cos(p2) * math.cos(rad_lng_1 - rad_lng_2))
c1 = (math.sin(xx) - xx) * (math.sin(p1) + math.sin(p2)) ** 2 / math.cos(xx / 2) ** 2
c2 = (math.sin(xx) + xx) * (math.sin(p1) - math.sin(p2)) ** 2 / math.sin(xx / 2) ** 2
dr = flatten / 8 * (c1 - c2)
distance = ra * (xx + dr)
return distance | ['def', 'calc_distance', '(', 'lng1', ',', 'lat1', ',', 'lng2', ',', 'lat2', ')', ':', 'ra', '=', '6378.140', '# 赤道半径 (km)', 'rb', '=', '6356.755', '# 极半径 (km)', 'flatten', '=', '(', 'ra', '-', 'rb', ')', '/', 'ra', '# 地球扁率', 'rad_lat_1', '=', 'math', '.', 'radians', '(', 'lat1', ')', 'rad_lng_1', '=', 'math', '.', 'radians', '(', 'lng1', ')', 'rad_lat_2', '=', 'math', '.', 'radians', '(', 'lat2', ')', 'rad_lng_2', '=', 'math', '.', 'radians', '(', 'lng2', ')', 'p1', '=', 'math', '.', 'atan', '(', 'rb', '/', 'ra', '*', 'math', '.', 'tan', '(', 'rad_lat_1', ')', ')', 'p2', '=', 'math', '.', 'atan', '(', 'rb', '/', 'ra', '*', 'math', '.', 'tan', '(', 'rad_lat_2', ')', ')', 'xx', '=', 'math', '.', 'acos', '(', 'math', '.', 'sin', '(', 'p1', ')', '*', 'math', '.', 'sin', '(', 'p2', ')', '+', 'math', '.', 'cos', '(', 'p1', ')', '*', 'math', '.', 'cos', '(', 'p2', ')', '*', 'math', '.', 'cos', '(', 'rad_lng_1', '-', 'rad_lng_2', ')', ')', 'c1', '=', '(', 'math', '.', 'sin', '(', 'xx', ')', '-', 'xx', ')', '*', '(', 'math', '.', 'sin', '(', 'p1', ')', '+', 'math', '.', 'sin', '(', 'p2', ')', ')', '**', '2', '/', 'math', '.', 'cos', '(', 'xx', '/', '2', ')', '**', '2', 'c2', '=', '(', 'math', '.', 'sin', '(', 'xx', ')', '+', 'xx', ')', '*', '(', 'math', '.', 'sin', '(', 'p1', ')', '-', 'math', '.', 'sin', '(', 'p2', ')', ')', '**', '2', '/', 'math', '.', 'sin', '(', 'xx', '/', '2', ')', '**', '2', 'dr', '=', 'flatten', '/', '8', '*', '(', 'c1', '-', 'c2', ')', 'distance', '=', 'ra', '*', '(', 'xx', '+', 'dr', ')', 'return', 'distance'] | Calc distance (km) by geo-coordinates.
@:param lng1: first coordinate.lng
@:param lat1: first coordinate.lat
@:param lng2: second coordinate.lng
@:param lat2: second coordinate.lat
@:return distance: km | ['Calc', 'distance', '(', 'km', ')', 'by', 'geo', '-', 'coordinates', '.'] | train | https://github.com/Vito2015/pyextend/blob/36861dfe1087e437ffe9b5a1da9345c85b4fa4a1/pyextend/formula/lbstools.py#L32-L54 |
1,385 | edoburu/django-any-urlfield | any_urlfield/templatetags/any_urlfield_tags.py | WithDictNode.render | def render(self, context):
"""
Render the tag, with extra context layer.
"""
extra_context = self.context_expr.resolve(context)
if not isinstance(extra_context, dict):
raise TemplateSyntaxError("{% withdict %} expects the argument to be a dictionary.")
with context.push(**extra_context):
return self.nodelist.render(context) | python | def render(self, context):
"""
Render the tag, with extra context layer.
"""
extra_context = self.context_expr.resolve(context)
if not isinstance(extra_context, dict):
raise TemplateSyntaxError("{% withdict %} expects the argument to be a dictionary.")
with context.push(**extra_context):
return self.nodelist.render(context) | ['def', 'render', '(', 'self', ',', 'context', ')', ':', 'extra_context', '=', 'self', '.', 'context_expr', '.', 'resolve', '(', 'context', ')', 'if', 'not', 'isinstance', '(', 'extra_context', ',', 'dict', ')', ':', 'raise', 'TemplateSyntaxError', '(', '"{% withdict %} expects the argument to be a dictionary."', ')', 'with', 'context', '.', 'push', '(', '*', '*', 'extra_context', ')', ':', 'return', 'self', '.', 'nodelist', '.', 'render', '(', 'context', ')'] | Render the tag, with extra context layer. | ['Render', 'the', 'tag', 'with', 'extra', 'context', 'layer', '.'] | train | https://github.com/edoburu/django-any-urlfield/blob/8d7d36c8a1fc251930f6dbdcc8b5b5151d20e3ab/any_urlfield/templatetags/any_urlfield_tags.py#L18-L27 |
1,386 | markovmodel/PyEMMA | pyemma/coordinates/estimation/koopman.py | _compute_u | def _compute_u(K):
"""
Estimate an approximation of the ratio of stationary over empirical distribution from the basis.
Parameters:
-----------
K0, ndarray(M+1, M+1),
time-lagged correlation matrix for the whitened and padded data set.
Returns:
--------
u : ndarray(M,)
coefficients of the ratio stationary / empirical dist. from the whitened and expanded basis.
"""
M = K.shape[0] - 1
# Compute right and left eigenvectors:
l, U = scl.eig(K.T)
l, U = sort_by_norm(l, U)
# Extract the eigenvector for eigenvalue one and normalize:
u = np.real(U[:, 0])
v = np.zeros(M+1)
v[M] = 1.0
u = u / np.dot(u, v)
return u | python | def _compute_u(K):
"""
Estimate an approximation of the ratio of stationary over empirical distribution from the basis.
Parameters:
-----------
K0, ndarray(M+1, M+1),
time-lagged correlation matrix for the whitened and padded data set.
Returns:
--------
u : ndarray(M,)
coefficients of the ratio stationary / empirical dist. from the whitened and expanded basis.
"""
M = K.shape[0] - 1
# Compute right and left eigenvectors:
l, U = scl.eig(K.T)
l, U = sort_by_norm(l, U)
# Extract the eigenvector for eigenvalue one and normalize:
u = np.real(U[:, 0])
v = np.zeros(M+1)
v[M] = 1.0
u = u / np.dot(u, v)
return u | ['def', '_compute_u', '(', 'K', ')', ':', 'M', '=', 'K', '.', 'shape', '[', '0', ']', '-', '1', '# Compute right and left eigenvectors:', 'l', ',', 'U', '=', 'scl', '.', 'eig', '(', 'K', '.', 'T', ')', 'l', ',', 'U', '=', 'sort_by_norm', '(', 'l', ',', 'U', ')', '# Extract the eigenvector for eigenvalue one and normalize:', 'u', '=', 'np', '.', 'real', '(', 'U', '[', ':', ',', '0', ']', ')', 'v', '=', 'np', '.', 'zeros', '(', 'M', '+', '1', ')', 'v', '[', 'M', ']', '=', '1.0', 'u', '=', 'u', '/', 'np', '.', 'dot', '(', 'u', ',', 'v', ')', 'return', 'u'] | Estimate an approximation of the ratio of stationary over empirical distribution from the basis.
Parameters:
-----------
K0, ndarray(M+1, M+1),
time-lagged correlation matrix for the whitened and padded data set.
Returns:
--------
u : ndarray(M,)
coefficients of the ratio stationary / empirical dist. from the whitened and expanded basis. | ['Estimate', 'an', 'approximation', 'of', 'the', 'ratio', 'of', 'stationary', 'over', 'empirical', 'distribution', 'from', 'the', 'basis', '.', 'Parameters', ':', '-----------', 'K0', 'ndarray', '(', 'M', '+', '1', 'M', '+', '1', ')', 'time', '-', 'lagged', 'correlation', 'matrix', 'for', 'the', 'whitened', 'and', 'padded', 'data', 'set', '.', 'Returns', ':', '--------', 'u', ':', 'ndarray', '(', 'M', ')', 'coefficients', 'of', 'the', 'ratio', 'stationary', '/', 'empirical', 'dist', '.', 'from', 'the', 'whitened', 'and', 'expanded', 'basis', '.'] | train | https://github.com/markovmodel/PyEMMA/blob/5c3124398217de05ba5ce9c8fb01519222481ab8/pyemma/coordinates/estimation/koopman.py#L29-L50 |
1,387 | ZELLMECHANIK-DRESDEN/dclab | dclab/isoelastics/__init__.py | Isoelastics.load_data | def load_data(self, path):
"""Load isoelastics from a text file
The text file is loaded with `numpy.loadtxt` and must have
three columns, representing the two data columns and the
elastic modulus with units defined in `definitions.py`.
The file header must have a section defining meta data of the
content like so:
# [...]
#
# - column 1: area_um
# - column 2: deform
# - column 3: emodulus
# - channel width [um]: 20
# - flow rate [ul/s]: 0.04
# - viscosity [mPa*s]: 15
# - method: analytical
#
# [...]
Parameters
----------
path: str
Path to a isoelastics text file
"""
path = pathlib.Path(path).resolve()
# Get metadata
meta = {}
with path.open() as fd:
while True:
line = fd.readline().strip()
if line.startswith("# - "):
line = line.strip("#- ")
var, val = line.split(":")
if val.strip().replace(".", "").isdigit():
# channel width, flow rate, viscosity
val = float(val)
else:
# columns, calculation
val = val.strip().lower()
meta[var.strip()] = val
elif line and not line.startswith("#"):
break
assert meta["column 1"] in dfn.scalar_feature_names
assert meta["column 2"] in dfn.scalar_feature_names
assert meta["column 3"] == "emodulus"
assert meta["method"] in VALID_METHODS
# Load isoelasics
with path.open("rb") as isfd:
isodata = np.loadtxt(isfd)
# Slice out individual isoelastics
emoduli = np.unique(isodata[:, 2])
isoel = []
for emod in emoduli:
where = isodata[:, 2] == emod
isoel.append(isodata[where])
# Add isoelastics to instance
self.add(isoel=isoel,
col1=meta["column 1"],
col2=meta["column 2"],
channel_width=meta["channel width [um]"],
flow_rate=meta["flow rate [ul/s]"],
viscosity=meta["viscosity [mPa*s]"],
method=meta["method"]) | python | def load_data(self, path):
"""Load isoelastics from a text file
The text file is loaded with `numpy.loadtxt` and must have
three columns, representing the two data columns and the
elastic modulus with units defined in `definitions.py`.
