prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  Remove use of Bio._py3k (Python 2 / 3 compatibility)
  As of Biopython 1.76 (released December 2019), we are dropping Python 2 support and focusing on Python 3.6 or later. This means we no longer need our (internal) Python 2 vs 3 compatibility library ``Bio._py3k`` (which is a bit like the third party library ``six``).
  
  This issue is suitable and specifically targeting first time contributors.
  
  There are lots of cases:
  
  ```
  $ grep _py3k Bio*/*.py Bio/*/*.py Bio/*/*/*.py
  Bio/File.py:from Bio._py3k import basestring
  Bio/MarkovModel.py:        from Bio._py3k import StringIO
  Bio/Seq.py:from Bio._py3k import range
  Bio/Seq.py:from Bio._py3k import basestring
  ...
  ```
  
  Example One
  ------------
  
  Taking the first example, ``from Bio._py3k import basestring`` we see that this is defined under Python 3 as an alias of ``str``:
  
  https://github.com/biopython/biopython/blob/biopython-176/Bio/_py3k/__init__.py#L56
  
  ```python
      # Lots of our Python 2 code uses isinstance(x, basestring)
      # which after 2to3 becomes isinstance(x, str)
      basestring = str
      unicode = str
  ```
  
  Therefore the fix for ``Bio/File.py`` is to remove the ``from Bio._py3k import basestring`` line, and update where ``basestring`` was used to instead use ``str``, which in this case means editing one line:
  
  ```python
  if isinstance(handleish, basestring):
  ```
  
  with:
  
  ```python
  if isinstance(handleish, str):
  ```
  
  Example Two
  ------------
  
  Taking the second example, ``Bio/MarkovModel.py`` has ``from Bio._py3k import StringIO`` which we find on Python 3 can just be replaced with ``from io import StringIO``
  
  https://github.com/biopython/biopython/blob/biopython-176/Bio/_py3k/__init__.py#L130
  
  Contributing
  -----------
  
  Could any newcomer wanting to work on this first comment on this issue saying which file(s) they are going to start with (e.g. ``Bio/File.py``, or ``BioSQL/``) to avoid duplication of effort.
  
  (*Update: The consensus was to switch to be function or constant instead, since they generally require the same technique/fix each time*)
  
  Then read https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst and setup ``flake8`` on your machine.
  
  Then make a pull request making the necessary changes so that those files no longer import from ``Bio._py3k``. Once that's done, you could pick some more to work on.
  
  Eventually there will be nothing using ``Bio._py3k`` and that code itself can be removed, and this issue closed.
  
  </issue>
  <code>
  [start of Bio/_py3k/__init__.py]
  1 # Copyright 2010-2018 by Peter Cock.  All rights reserved.
  2 #
  3 # This file is part of the Biopython distribution and governed by your
  4 # choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
  5 # Please see the LICENSE file that should have been included as part of this
  6 # package.
  7 """Python 3 compatibility tools (PRIVATE).
  8 
  9 Once we drop support for Python 2, the whole of Bio._py3k will
  10 go away.
  11 """
  12 
  13 # From the point of view of pep8 and flake8, there are lots of issues with
  14 # this file. This line tells flake8 to ignore it for quality assurance:
  15 # flake8: noqa
  16 
  17 import sys
  18 
  19 import codecs
  20 
  21 
  22 def _bytes_bytearray_to_str(s):
  23     """If s is bytes or bytearray, convert to a unicode string (PRIVATE)."""
  24     if isinstance(s, (bytes, bytearray)):
  25         return s.decode()
  26     return s
  27 
  28 
  29 import io
  30 import locale
  31 
  32 # Python 3.4 onwards, the standard library wrappers should work:
  33 def _binary_to_string_handle(handle):
  34     """Treat a binary (bytes) handle like a text (unicode) handle (PRIVATE)."""
  35     try:
  36         # If this is a network handle from urllib,
  37         # the HTTP headers may tell us the encoding.
  38         encoding = handle.headers.get_content_charset()
  39     except AttributeError:
  40         encoding = None
  41     if encoding is None:
  42         # The W3C recommendation is:
  43         # When no explicit charset parameter is provided by the sender,
  44         # media subtypes of the "text" type are defined to have a default
  45         # charset value of "ISO-8859-1" when received via HTTP.
  46         # "ISO-8859-1" is also known as 'latin-1'
  47         # See the following for more detail:
  48         # https://www.w3.org/Protocols/rfc2616/rfc2616-sec3.html#sec3.7.1
  49         encoding = "latin-1"
  50     wrapped = io.TextIOWrapper(io.BufferedReader(handle), encoding=encoding)
  51     try:
  52         # If wrapping an online handle, this is nice to have:
  53         wrapped.url = handle.url
  54     except AttributeError:
  55         pass
  56     return wrapped
  57 
  58 
  59 # On Python 3 urllib, urllib2, and urlparse were merged:
  60 from urllib.request import urlopen, Request, urlparse, urlcleanup
  61 from urllib.parse import urlencode, quote
  62 from urllib.error import URLError, HTTPError
  63
  [end of Bio/_py3k/__init__.py]
  </code>
  
  I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply. Please respond with a single patch file in the following format.
  <patch>
  diff --git a/file.py b/file.py
  --- a/file.py
  +++ b/file.py
  @@ -1,27 +1,35 @@
   def euclidean(a, b):
  -    while b:
  -        a, b = b, a % b
  -    return a
  +    if b == 0:
  +        return a
  +    return euclidean(b, a % b)
   
   
   def bresenham(x0, y0, x1, y1