The file header must have a section defining meta data of the
content like so:
# [...]
#
# - column 1: area_um
# - column 2: deform
# - column 3: emodulus
# - channel width [um]: 20
# - flow rate [ul/s]: 0.04
# - viscosity [mPa*s]: 15
# - method: analytical
#
# [...]
Parameters
----------
path: str
Path to a isoelastics text file
"""
path = pathlib.Path(path).resolve()
# Get metadata
meta = {}
with path.open() as fd:
while True:
line = fd.readline().strip()
if line.startswith("# - "):
line = line.strip("#- ")
var, val = line.split(":")
if val.strip().replace(".", "").isdigit():
# channel width, flow rate, viscosity
val = float(val)
else:
# columns, calculation
val = val.strip().lower()
meta[var.strip()] = val
elif line and not line.startswith("#"):
break
assert meta["column 1"] in dfn.scalar_feature_names
assert meta["column 2"] in dfn.scalar_feature_names
assert meta["column 3"] == "emodulus"
assert meta["method"] in VALID_METHODS
# Load isoelasics
with path.open("rb") as isfd:
isodata = np.loadtxt(isfd)
# Slice out individual isoelastics
emoduli = np.unique(isodata[:, 2])
isoel = []
for emod in emoduli:
where = isodata[:, 2] == emod
isoel.append(isodata[where])
# Add isoelastics to instance
self.add(isoel=isoel,
col1=meta["column 1"],
col2=meta["column 2"],
channel_width=meta["channel width [um]"],
flow_rate=meta["flow rate [ul/s]"],
viscosity=meta["viscosity [mPa*s]"],
method=meta["method"]) | ['def', 'load_data', '(', 'self', ',', 'path', ')', ':', 'path', '=', 'pathlib', '.', 'Path', '(', 'path', ')', '.', 'resolve', '(', ')', '# Get metadata', 'meta', '=', '{', '}', 'with', 'path', '.', 'open', '(', ')', 'as', 'fd', ':', 'while', 'True', ':', 'line', '=', 'fd', '.', 'readline', '(', ')', '.', 'strip', '(', ')', 'if', 'line', '.', 'startswith', '(', '"# - "', ')', ':', 'line', '=', 'line', '.', 'strip', '(', '"#- "', ')', 'var', ',', 'val', '=', 'line', '.', 'split', '(', '":"', ')', 'if', 'val', '.', 'strip', '(', ')', '.', 'replace', '(', '"."', ',', '""', ')', '.', 'isdigit', '(', ')', ':', '# channel width, flow rate, viscosity', 'val', '=', 'float', '(', 'val', ')', 'else', ':', '# columns, calculation', 'val', '=', 'val', '.', 'strip', '(', ')', '.', 'lower', '(', ')', 'meta', '[', 'var', '.', 'strip', '(', ')', ']', '=', 'val', 'elif', 'line', 'and', 'not', 'line', '.', 'startswith', '(', '"#"', ')', ':', 'break', 'assert', 'meta', '[', '"column 1"', ']', 'in', 'dfn', '.', 'scalar_feature_names', 'assert', 'meta', '[', '"column 2"', ']', 'in', 'dfn', '.', 'scalar_feature_names', 'assert', 'meta', '[', '"column 3"', ']', '==', '"emodulus"', 'assert', 'meta', '[', '"method"', ']', 'in', 'VALID_METHODS', '# Load isoelasics', 'with', 'path', '.', 'open', '(', '"rb"', ')', 'as', 'isfd', ':', 'isodata', '=', 'np', '.', 'loadtxt', '(', 'isfd', ')', '# Slice out individual isoelastics', 'emoduli', '=', 'np', '.', 'unique', '(', 'isodata', '[', ':', ',', '2', ']', ')', 'isoel', '=', '[', ']', 'for', 'emod', 'in', 'emoduli', ':', 'where', '=', 'isodata', '[', ':', ',', '2', ']', '==', 'emod', 'isoel', '.', 'append', '(', 'isodata', '[', 'where', ']', ')', '# Add isoelastics to instance', 'self', '.', 'add', '(', 'isoel', '=', 'isoel', ',', 'col1', '=', 'meta', '[', '"column 1"', ']', ',', 'col2', '=', 'meta', '[', '"column 2"', ']', ',', 'channel_width', '=', 'meta', '[', '"channel width [um]"', ']', ',', 'flow_rate', '=', 'meta', '[', '"flow rate [ul/s]"', ']', ',', 'viscosity', '=', 'meta', '[', '"viscosity [mPa*s]"', ']', ',', 'method', '=', 'meta', '[', '"method"', ']', ')'] | Load isoelastics from a text file
The text file is loaded with `numpy.loadtxt` and must have
three columns, representing the two data columns and the
elastic modulus with units defined in `definitions.py`.
The file header must have a section defining meta data of the
content like so:
# [...]
#
# - column 1: area_um
# - column 2: deform
# - column 3: emodulus
# - channel width [um]: 20
# - flow rate [ul/s]: 0.04
# - viscosity [mPa*s]: 15
# - method: analytical
#
# [...]
Parameters
----------
path: str
Path to a isoelastics text file | ['Load', 'isoelastics', 'from', 'a', 'text', 'file'] | train | https://github.com/ZELLMECHANIK-DRESDEN/dclab/blob/79002c4356e7020c2ba73ab0a3819c9abd4affec/dclab/isoelastics/__init__.py#L348-L417 |
1,388 | pettarin/ipapy | ipapy/compatibility.py | is_unicode_string | def is_unicode_string(string):
"""
Return ``True`` if the given string is a Unicode string,
that is, of type ``unicode`` in Python 2 or ``str`` in Python 3.
Return ``None`` if ``string`` is ``None``.
:param str string: the string to be checked
:rtype: bool
"""
if string is None:
return None
if PY2:
return isinstance(string, unicode)
return isinstance(string, str) | python | def is_unicode_string(string):
"""
Return ``True`` if the given string is a Unicode string,
that is, of type ``unicode`` in Python 2 or ``str`` in Python 3.
Return ``None`` if ``string`` is ``None``.
:param str string: the string to be checked
:rtype: bool
"""
if string is None:
return None
if PY2:
return isinstance(string, unicode)
return isinstance(string, str) | ['def', 'is_unicode_string', '(', 'string', ')', ':', 'if', 'string', 'is', 'None', ':', 'return', 'None', 'if', 'PY2', ':', 'return', 'isinstance', '(', 'string', ',', 'unicode', ')', 'return', 'isinstance', '(', 'string', ',', 'str', ')'] | Return ``True`` if the given string is a Unicode string,
that is, of type ``unicode`` in Python 2 or ``str`` in Python 3.
Return ``None`` if ``string`` is ``None``.
:param str string: the string to be checked
:rtype: bool | ['Return', 'True', 'if', 'the', 'given', 'string', 'is', 'a', 'Unicode', 'string', 'that', 'is', 'of', 'type', 'unicode', 'in', 'Python', '2', 'or', 'str', 'in', 'Python', '3', '.'] | train | https://github.com/pettarin/ipapy/blob/ede4b3c40636f6eb90068369d31a2e75c7115324/ipapy/compatibility.py#L25-L39 |
1,389 | zsethna/OLGA | olga/generate_sequences.py | main | def main():
""" Generate sequences."""
parser = OptionParser(conflict_handler="resolve")
parser.add_option('--humanTRA', '--human_T_alpha', action='store_true', dest='humanTRA', default=False, help='use default human TRA model (T cell alpha chain)')
parser.add_option('--humanTRB', '--human_T_beta', action='store_true', dest='humanTRB', default=False, help='use default human TRB model (T cell beta chain)')
parser.add_option('--mouseTRB', '--mouse_T_beta', action='store_true', dest='mouseTRB', default=False, help='use default mouse TRB model (T cell beta chain)')
parser.add_option('--humanIGH', '--human_B_heavy', action='store_true', dest='humanIGH', default=False, help='use default human IGH model (B cell heavy chain)')
parser.add_option('--VDJ_model_folder', dest='vdj_model_folder', metavar='PATH/TO/FOLDER/', help='specify PATH/TO/FOLDER/ for a custom VDJ generative model')
parser.add_option('--VJ_model_folder', dest='vj_model_folder', metavar='PATH/TO/FOLDER/', help='specify PATH/TO/FOLDER/ for a custom VJ generative model')
parser.add_option('-o', '--outfile', dest = 'outfile_name', metavar='PATH/TO/FILE', help='write CDR3 sequences to PATH/TO/FILE')
parser.add_option('-n', '--num_seqs', type='float', metavar='N', default = 0, dest='num_seqs_to_generate', help='specify the number of sequences to generate.')
parser.add_option('--seed', type='int', dest='seed', help='set seed for pseudorandom number generator. Default is to not set a seed.')
parser.add_option('--seqs_per_time_update', type='float', default = 100000, dest='seqs_per_time_update', help='specify the number of sequences between time updates. Default is 1e5')
parser.add_option('--conserved_J_residues', type='string', default = 'FVW', dest='conserved_J_residues', help="specify conserved J residues. Default is 'FVW'.")
parser.add_option('--time_updates_off', action='store_false', dest='time_updates', default=True, help='turn time updates off.')
parser.add_option('--seq_type', type='choice', default = 'all', dest='seq_type', choices=['all', 'ntseq', 'nucleotide', 'aaseq', 'amino_acid'], help="declare sequence type for output sequences. Choices: 'all' [default], 'ntseq', 'nucleotide', 'aaseq', 'amino_acid'")
parser.add_option('--record_genes_off', action='store_false', dest="record_genes", default=True, help='turn off recording V and J gene info.')
parser.add_option('-d', '--delimiter', type='choice', dest='delimiter', choices=['tab', 'space', ',', ';', ':'], help="declare delimiter choice. Default is tab for .tsv output files, comma for .csv files, and tab for all others. Choices: 'tab', 'space', ',', ';', ':'")
parser.add_option('--raw_delimiter', type='str', dest='delimiter', help="declare delimiter choice as a raw string.")
(options, args) = parser.parse_args()
main_folder = os.path.dirname(__file__)
default_models = {}
default_models['humanTRA'] = [os.path.join(main_folder, 'default_models', 'human_T_alpha'), 'VJ']
default_models['humanTRB'] = [os.path.join(main_folder, 'default_models', 'human_T_beta'), 'VDJ']
default_models['mouseTRB'] = [os.path.join(main_folder, 'default_models', 'mouse_T_beta'), 'VDJ']
default_models['humanIGH'] = [os.path.join(main_folder, 'default_models', 'human_B_heavy'), 'VDJ']
num_models_specified = sum([1 for x in default_models.keys() + ['vj_model_folder', 'vdj_model_folder'] if getattr(options, x)])
if num_models_specified == 1: #exactly one model specified
try:
d_model = [x for x in default_models.keys() if getattr(options, x)][0]
model_folder = default_models[d_model][0]
recomb_type = default_models[d_model][1]
except IndexError:
if options.vdj_model_folder: #custom VDJ model specified
model_folder = options.vdj_model_folder
recomb_type = 'VDJ'
elif options.vj_model_folder: #custom VJ model specified
model_folder = options.vj_model_folder
recomb_type = 'VJ'
elif num_models_specified == 0:
print 'Need to indicate generative model.'
print 'Exiting...'
return -1
elif num_models_specified > 1:
print 'Only specify one model'
print 'Exiting...'
return -1
#Check that all model and genomic files exist in the indicated model folder
if not os.path.isdir(model_folder):
print 'Check pathing... cannot find the model folder: ' + model_folder
print 'Exiting...'
return -1
params_file_name = os.path.join(model_folder,'model_params.txt')
marginals_file_name = os.path.join(model_folder,'model_marginals.txt')
V_anchor_pos_file = os.path.join(model_folder,'V_gene_CDR3_anchors.csv')
J_anchor_pos_file = os.path.join(model_folder,'J_gene_CDR3_anchors.csv')
for x in [params_file_name, marginals_file_name, V_anchor_pos_file, J_anchor_pos_file]:
if not os.path.isfile(x):
print 'Cannot find: ' + x
print 'Please check the files (and naming conventions) in the model folder ' + model_folder
print 'Exiting...'
return -1
if options.outfile_name is not None:
outfile_name = options.outfile_name
if os.path.isfile(outfile_name):
if not raw_input(outfile_name + ' already exists. Overwrite (y/n)? ').strip().lower() in ['y', 'yes']:
print 'Exiting...'
return -1
#Parse arguments
num_seqs_to_generate = int(options.num_seqs_to_generate)
if num_seqs_to_generate <= 0:
print 'Need to specify num_seqs (number of sequences to generate).'
print 'Exiting...'
return -1
#Parse default delimiter
delimiter = options.delimiter
if delimiter is None:
delimiter = '\t'
if options.outfile_name is not None:
if outfile_name.endswith('.tsv'):
delimiter = '\t'
elif outfile_name.endswith('.csv'):
delimiter = ','
else:
try:
delimiter = {'tab': '\t', 'space': ' ', ',': ',', ';': ';', ':': ':'}[delimiter]
except KeyError:
pass #Other raw string.
#Optional flags
seq_type = {'all': 'all', 'ntseq': 'ntseq', 'nucleotide': 'ntseq', 'aaseq': 'aaseq', 'amino_acid': 'aaseq'}[options.seq_type]
record_genes = options.record_genes
seqs_per_time_update = int(options.seqs_per_time_update)
time_updates = options.time_updates
conserved_J_residues = options.conserved_J_residues
if options.seed is not None:
np.random.seed(options.seed)
#VDJ recomb case --- used for TCRB and IGH
if recomb_type == 'VDJ':
genomic_data = load_model.GenomicDataVDJ()
genomic_data.load_igor_genomic_data(params_file_name, V_anchor_pos_file, J_anchor_pos_file)
generative_model = load_model.GenerativeModelVDJ()
generative_model.load_and_process_igor_model(marginals_file_name)
seq_gen = sequence_generation.SequenceGenerationVDJ(generative_model, genomic_data)
#VJ recomb case --- used for TCRA and light chain
elif recomb_type == 'VJ':
genomic_data = load_model.GenomicDataVJ()
genomic_data.load_igor_genomic_data(params_file_name, V_anchor_pos_file, J_anchor_pos_file)
generative_model = load_model.GenerativeModelVJ()
generative_model.load_and_process_igor_model(marginals_file_name)
seq_gen = sequence_generation.SequenceGenerationVJ(generative_model, genomic_data)
V_gene_names = [V[0].split('*')[0] for V in genomic_data.genV]
J_gene_names = [J[0].split('*')[0] for J in genomic_data.genJ]
if options.outfile_name is not None:
outfile = open(outfile_name, 'w')
print 'Starting sequence generation... '
start_time = time.time()
for i in range(num_seqs_to_generate):
ntseq, aaseq, V_in, J_in = seq_gen.gen_rnd_prod_CDR3(conserved_J_residues)
if seq_type == 'all': #default, include both ntseq and aaseq
current_line_out = ntseq + delimiter + aaseq
elif seq_type == 'ntseq': #only record ntseq
current_line_out = ntseq
elif seq_type == 'aaseq': #only record aaseq
current_line_out = aaseq
if record_genes:
current_line_out += delimiter + V_gene_names[V_in] + delimiter + J_gene_names[J_in]
outfile.write(current_line_out + '\n')
if (i+1)%seqs_per_time_update == 0 and time_updates:
c_time = time.time() - start_time
eta = ((num_seqs_to_generate - (i+1))/float(i+1))*c_time
if c_time > 86400: #more than a day
c_time_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(c_time)/86400, (int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 3600: #more than an hr
c_time_str = '%d hours, %d minutes, and %.2f seconds.'%((int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 60: #more than a min
c_time_str = '%d minutes and %.2f seconds.'%((int(c_time)/60)%60, c_time%60)
else:
c_time_str = '%.2f seconds.'%(c_time)
if eta > 86400: #more than a day
eta_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(eta)/86400, (int(eta)/3600)%24, (int(eta)/60)%60, eta%60)
elif eta > 3600: #more than an hr
eta_str = '%d hours, %d minutes, and %.2f seconds.'%((int(eta)/3600)%24, (int(eta)/60)%60, eta%60)
elif eta > 60: #more than a min
eta_str = '%d minutes and %.2f seconds.'%((int(eta)/60)%60, eta%60)
else:
eta_str = '%.2f seconds.'%(eta)
print '%d sequences generated in %s Estimated time remaining: %s'%(i+1, c_time_str, eta_str)
c_time = time.time() - start_time
if c_time > 86400: #more than a day
c_time_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(c_time)/86400, (int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 3600: #more than an hr
c_time_str = '%d hours, %d minutes, and %.2f seconds.'%((int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 60: #more than a min
c_time_str = '%d minutes and %.2f seconds.'%((int(c_time)/60)%60, c_time%60)
else:
c_time_str = '%.2f seconds.'%(c_time)
print 'Completed generating all %d sequences in %s'%(num_seqs_to_generate, c_time_str)
outfile.close()
else: #print to stdout
for i in range(num_seqs_to_generate):
ntseq, aaseq, V_in, J_in = seq_gen.gen_rnd_prod_CDR3(conserved_J_residues)
if seq_type == 'all': #default, include both ntseq and aaseq
current_line_out = ntseq + delimiter + aaseq
elif seq_type == 'ntseq': #only record ntseq
current_line_out = ntseq
elif seq_type == 'aaseq': #only record aaseq
current_line_out = aaseq
if record_genes:
current_line_out += delimiter + V_gene_names[V_in] + delimiter + J_gene_names[J_in]
print current_line_out | python | def main():
""" Generate sequences."""
parser = OptionParser(conflict_handler="resolve")
parser.add_option('--humanTRA', '--human_T_alpha', action='store_true', dest='humanTRA', default=False, help='use default human TRA model (T cell alpha chain)')
parser.add_option('--humanTRB', '--human_T_beta', action='store_true', dest='humanTRB', default=False, help='use default human TRB model (T cell beta chain)')
parser.add_option('--mouseTRB', '--mouse_T_beta', action='store_true', dest='mouseTRB', default=False, help='use default mouse TRB model (T cell beta chain)')
parser.add_option('--humanIGH', '--human_B_heavy', action='store_true', dest='humanIGH', default=False, help='use default human IGH model (B cell heavy chain)')
parser.add_option('--VDJ_model_folder', dest='vdj_model_folder', metavar='PATH/TO/FOLDER/', help='specify PATH/TO/FOLDER/ for a custom VDJ generative model')
parser.add_option('--VJ_model_folder', dest='vj_model_folder', metavar='PATH/TO/FOLDER/', help='specify PATH/TO/FOLDER/ for a custom VJ generative model')
parser.add_option('-o', '--outfile', dest = 'outfile_name', metavar='PATH/TO/FILE', help='write CDR3 sequences to PATH/TO/FILE')
parser.add_option('-n', '--num_seqs', type='float', metavar='N', default = 0, dest='num_seqs_to_generate', help='specify the number of sequences to generate.')
parser.add_option('--seed', type='int', dest='seed', help='set seed for pseudorandom number generator. Default is to not set a seed.')
parser.add_option('--seqs_per_time_update', type='float', default = 100000, dest='seqs_per_time_update', help='specify the number of sequences between time updates. Default is 1e5')
parser.add_option('--conserved_J_residues', type='string', default = 'FVW', dest='conserved_J_residues', help="specify conserved J residues. Default is 'FVW'.")
parser.add_option('--time_updates_off', action='store_false', dest='time_updates', default=True, help='turn time updates off.')
parser.add_option('--seq_type', type='choice', default = 'all', dest='seq_type', choices=['all', 'ntseq', 'nucleotide', 'aaseq', 'amino_acid'], help="declare sequence type for output sequences. Choices: 'all' [default], 'ntseq', 'nucleotide', 'aaseq', 'amino_acid'")
parser.add_option('--record_genes_off', action='store_false', dest="record_genes", default=True, help='turn off recording V and J gene info.')
parser.add_option('-d', '--delimiter', type='choice', dest='delimiter', choices=['tab', 'space', ',', ';', ':'], help="declare delimiter choice. Default is tab for .tsv output files, comma for .csv files, and tab for all others. Choices: 'tab', 'space', ',', ';', ':'")
parser.add_option('--raw_delimiter', type='str', dest='delimiter', help="declare delimiter choice as a raw string.")
(options, args) = parser.parse_args()
main_folder = os.path.dirname(__file__)
default_models = {}
default_models['humanTRA'] = [os.path.join(main_folder, 'default_models', 'human_T_alpha'), 'VJ']
default_models['humanTRB'] = [os.path.join(main_folder, 'default_models', 'human_T_beta'), 'VDJ']
default_models['mouseTRB'] = [os.path.join(main_folder, 'default_models', 'mouse_T_beta'), 'VDJ']
default_models['humanIGH'] = [os.path.join(main_folder, 'default_models', 'human_B_heavy'), 'VDJ']
num_models_specified = sum([1 for x in default_models.keys() + ['vj_model_folder', 'vdj_model_folder'] if getattr(options, x)])
if num_models_specified == 1: #exactly one model specified
try:
d_model = [x for x in default_models.keys() if getattr(options, x)][0]
model_folder = default_models[d_model][0]
recomb_type = default_models[d_model][1]
except IndexError:
if options.vdj_model_folder: #custom VDJ model specified
model_folder = options.vdj_model_folder
recomb_type = 'VDJ'
elif options.vj_model_folder: #custom VJ model specified
model_folder = options.vj_model_folder
recomb_type = 'VJ'
elif num_models_specified == 0:
print 'Need to indicate generative model.'
print 'Exiting...'
return -1
elif num_models_specified > 1:
print 'Only specify one model'
print 'Exiting...'
return -1
#Check that all model and genomic files exist in the indicated model folder
if not os.path.isdir(model_folder):
print 'Check pathing... cannot find the model folder: ' + model_folder
print 'Exiting...'
return -1
params_file_name = os.path.join(model_folder,'model_params.txt')
marginals_file_name = os.path.join(model_folder,'model_marginals.txt')
V_anchor_pos_file = os.path.join(model_folder,'V_gene_CDR3_anchors.csv')
J_anchor_pos_file = os.path.join(model_folder,'J_gene_CDR3_anchors.csv')
for x in [params_file_name, marginals_file_name, V_anchor_pos_file, J_anchor_pos_file]:
if not os.path.isfile(x):
print 'Cannot find: ' + x
print 'Please check the files (and naming conventions) in the model folder ' + model_folder
print 'Exiting...'
return -1
if options.outfile_name is not None:
outfile_name = options.outfile_name
if os.path.isfile(outfile_name):
if not raw_input(outfile_name + ' already exists. Overwrite (y/n)? ').strip().lower() in ['y', 'yes']:
print 'Exiting...'
return -1
#Parse arguments
num_seqs_to_generate = int(options.num_seqs_to_generate)
if num_seqs_to_generate <= 0:
print 'Need to specify num_seqs (number of sequences to generate).'
print 'Exiting...'
return -1
#Parse default delimiter
delimiter = options.delimiter
if delimiter is None:
delimiter = '\t'
if options.outfile_name is not None:
if outfile_name.endswith('.tsv'):
delimiter = '\t'
elif outfile_name.endswith('.csv'):
delimiter = ','
else:
try:
delimiter = {'tab': '\t', 'space': ' ', ',': ',', ';': ';', ':': ':'}[delimiter]
except KeyError:
pass #Other raw string.
#Optional flags
seq_type = {'all': 'all', 'ntseq': 'ntseq', 'nucleotide': 'ntseq', 'aaseq': 'aaseq', 'amino_acid': 'aaseq'}[options.seq_type]
record_genes = options.record_genes
seqs_per_time_update = int(options.seqs_per_time_update)
time_updates = options.time_updates
conserved_J_residues = options.conserved_J_residues
if options.seed is not None:
np.random.seed(options.seed)
#VDJ recomb case --- used for TCRB and IGH
if recomb_type == 'VDJ':
genomic_data = load_model.GenomicDataVDJ()
genomic_data.load_igor_genomic_data(params_file_name, V_anchor_pos_file, J_anchor_pos_file)
generative_model = load_model.GenerativeModelVDJ()
generative_model.load_and_process_igor_model(marginals_file_name)
seq_gen = sequence_generation.SequenceGenerationVDJ(generative_model, genomic_data)
#VJ recomb case --- used for TCRA and light chain
elif recomb_type == 'VJ':
genomic_data = load_model.GenomicDataVJ()
genomic_data.load_igor_genomic_data(params_file_name, V_anchor_pos_file, J_anchor_pos_file)
generative_model = load_model.GenerativeModelVJ()
generative_model.load_and_process_igor_model(marginals_file_name)
seq_gen = sequence_generation.SequenceGenerationVJ(generative_model, genomic_data)
V_gene_names = [V[0].split('*')[0] for V in genomic_data.genV]
J_gene_names = [J[0].split('*')[0] for J in genomic_data.genJ]
if options.outfile_name is not None:
outfile = open(outfile_name, 'w')
print 'Starting sequence generation... '
start_time = time.time()
for i in range(num_seqs_to_generate):
ntseq, aaseq, V_in, J_in = seq_gen.gen_rnd_prod_CDR3(conserved_J_residues)
if seq_type == 'all': #default, include both ntseq and aaseq
current_line_out = ntseq + delimiter + aaseq
elif seq_type == 'ntseq': #only record ntseq
current_line_out = ntseq
elif seq_type == 'aaseq': #only record aaseq
current_line_out = aaseq
if record_genes:
current_line_out += delimiter + V_gene_names[V_in] + delimiter + J_gene_names[J_in]
outfile.write(current_line_out + '\n')
if (i+1)%seqs_per_time_update == 0 and time_updates:
c_time = time.time() - start_time
eta = ((num_seqs_to_generate - (i+1))/float(i+1))*c_time
if c_time > 86400: #more than a day
c_time_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(c_time)/86400, (int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 3600: #more than an hr
c_time_str = '%d hours, %d minutes, and %.2f seconds.'%((int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 60: #more than a min
c_time_str = '%d minutes and %.2f seconds.'%((int(c_time)/60)%60, c_time%60)
else:
c_time_str = '%.2f seconds.'%(c_time)
if eta > 86400: #more than a day
eta_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(eta)/86400, (int(eta)/3600)%24, (int(eta)/60)%60, eta%60)
elif eta > 3600: #more than an hr
eta_str = '%d hours, %d minutes, and %.2f seconds.'%((int(eta)/3600)%24, (int(eta)/60)%60, eta%60)
elif eta > 60: #more than a min
eta_str = '%d minutes and %.2f seconds.'%((int(eta)/60)%60, eta%60)
else:
eta_str = '%.2f seconds.'%(eta)
print '%d sequences generated in %s Estimated time remaining: %s'%(i+1, c_time_str, eta_str)
c_time = time.time() - start_time
if c_time > 86400: #more than a day
c_time_str = '%d days, %d hours, %d minutes, and %.2f seconds.'%(int(c_time)/86400, (int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 3600: #more than an hr
c_time_str = '%d hours, %d minutes, and %.2f seconds.'%((int(c_time)/3600)%24, (int(c_time)/60)%60, c_time%60)
elif c_time > 60: #more than a min
c_time_str = '%d minutes and %.2f seconds.'%((int(c_time)/60)%60, c_time%60)
else:
c_time_str = '%.2f seconds.'%(c_time)
print 'Completed generating all %d sequences in %s'%(num_seqs_to_generate, c_time_str)
outfile.close()
else: #print to stdout
for i in range(num_seqs_to_generate):
ntseq, aaseq, V_in, J_in = seq_gen.gen_rnd_prod_CDR3(conserved_J_residues)
if seq_type == 'all': #default, include both ntseq and aaseq
current_line_out = ntseq + delimiter + aaseq
elif seq_type == 'ntseq': #only record ntseq
current_line_out = ntseq
elif seq_type == 'aaseq': #only record aaseq
current_line_out = aaseq
if record_genes:
current_line_out += delimiter + V_gene_names[V_in] + delimiter + J_gene_names[J_in]
print current_line_out | ['def', 'main', '(', ')', ':', 'parser', '=', 'OptionParser', '(', 'conflict_handler', '=', '"resolve"', ')', 'parser', '.', 'add_option', '(', "'--humanTRA'", ',', "'--human_T_alpha'", ',', 'action', '=', "'store_true'", ',', 'dest', '=', "'humanTRA'", ',', 'default', '=', 'False', ',', 'help', '=', "'use default human TRA model (T cell alpha chain)'", ')', 'parser', '.', 'add_option', '(', "'--humanTRB'", ',', "'--human_T_beta'", ',', 'action', '=', "'store_true'", ',', 'dest', '=', "'humanTRB'", ',', 'default', '=', 'False', ',', 'help', '=', "'use default human TRB model (T cell beta chain)'", ')', 'parser', '.', 'add_option', '(', "'--mouseTRB'", ',', "'--mouse_T_beta'", ',', 'action', '=', "'store_true'", ',', 'dest', '=', "'mouseTRB'", ',', 'default', '=', 'False', ',', 'help', '=', "'use default mouse TRB model (T cell beta chain)'", ')', 'parser', '.', 'add_option', '(', "'--humanIGH'", ',', "'--human_B_heavy'", ',', 'action', '=', "'store_true'", ',', 'dest', '=', "'humanIGH'", ',', 'default', '=', 'False', ',', 'help', '=', "'use default human IGH model (B cell heavy chain)'", ')', 'parser', '.', 'add_option', '(', "'--VDJ_model_folder'", ',', 'dest', '=', "'vdj_model_folder'", ',', 'metavar', '=', "'PATH/TO/FOLDER/'", ',', 'help', '=', "'specify PATH/TO/FOLDER/ for a custom VDJ generative model'", ')', 'parser', '.', 'add_option', '(', "'--VJ_model_folder'", ',', 'dest', '=', "'vj_model_folder'", ',', 'metavar', '=', "'PATH/TO/FOLDER/'", ',', 'help', '=', "'specify PATH/TO/FOLDER/ for a custom VJ generative model'", ')', 'parser', '.', 'add_option', '(', "'-o'", ',', "'--outfile'", ',', 'dest', '=', "'outfile_name'", ',', 'metavar', '=', "'PATH/TO/FILE'", ',', 'help', '=', "'write CDR3 sequences to PATH/TO/FILE'", ')', 'parser', '.', 'add_option', '(', "'-n'", ',', "'--num_seqs'", ',', 'type', '=', "'float'", ',', 'metavar', '=', "'N'", ',', 'default', '=', '0', ',', 'dest', '=', "'num_seqs_to_generate'", ',', 'help', '=', "'specify the number of sequences to generate.'", ')', 'parser', '.', 'add_option', '(', "'--seed'", ',', 'type', '=', "'int'", ',', 'dest', '=', "'seed'", ',', 'help', '=', "'set seed for pseudorandom number generator. Default is to not set a seed.'", ')', 'parser', '.', 'add_option', '(', "'--seqs_per_time_update'", ',', 'type', '=', "'float'", ',', 'default', '=', '100000', ',', 'dest', '=', "'seqs_per_time_update'", ',', 'help', '=', "'specify the number of sequences between time updates. Default is 1e5'", ')', 'parser', '.', 'add_option', '(', "'--conserved_J_residues'", ',', 'type', '=', "'string'", ',', 'default', '=', "'FVW'", ',', 'dest', '=', "'conserved_J_residues'", ',', 'help', '=', '"specify conserved J residues. Default is \'FVW\'."', ')', 'parser', '.', 'add_option', '(', "'--time_updates_off'", ',', 'action', '=', "'store_false'", ',', 'dest', '=', "'time_updates'", ',', 'default', '=', 'True', ',', 'help', '=', "'turn time updates off.'", ')', 'parser', '.', 'add_option', '(', "'--seq_type'", ',', 'type', '=', "'choice'", ',', 'default', '=', "'all'", ',', 'dest', '=', "'seq_type'", ',', 'choices', '=', '[', "'all'", ',', "'ntseq'", ',', "'nucleotide'", ',', "'aaseq'", ',', "'amino_acid'", ']', ',', 'help', '=', '"declare sequence type for output sequences. Choices: \'all\' [default], \'ntseq\', \'nucleotide\', \'aaseq\', \'amino_acid\'"', ')', 'parser', '.', 'add_option', '(', "'--record_genes_off'", ',', 'action', '=', "'store_false'", ',', 'dest', '=', '"record_genes"', ',', 'default', '=', 'True', ',', 'help', '=', "'turn off recording V and J gene info.'", ')', 'parser', '.', 'add_option', '(', "'-d'", ',', "'--delimiter'", ',', 'type', '=', "'choice'", ',', 'dest', '=', "'delimiter'", ',', 'choices', '=', '[', "'tab'", ',', "'space'", ',', "','", ',', "';'", ',', "':'", ']', ',', 'help', '=', '"declare delimiter choice. Default is tab for .tsv output files, comma for .csv files, and tab for all others. Choices: \'tab\', \'space\', \',\', \';\', \':\'"', ')', 'parser', '.', 'add_option', '(', "'--raw_delimiter'", ',', 'type', '=', "'str'", ',', 'dest', '=', "'delimiter'", ',', 'help', '=', '"declare delimiter choice as a raw string."', ')', '(', 'options', ',', 'args', ')', '=', 'parser', '.', 'parse_args', '(', ')', 'main_folder', '=', 'os', '.', 'path', '.', 'dirname', '(', '__file__', ')', 'default_models', '=', '{', '}', 'default_models', '[', "'humanTRA'", ']', '=', '[', 'os', '.', 'path', '.', 'join', '(', 'main_folder', ',', "'default_models'", ',', "'human_T_alpha'", ')', ',', "'VJ'", ']', 'default_models', '[', "'humanTRB'", ']', '=', '[', 'os', '.', 'path', '.', 'join', '(', 'main_folder', ',', "'default_models'", ',', "'human_T_beta'", ')', ',', "'VDJ'", ']', 'default_models', '[', "'mouseTRB'", ']', '=', '[', 'os', '.', 'path', '.', 'join', '(', 'main_folder', ',', "'default_models'", ',', "'mouse_T_beta'", ')', ',', "'VDJ'", ']', 'default_models', '[', "'humanIGH'", ']', '=', '[', 'os', '.', 'path', '.', 'join', '(', 'main_folder', ',', "'default_models'", ',', "'human_B_heavy'", ')', ',', "'VDJ'", ']', 'num_models_specified', '=', 'sum', '(', '[', '1', 'for', 'x', 'in', 'default_models', '.', 'keys', '(', ')', '+', '[', "'vj_model_folder'", ',', "'vdj_model_folder'", ']', 'if', 'getattr', '(', 'options', ',', 'x', ')', ']', ')', 'if', 'num_models_specified', '==', '1', ':', '#exactly one model specified', 'try', ':', 'd_model', '=', '[', 'x', 'for', 'x', 'in', 'default_models', '.', 'keys', '(', ')', 'if', 'getattr', '(', 'options', ',', 'x', ')', ']', '[', '0', ']', 'model_folder', '=', 'default_models', '[', 'd_model', ']', '[', '0', ']', 'recomb_type', '=', 'default_models', '[', 'd_model', ']', '[', '1', ']', 'except', 'IndexError', ':', 'if', 'options', '.', 'vdj_model_folder', ':', '#custom VDJ model specified', 'model_folder', '=', 'options', '.', 'vdj_model_folder', 'recomb_type', '=', "'VDJ'", 'elif', 'options', '.', 'vj_model_folder', ':', '#custom VJ model specified', 'model_folder', '=', 'options', '.', 'vj_model_folder', 'recomb_type', '=', "'VJ'", 'elif', 'num_models_specified', '==', '0', ':', 'print', "'Need to indicate generative model.'", 'print', "'Exiting...'", 'return', '-', '1', 'elif', 'num_models_specified', '>', '1', ':', 'print', "'Only specify one model'", 'print', "'Exiting...'", 'return', '-', '1', '#Check that all model and genomic files exist in the indicated model folder', 'if', 'not', 'os', '.', 'path', '.', 'isdir', '(', 'model_folder', ')', ':', 'print', "'Check pathing... cannot find the model folder: '", '+', 'model_folder', 'print', "'Exiting...'", 'return', '-', '1', 'params_file_name', '=', 'os', '.', 'path', '.', 'join', '(', 'model_folder', ',', "'model_params.txt'", ')', 'marginals_file_name', '=', 'os', '.', 'path', '.', 'join', '(', 'model_folder', ',', "'model_marginals.txt'", ')', 'V_anchor_pos_file', '=', 'os', '.', 'path', '.', 'join', '(', 'model_folder', ',', "'V_gene_CDR3_anchors.csv'", ')', 'J_anchor_pos_file', '=', 'os', '.', 'path', '.', 'join', '(', 'model_folder', ',', "'J_gene_CDR3_anchors.csv'", ')', 'for', 'x', 'in', '[', 'params_file_name', ',', 'marginals_file_name', ',', 'V_anchor_pos_file', ',', 'J_anchor_pos_file', ']', ':', 'if', 'not', 'os', '.', 'path', '.', 'isfile', '(', 'x', ')', ':', 'print', "'Cannot find: '", '+', 'x', 'print', "'Please check the files (and naming conventions) in the model folder '", '+', 'model_folder', 'print', "'Exiting...'", 'return', '-', '1', 'if', 'options', '.', 'outfile_name', 'is', 'not', 'None', ':', 'outfile_name', '=', 'options', '.', 'outfile_name', 'if', 'os', '.', 'path', '.', 'isfile', '(', 'outfile_name', ')', ':', 'if', 'not', 'raw_input', '(', 'outfile_name', '+', "' already exists. Overwrite (y/n)? '", ')', '.', 'strip', '(', ')', '.', 'lower', '(', ')', 'in', '[', "'y'", ',', "'yes'", ']', ':', 'print', "'Exiting...'", 'return', '-', '1', '#Parse arguments', 'num_seqs_to_generate', '=', 'int', '(', 'options', '.', 'num_seqs_to_generate', ')', 'if', 'num_seqs_to_generate', '<=', '0', ':', 'print', "'Need to specify num_seqs (number of sequences to generate).'", 'print', "'Exiting...'", 'return', '-', '1', '#Parse default delimiter', 'delimiter', '=', 'options', '.', 'delimiter', 'if', 'delimiter', 'is', 'None', ':', 'delimiter', '=', "'\\t'", 'if', 'options', '.', 'outfile_name', 'is', 'not', 'None', ':', 'if', 'outfile_name', '.', 'endswith', '(', "'.tsv'", ')', ':', 'delimiter', '=', "'\\t'", 'elif', 'outfile_name', '.', 'endswith', '(', "'.csv'", ')', ':', 'delimiter', '=', "','", 'else', ':', 'try', ':', 'delimiter', '=', '{', "'tab'", ':', "'\\t'", ',', "'space'", ':', "' '", ',', "','", ':', "','", ',', "';'", ':', "';'", ',', "':'", ':', "':'", '}', '[', 'delimiter', ']', 'except', 'KeyError', ':', 'pass', '#Other raw string.', '#Optional flags', 'seq_type', '=', '{', "'all'", ':', "'all'", ',', "'ntseq'", ':', "'ntseq'", ',', "'nucleotide'", ':', "'ntseq'", ',', "'aaseq'", ':', "'aaseq'", ',', "'amino_acid'", ':', "'aaseq'", '}', '[', 'options', '.', 'seq_type', ']', 'record_genes', '=', 'options', '.', 'record_genes', 'seqs_per_time_update', '=', 'int', '(', 'options', '.', 'seqs_per_time_update', ')', 'time_updates', '=', 'options', '.', 'time_updates', 'conserved_J_residues', '=', 'options', '.', 'conserved_J_residues', 'if', 'options', '.', 'seed', 'is', 'not', 'None', ':', 'np', '.', 'random', '.', 'seed', '(', 'options', '.', 'seed', ')', '#VDJ recomb case --- used for TCRB and IGH', 'if', 'recomb_type', '==', "'VDJ'", ':', 'genomic_data', '=', 'load_model', '.', 'GenomicDataVDJ', '(', ')', 'genomic_data', '.', 'load_igor_genomic_data', '(', 'params_file_name', ',', 'V_anchor_pos_file', ',', 'J_anchor_pos_file', ')', 'generative_model', '=', 'load_model', '.', 'GenerativeModelVDJ', '(', ')', 'generative_model', '.', 'load_and_process_igor_model', '(', 'marginals_file_name', ')', 'seq_gen', '=', 'sequence_generation', '.', 'SequenceGenerationVDJ', '(', 'generative_model', ',', 'genomic_data', ')', '#VJ recomb case --- used for TCRA and light chain', 'elif', 'recomb_type', '==', "'VJ'", ':', 'genomic_data', '=', 'load_model', '.', 'GenomicDataVJ', '(', ')', 'genomic_data', '.', 'load_igor_genomic_data', '(', 'params_file_name', ',', 'V_anchor_pos_file', ',', 'J_anchor_pos_file', ')', 'generative_model', '=', 'load_model', '.', 'GenerativeModelVJ', '(', ')', 'generative_model', '.', 'load_and_process_igor_model', '(', 'marginals_file_name', ')', 'seq_gen', '=', 'sequence_generation', '.', 'SequenceGenerationVJ', '(', 'generative_model', ',', 'genomic_data', ')', 'V_gene_names', '=', '[', 'V', '[', '0', ']', '.', 'split', '(', "'*'", ')', '[', '0', ']', 'for', 'V', 'in', 'genomic_data', '.', 'genV', ']', 'J_gene_names', '=', '[', 'J', '[', '0', ']', '.', 'split', '(', "'*'", ')', '[', '0', ']', 'for', 'J', 'in', 'genomic_data', '.', 'genJ', ']', 'if', 'options', '.', 'outfile_name', 'is', 'not', 'None', ':', 'outfile', '=', 'open', '(', 'outfile_name', ',', "'w'", ')', 'print', "'Starting sequence generation... '", 'start_time', '=', 'time', '.', 'time', '(', ')', 'for', 'i', 'in', 'range', '(', 'num_seqs_to_generate', ')', ':', 'ntseq', ',', 'aaseq', ',', 'V_in', ',', 'J_in', '=', 'seq_gen', '.', 'gen_rnd_prod_CDR3', '(', 'conserved_J_residues', ')', 'if', 'seq_type', '==', "'all'", ':', '#default, include both ntseq and aaseq', 'current_line_out', '=', 'ntseq', '+', 'delimiter', '+', 'aaseq', 'elif', 'seq_type', '==', "'ntseq'", ':', '#only record ntseq', 'current_line_out', '=', 'ntseq', 'elif', 'seq_type', '==', "'aaseq'", ':', '#only record aaseq', 'current_line_out', '=', 'aaseq', 'if', 'record_genes', ':', 'current_line_out', '+=', 'delimiter', '+', 'V_gene_names', '[', 'V_in', ']', '+', 'delimiter', '+', 'J_gene_names', '[', 'J_in', ']', 'outfile', '.', 'write', '(', 'current_line_out', '+', "'\\n'", ')', 'if', '(', 'i', '+', '1', ')', '%', 'seqs_per_time_update', '==', '0', 'and', 'time_updates', ':', 'c_time', '=', 'time', '.', 'time', '(', ')', '-', 'start_time', 'eta', '=', '(', '(', 'num_seqs_to_generate', '-', '(', 'i', '+', '1', ')', ')', '/', 'float', '(', 'i', '+', '1', ')', ')', '*', 'c_time', 'if', 'c_time', '>', '86400', ':', '#more than a day', 'c_time_str', '=', "'%d days, %d hours, %d minutes, and %.2f seconds.'", '%', '(', 'int', '(', 'c_time', ')', '/', '86400', ',', '(', 'int', '(', 'c_time', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'elif', 'c_time', '>', '3600', ':', '#more than an hr', 'c_time_str', '=', "'%d hours, %d minutes, and %.2f seconds.'", '%', '(', '(', 'int', '(', 'c_time', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'elif', 'c_time', '>', '60', ':', '#more than a min', 'c_time_str', '=', "'%d minutes and %.2f seconds.'", '%', '(', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'else', ':', 'c_time_str', '=', "'%.2f seconds.'", '%', '(', 'c_time', ')', 'if', 'eta', '>', '86400', ':', '#more than a day', 'eta_str', '=', "'%d days, %d hours, %d minutes, and %.2f seconds.'", '%', '(', 'int', '(', 'eta', ')', '/', '86400', ',', '(', 'int', '(', 'eta', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'eta', ')', '/', '60', ')', '%', '60', ',', 'eta', '%', '60', ')', 'elif', 'eta', '>', '3600', ':', '#more than an hr', 'eta_str', '=', "'%d hours, %d minutes, and %.2f seconds.'", '%', '(', '(', 'int', '(', 'eta', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'eta', ')', '/', '60', ')', '%', '60', ',', 'eta', '%', '60', ')', 'elif', 'eta', '>', '60', ':', '#more than a min', 'eta_str', '=', "'%d minutes and %.2f seconds.'", '%', '(', '(', 'int', '(', 'eta', ')', '/', '60', ')', '%', '60', ',', 'eta', '%', '60', ')', 'else', ':', 'eta_str', '=', "'%.2f seconds.'", '%', '(', 'eta', ')', 'print', "'%d sequences generated in %s Estimated time remaining: %s'", '%', '(', 'i', '+', '1', ',', 'c_time_str', ',', 'eta_str', ')', 'c_time', '=', 'time', '.', 'time', '(', ')', '-', 'start_time', 'if', 'c_time', '>', '86400', ':', '#more than a day', 'c_time_str', '=', "'%d days, %d hours, %d minutes, and %.2f seconds.'", '%', '(', 'int', '(', 'c_time', ')', '/', '86400', ',', '(', 'int', '(', 'c_time', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'elif', 'c_time', '>', '3600', ':', '#more than an hr', 'c_time_str', '=', "'%d hours, %d minutes, and %.2f seconds.'", '%', '(', '(', 'int', '(', 'c_time', ')', '/', '3600', ')', '%', '24', ',', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'elif', 'c_time', '>', '60', ':', '#more than a min', 'c_time_str', '=', "'%d minutes and %.2f seconds.'", '%', '(', '(', 'int', '(', 'c_time', ')', '/', '60', ')', '%', '60', ',', 'c_time', '%', '60', ')', 'else', ':', 'c_time_str', '=', "'%.2f seconds.'", '%', '(', 'c_time', ')', 'print', "'Completed generating all %d sequences in %s'", '%', '(', 'num_seqs_to_generate', ',', 'c_time_str', ')', 'outfile', '.', 'close', '(', ')', 'else', ':', '#print to stdout', 'for', 'i', 'in', 'range', '(', 'num_seqs_to_generate', ')', ':', 'ntseq', ',', 'aaseq', ',', 'V_in', ',', 'J_in', '=', 'seq_gen', '.', 'gen_rnd_prod_CDR3', '(', 'conserved_J_residues', ')', 'if', 'seq_type', '==', "'all'", ':', '#default, include both ntseq and aaseq', 'current_line_out', '=', 'ntseq', '+', 'delimiter', '+', 'aaseq', 'elif', 'seq_type', '==', "'ntseq'", ':', '#only record ntseq', 'current_line_out', '=', 'ntseq', 'elif', 'seq_type', '==', "'aaseq'", ':', '#only record aaseq', 'current_line_out', '=', 'aaseq', 'if', 'record_genes', ':', 'current_line_out', '+=', 'delimiter', '+', 'V_gene_names', '[', 'V_in', ']', '+', 'delimiter', '+', 'J_gene_names', '[', 'J_in', ']', 'print', 'current_line_out'] | Generate sequences. | ['Generate', 'sequences', '.'] | train | https://github.com/zsethna/OLGA/blob/e825c333f0f9a4eb02132e0bcf86f0dca9123114/olga/generate_sequences.py#L144-L345 |
1,390 | tyarkoni/pliers | pliers/diagnostics/diagnostics.py | Diagnostics.flag_all | def flag_all(self, thresh_dict=None, include=None, exclude=None):
'''
Returns indices of (rows, columns) that satisfy flag() on any
diagnostic. Uses user-provided thresholds in thresh_dict/
Args:
thresh_dict (dict): dictionary of diagnostic->threshold functions
include (list): optional sublist of diagnostics to flag
exclude (list): optional sublist of diagnostics to not flag
'''
if thresh_dict is None:
thresh_dict = {}
row_idx = set()
col_idx = set()
include = self.results if include is None else include
include = list(
set(include) - set(exclude)) if exclude is not None else include
for diagnostic in include:
if diagnostic in thresh_dict:
flagged = self.flag(diagnostic, thresh_dict[diagnostic])
else:
flagged = self.flag(diagnostic)
if diagnostic == 'RowMahalanobisDistances':
row_idx = row_idx.union(flagged)
else:
col_idx = col_idx.union(flagged)
return sorted(list(row_idx)), sorted(list(col_idx)) | python | def flag_all(self, thresh_dict=None, include=None, exclude=None):
'''
Returns indices of (rows, columns) that satisfy flag() on any
diagnostic. Uses user-provided thresholds in thresh_dict/
Args:
thresh_dict (dict): dictionary of diagnostic->threshold functions
include (list): optional sublist of diagnostics to flag
exclude (list): optional sublist of diagnostics to not flag
'''
if thresh_dict is None:
thresh_dict = {}
row_idx = set()
col_idx = set()
include = self.results if include is None else include
include = list(
set(include) - set(exclude)) if exclude is not None else include
for diagnostic in include:
if diagnostic in thresh_dict:
flagged = self.flag(diagnostic, thresh_dict[diagnostic])
else:
flagged = self.flag(diagnostic)
if diagnostic == 'RowMahalanobisDistances':
row_idx = row_idx.union(flagged)
else:
col_idx = col_idx.union(flagged)
return sorted(list(row_idx)), sorted(list(col_idx)) | ['def', 'flag_all', '(', 'self', ',', 'thresh_dict', '=', 'None', ',', 'include', '=', 'None', ',', 'exclude', '=', 'None', ')', ':', 'if', 'thresh_dict', 'is', 'None', ':', 'thresh_dict', '=', '{', '}', 'row_idx', '=', 'set', '(', ')', 'col_idx', '=', 'set', '(', ')', 'include', '=', 'self', '.', 'results', 'if', 'include', 'is', 'None', 'else', 'include', 'include', '=', 'list', '(', 'set', '(', 'include', ')', '-', 'set', '(', 'exclude', ')', ')', 'if', 'exclude', 'is', 'not', 'None', 'else', 'include', 'for', 'diagnostic', 'in', 'include', ':', 'if', 'diagnostic', 'in', 'thresh_dict', ':', 'flagged', '=', 'self', '.', 'flag', '(', 'diagnostic', ',', 'thresh_dict', '[', 'diagnostic', ']', ')', 'else', ':', 'flagged', '=', 'self', '.', 'flag', '(', 'diagnostic', ')', 'if', 'diagnostic', '==', "'RowMahalanobisDistances'", ':', 'row_idx', '=', 'row_idx', '.', 'union', '(', 'flagged', ')', 'else', ':', 'col_idx', '=', 'col_idx', '.', 'union', '(', 'flagged', ')', 'return', 'sorted', '(', 'list', '(', 'row_idx', ')', ')', ',', 'sorted', '(', 'list', '(', 'col_idx', ')', ')'] | Returns indices of (rows, columns) that satisfy flag() on any
diagnostic. Uses user-provided thresholds in thresh_dict/
Args:
thresh_dict (dict): dictionary of diagnostic->threshold functions
include (list): optional sublist of diagnostics to flag
exclude (list): optional sublist of diagnostics to not flag | ['Returns', 'indices', 'of', '(', 'rows', 'columns', ')', 'that', 'satisfy', 'flag', '()', 'on', 'any', 'diagnostic', '.', 'Uses', 'user', '-', 'provided', 'thresholds', 'in', 'thresh_dict', '/'] | train | https://github.com/tyarkoni/pliers/blob/5b3385960ebd8c6ef1e86dd5e1be0080b2cb7f2b/pliers/diagnostics/diagnostics.py#L186-L214 |
1,391 | contentful/contentful-management.py | contentful_management/space.py | Space.create_attributes | def create_attributes(klass, attributes, previous_object=None):
"""Attributes for space creation."""
if previous_object is not None:
return {'name': attributes.get('name', previous_object.name)}
return {
'name': attributes.get('name', ''),
'defaultLocale': attributes['default_locale']
} | python | def create_attributes(klass, attributes, previous_object=None):
"""Attributes for space creation."""
if previous_object is not None:
return {'name': attributes.get('name', previous_object.name)}
return {
'name': attributes.get('name', ''),
'defaultLocale': attributes['default_locale']
} | ['def', 'create_attributes', '(', 'klass', ',', 'attributes', ',', 'previous_object', '=', 'None', ')', ':', 'if', 'previous_object', 'is', 'not', 'None', ':', 'return', '{', "'name'", ':', 'attributes', '.', 'get', '(', "'name'", ',', 'previous_object', '.', 'name', ')', '}', 'return', '{', "'name'", ':', 'attributes', '.', 'get', '(', "'name'", ',', "''", ')', ',', "'defaultLocale'", ':', 'attributes', '[', "'default_locale'", ']', '}'] | Attributes for space creation. | ['Attributes', 'for', 'space', 'creation', '.'] | train | https://github.com/contentful/contentful-management.py/blob/707dd30883b98a10c7ff0f7f5bdb8edbdc1d8df0/contentful_management/space.py#L54-L62 |
1,392 | inveniosoftware/invenio-files-rest | invenio_files_rest/models.py | MultipartObject.merge_parts | def merge_parts(self, version_id=None, **kwargs):
"""Merge parts into object version."""
self.file.update_checksum(**kwargs)
with db.session.begin_nested():
obj = ObjectVersion.create(
self.bucket,
self.key,
_file_id=self.file_id,
version_id=version_id
)
self.delete()
return obj | python | def merge_parts(self, version_id=None, **kwargs):
"""Merge parts into object version."""
self.file.update_checksum(**kwargs)
with db.session.begin_nested():
obj = ObjectVersion.create(
self.bucket,
self.key,
_file_id=self.file_id,
version_id=version_id
)
self.delete()
return obj | ['def', 'merge_parts', '(', 'self', ',', 'version_id', '=', 'None', ',', '*', '*', 'kwargs', ')', ':', 'self', '.', 'file', '.', 'update_checksum', '(', '*', '*', 'kwargs', ')', 'with', 'db', '.', 'session', '.', 'begin_nested', '(', ')', ':', 'obj', '=', 'ObjectVersion', '.', 'create', '(', 'self', '.', 'bucket', ',', 'self', '.', 'key', ',', '_file_id', '=', 'self', '.', 'file_id', ',', 'version_id', '=', 'version_id', ')', 'self', '.', 'delete', '(', ')', 'return', 'obj'] | Merge parts into object version. | ['Merge', 'parts', 'into', 'object', 'version', '.'] | train | https://github.com/inveniosoftware/invenio-files-rest/blob/59a950da61cc8d5882a03c6fde6db2e2ed10befd/invenio_files_rest/models.py#L1490-L1501 |
1,393 | fabioz/PyDev.Debugger | third_party/pep8/pycodestyle.py | whitespace_around_comma | def whitespace_around_comma(logical_line):
r"""Avoid extraneous whitespace after a comma or a colon.
Note: these checks are disabled by default
Okay: a = (1, 2)
E241: a = (1, 2)
E242: a = (1,\t2)
"""
line = logical_line
for m in WHITESPACE_AFTER_COMMA_REGEX.finditer(line):
found = m.start() + 1
if '\t' in m.group():
yield found, "E242 tab after '%s'" % m.group()[0]
else:
yield found, "E241 multiple spaces after '%s'" % m.group()[0] | python | def whitespace_around_comma(logical_line):
r"""Avoid extraneous whitespace after a comma or a colon.
Note: these checks are disabled by default
Okay: a = (1, 2)
E241: a = (1, 2)
E242: a = (1,\t2)
"""
line = logical_line
for m in WHITESPACE_AFTER_COMMA_REGEX.finditer(line):
found = m.start() + 1
if '\t' in m.group():
yield found, "E242 tab after '%s'" % m.group()[0]
else:
yield found, "E241 multiple spaces after '%s'" % m.group()[0] | ['def', 'whitespace_around_comma', '(', 'logical_line', ')', ':', 'line', '=', 'logical_line', 'for', 'm', 'in', 'WHITESPACE_AFTER_COMMA_REGEX', '.', 'finditer', '(', 'line', ')', ':', 'found', '=', 'm', '.', 'start', '(', ')', '+', '1', 'if', "'\\t'", 'in', 'm', '.', 'group', '(', ')', ':', 'yield', 'found', ',', '"E242 tab after \'%s\'"', '%', 'm', '.', 'group', '(', ')', '[', '0', ']', 'else', ':', 'yield', 'found', ',', '"E241 multiple spaces after \'%s\'"', '%', 'm', '.', 'group', '(', ')', '[', '0', ']'] | r"""Avoid extraneous whitespace after a comma or a colon.
Note: these checks are disabled by default
Okay: a = (1, 2)
E241: a = (1, 2)
E242: a = (1,\t2) | ['r', 'Avoid', 'extraneous', 'whitespace', 'after', 'a', 'comma', 'or', 'a', 'colon', '.'] | train | https://github.com/fabioz/PyDev.Debugger/blob/ed9c4307662a5593b8a7f1f3389ecd0e79b8c503/third_party/pep8/pycodestyle.py#L791-L806 |
1,394 | Accelize/pycosio | pycosio/storage/s3.py | _S3System._remove | def _remove(self, client_kwargs):
"""
Remove an object.
args:
client_kwargs (dict): Client arguments.
"""
with _handle_client_error():
# Object
if 'Key' in client_kwargs:
return self.client.delete_object(**client_kwargs)
# Bucket
return self.client.delete_bucket(Bucket=client_kwargs['Bucket']) | python | def _remove(self, client_kwargs):
"""
Remove an object.
args:
client_kwargs (dict): Client arguments.
"""
with _handle_client_error():
# Object
if 'Key' in client_kwargs:
return self.client.delete_object(**client_kwargs)
# Bucket
return self.client.delete_bucket(Bucket=client_kwargs['Bucket']) | ['def', '_remove', '(', 'self', ',', 'client_kwargs', ')', ':', 'with', '_handle_client_error', '(', ')', ':', '# Object', 'if', "'Key'", 'in', 'client_kwargs', ':', 'return', 'self', '.', 'client', '.', 'delete_object', '(', '*', '*', 'client_kwargs', ')', '# Bucket', 'return', 'self', '.', 'client', '.', 'delete_bucket', '(', 'Bucket', '=', 'client_kwargs', '[', "'Bucket'", ']', ')'] | Remove an object.
args:
client_kwargs (dict): Client arguments. | ['Remove', 'an', 'object', '.'] | train | https://github.com/Accelize/pycosio/blob/1cc1f8fdf5394d92918b7bae2bfa682169ccc48c/pycosio/storage/s3.py#L247-L260 |
1,395 | aws/sagemaker-containers | src/sagemaker_containers/_env.py | read_hyperparameters | def read_hyperparameters(): # type: () -> dict
"""Read the hyperparameters from /opt/ml/input/config/hyperparameters.json.
For more information about hyperparameters.json:
https://docs.aws.amazon.com/sagemaker/latest/dg/your-algorithms-training-algo.html#your-algorithms-training-algo-running-container-hyperparameters
Returns:
(dict[string, object]): a dictionary containing the hyperparameters.
"""
hyperparameters = _read_json(hyperparameters_file_dir)
deserialized_hps = {}
for k, v in hyperparameters.items():
try:
v = json.loads(v)
except (ValueError, TypeError):
logger.info("Failed to parse hyperparameter %s value %s to Json.\n"
"Returning the value itself", k, v)
deserialized_hps[k] = v
return deserialized_hps | python | def read_hyperparameters(): # type: () -> dict
"""Read the hyperparameters from /opt/ml/input/config/hyperparameters.json.
For more information about hyperparameters.json:
https://docs.aws.amazon.com/sagemaker/latest/dg/your-algorithms-training-algo.html#your-algorithms-training-algo-running-container-hyperparameters
Returns:
(dict[string, object]): a dictionary containing the hyperparameters.
"""
hyperparameters = _read_json(hyperparameters_file_dir)
deserialized_hps = {}
for k, v in hyperparameters.items():
try:
v = json.loads(v)
except (ValueError, TypeError):
logger.info("Failed to parse hyperparameter %s value %s to Json.\n"
"Returning the value itself", k, v)
deserialized_hps[k] = v
return deserialized_hps | ['def', 'read_hyperparameters', '(', ')', ':', '# type: () -> dict', 'hyperparameters', '=', '_read_json', '(', 'hyperparameters_file_dir', ')', 'deserialized_hps', '=', '{', '}', 'for', 'k', ',', 'v', 'in', 'hyperparameters', '.', 'items', '(', ')', ':', 'try', ':', 'v', '=', 'json', '.', 'loads', '(', 'v', ')', 'except', '(', 'ValueError', ',', 'TypeError', ')', ':', 'logger', '.', 'info', '(', '"Failed to parse hyperparameter %s value %s to Json.\\n"', '"Returning the value itself"', ',', 'k', ',', 'v', ')', 'deserialized_hps', '[', 'k', ']', '=', 'v', 'return', 'deserialized_hps'] | Read the hyperparameters from /opt/ml/input/config/hyperparameters.json.
For more information about hyperparameters.json:
https://docs.aws.amazon.com/sagemaker/latest/dg/your-algorithms-training-algo.html#your-algorithms-training-algo-running-container-hyperparameters
Returns:
(dict[string, object]): a dictionary containing the hyperparameters. | ['Read', 'the', 'hyperparameters', 'from', '/', 'opt', '/', 'ml', '/', 'input', '/', 'config', '/', 'hyperparameters', '.', 'json', '.'] | train | https://github.com/aws/sagemaker-containers/blob/0030f07abbaf22a55d986d97274d7a8d1aa1f10c/src/sagemaker_containers/_env.py#L197-L219 |
1,396 | googledatalab/pydatalab | solutionbox/ml_workbench/xgboost/trainer/feature_transforms.py | get_transformed_feature_indices | def get_transformed_feature_indices(features, stats):
"""Returns information about the transformed features.
Returns:
List in the from
[(transformed_feature_name, {size: int, index_start: int})]
"""
feature_indices = []
index_start = 1
for name, transform in sorted(six.iteritems(features)):
transform_name = transform['transform']
source_column = transform['source_column']
info = {}
if transform_name in [IDENTITY_TRANSFORM, SCALE_TRANSFORM]:
info['size'] = 1
elif transform_name in [ONE_HOT_TRANSFORM, MULTI_HOT_TRANSFORM]:
info['size'] = stats['column_stats'][source_column]['vocab_size']
elif transform_name == IMAGE_TRANSFORM:
info['size'] = IMAGE_BOTTLENECK_TENSOR_SIZE
elif transform_name == TARGET_TRANSFORM:
info['size'] = 0
else:
raise ValueError('xgboost does not support transform "%s"' % transform)
info['index_start'] = index_start
index_start += info['size']
feature_indices.append((name, info))
return feature_indices | python | def get_transformed_feature_indices(features, stats):
"""Returns information about the transformed features.
Returns:
List in the from
[(transformed_feature_name, {size: int, index_start: int})]
"""
feature_indices = []
index_start = 1
for name, transform in sorted(six.iteritems(features)):
transform_name = transform['transform']
source_column = transform['source_column']
info = {}
if transform_name in [IDENTITY_TRANSFORM, SCALE_TRANSFORM]:
info['size'] = 1
elif transform_name in [ONE_HOT_TRANSFORM, MULTI_HOT_TRANSFORM]:
info['size'] = stats['column_stats'][source_column]['vocab_size']
elif transform_name == IMAGE_TRANSFORM:
info['size'] = IMAGE_BOTTLENECK_TENSOR_SIZE
elif transform_name == TARGET_TRANSFORM:
info['size'] = 0
else:
raise ValueError('xgboost does not support transform "%s"' % transform)
info['index_start'] = index_start
index_start += info['size']
feature_indices.append((name, info))
return feature_indices | ['def', 'get_transformed_feature_indices', '(', 'features', ',', 'stats', ')', ':', 'feature_indices', '=', '[', ']', 'index_start', '=', '1', 'for', 'name', ',', 'transform', 'in', 'sorted', '(', 'six', '.', 'iteritems', '(', 'features', ')', ')', ':', 'transform_name', '=', 'transform', '[', "'transform'", ']', 'source_column', '=', 'transform', '[', "'source_column'", ']', 'info', '=', '{', '}', 'if', 'transform_name', 'in', '[', 'IDENTITY_TRANSFORM', ',', 'SCALE_TRANSFORM', ']', ':', 'info', '[', "'size'", ']', '=', '1', 'elif', 'transform_name', 'in', '[', 'ONE_HOT_TRANSFORM', ',', 'MULTI_HOT_TRANSFORM', ']', ':', 'info', '[', "'size'", ']', '=', 'stats', '[', "'column_stats'", ']', '[', 'source_column', ']', '[', "'vocab_size'", ']', 'elif', 'transform_name', '==', 'IMAGE_TRANSFORM', ':', 'info', '[', "'size'", ']', '=', 'IMAGE_BOTTLENECK_TENSOR_SIZE', 'elif', 'transform_name', '==', 'TARGET_TRANSFORM', ':', 'info', '[', "'size'", ']', '=', '0', 'else', ':', 'raise', 'ValueError', '(', '\'xgboost does not support transform "%s"\'', '%', 'transform', ')', 'info', '[', "'index_start'", ']', '=', 'index_start', 'index_start', '+=', 'info', '[', "'size'", ']', 'feature_indices', '.', 'append', '(', '(', 'name', ',', 'info', ')', ')', 'return', 'feature_indices'] | Returns information about the transformed features.
Returns:
List in the from
[(transformed_feature_name, {size: int, index_start: int})] | ['Returns', 'information', 'about', 'the', 'transformed', 'features', '.'] | train | https://github.com/googledatalab/pydatalab/blob/d9031901d5bca22fe0d5925d204e6698df9852e1/solutionbox/ml_workbench/xgboost/trainer/feature_transforms.py#L415-L444 |
1,397 | angr/angr | angr/state_plugins/heap/heap_ptmalloc.py | SimHeapPTMalloc._find_bck | def _find_bck(self, chunk):
"""
Simply finds the free chunk that would be the backwards chunk relative to the chunk at ptr. Hence, the free head
and all other metadata are unaltered by this function.
"""
cur = self.free_head_chunk
if cur is None:
return None
fwd = cur.fwd_chunk()
if cur == fwd:
return cur
# At this point there should be at least two free chunks in the heap
if cur < chunk:
while cur < fwd < chunk:
cur = fwd
fwd = cur.fwd_chunk()
return cur
else:
while fwd != self.free_head_chunk:
cur = fwd
fwd = cur.fwd_chunk()
return cur | python | def _find_bck(self, chunk):
"""
Simply finds the free chunk that would be the backwards chunk relative to the chunk at ptr. Hence, the free head
and all other metadata are unaltered by this function.
"""
cur = self.free_head_chunk
if cur is None:
return None
fwd = cur.fwd_chunk()
if cur == fwd:
return cur
# At this point there should be at least two free chunks in the heap
if cur < chunk:
while cur < fwd < chunk:
cur = fwd
fwd = cur.fwd_chunk()
return cur
else:
while fwd != self.free_head_chunk:
cur = fwd
fwd = cur.fwd_chunk()
return cur | ['def', '_find_bck', '(', 'self', ',', 'chunk', ')', ':', 'cur', '=', 'self', '.', 'free_head_chunk', 'if', 'cur', 'is', 'None', ':', 'return', 'None', 'fwd', '=', 'cur', '.', 'fwd_chunk', '(', ')', 'if', 'cur', '==', 'fwd', ':', 'return', 'cur', '# At this point there should be at least two free chunks in the heap', 'if', 'cur', '<', 'chunk', ':', 'while', 'cur', '<', 'fwd', '<', 'chunk', ':', 'cur', '=', 'fwd', 'fwd', '=', 'cur', '.', 'fwd_chunk', '(', ')', 'return', 'cur', 'else', ':', 'while', 'fwd', '!=', 'self', '.', 'free_head_chunk', ':', 'cur', '=', 'fwd', 'fwd', '=', 'cur', '.', 'fwd_chunk', '(', ')', 'return', 'cur'] | Simply finds the free chunk that would be the backwards chunk relative to the chunk at ptr. Hence, the free head
and all other metadata are unaltered by this function. | ['Simply', 'finds', 'the', 'free', 'chunk', 'that', 'would', 'be', 'the', 'backwards', 'chunk', 'relative', 'to', 'the', 'chunk', 'at', 'ptr', '.', 'Hence', 'the', 'free', 'head', 'and', 'all', 'other', 'metadata', 'are', 'unaltered', 'by', 'this', 'function', '.'] | train | https://github.com/angr/angr/blob/4e2f97d56af5419ee73bdb30482c8dd8ff5f3e40/angr/state_plugins/heap/heap_ptmalloc.py#L281-L302 |
1,398 | tomnor/channelpack | channelpack/pulltxt.py | PatternPull.file_rows | def file_rows(self, fo):
"""Return the lines in the file as a list.
fo is the open file object."""
rows = []
for i in range(NUMROWS):
line = fo.readline()
if not line:
break
rows += [line]
return rows | python | def file_rows(self, fo):
"""Return the lines in the file as a list.
fo is the open file object."""
rows = []
for i in range(NUMROWS):
line = fo.readline()
if not line:
break
rows += [line]
return rows | ['def', 'file_rows', '(', 'self', ',', 'fo', ')', ':', 'rows', '=', '[', ']', 'for', 'i', 'in', 'range', '(', 'NUMROWS', ')', ':', 'line', '=', 'fo', '.', 'readline', '(', ')', 'if', 'not', 'line', ':', 'break', 'rows', '+=', '[', 'line', ']', 'return', 'rows'] | Return the lines in the file as a list.
fo is the open file object. | ['Return', 'the', 'lines', 'in', 'the', 'file', 'as', 'a', 'list', '.'] | train | https://github.com/tomnor/channelpack/blob/9ad3cd11c698aed4c0fc178385b2ba38a7d0efae/channelpack/pulltxt.py#L101-L113 |
1,399 | larryng/narwal | narwal/reddit.py | Reddit.flair | def flair(self, r, name, text, css_class):
"""Login required. Sets flair for a user. See https://github.com/reddit/reddit/wiki/API%3A-flair. Returns True or raises :class:`exceptions.UnexpectedResponse` if non-"truthy" value in response.
URL: ``http://www.reddit.com/api/flair``
:param r: name of subreddit
:param name: name of the user
:param text: flair text to assign
:param css_class: CSS class to assign to flair text
"""
data = dict(r=r, name=name, text=text, css_class=css_class)
j = self.post('api', 'flair', data=data)
return assert_truthy(j) | python | def flair(self, r, name, text, css_class):
"""Login required. Sets flair for a user. See https://github.com/reddit/reddit/wiki/API%3A-flair. Returns True or raises :class:`exceptions.UnexpectedResponse` if non-"truthy" value in response.
URL: ``http://www.reddit.com/api/flair``
:param r: name of subreddit
:param name: name of the user
:param text: flair text to assign
:param css_class: CSS class to assign to flair text
"""
data = dict(r=r, name=name, text=text, css_class=css_class)
j = self.post('api', 'flair', data=data)
return assert_truthy(j) | ['def', 'flair', '(', 'self', ',', 'r', ',', 'name', ',', 'text', ',', 'css_class', ')', ':', 'data', '=', 'dict', '(', 'r', '=', 'r', ',', 'name', '=', 'name', ',', 'text', '=', 'text', ',', 'css_class', '=', 'css_class', ')', 'j', '=', 'self', '.', 'post', '(', "'api'", ',', "'flair'", ',', 'data', '=', 'data', ')', 'return', 'assert_truthy', '(', 'j', ')'] | Login required. Sets flair for a user. See https://github.com/reddit/reddit/wiki/API%3A-flair. Returns True or raises :class:`exceptions.UnexpectedResponse` if non-"truthy" value in response.
URL: ``http://www.reddit.com/api/flair``
:param r: name of subreddit
:param name: name of the user
:param text: flair text to assign
:param css_class: CSS class to assign to flair text | ['Login', 'required', '.', 'Sets', 'flair', 'for', 'a', 'user', '.', 'See', 'https', ':', '//', 'github', '.', 'com', '/', 'reddit', '/', 'reddit', '/', 'wiki', '/', 'API%3A', '-', 'flair', '.', 'Returns', 'True', 'or', 'raises', ':', 'class', ':', 'exceptions', '.', 'UnexpectedResponse', 'if', 'non', '-', 'truthy', 'value', 'in', 'response', '.', 'URL', ':', 'http', ':', '//', 'www', '.', 'reddit', '.', 'com', '/', 'api', '/', 'flair', ':', 'param', 'r', ':', 'name', 'of', 'subreddit', ':', 'param', 'name', ':', 'name', 'of', 'the', 'user', ':', 'param', 'text', ':', 'flair', 'text', 'to', 'assign', ':', 'param', 'css_class', ':', 'CSS', 'class', 'to', 'assign', 'to', 'flair', 'text'] | train | https://github.com/larryng/narwal/blob/58c409a475c8ed865579a61d7010162ed8cef597/narwal/reddit.py#L877-L889 |
Subsets and Splits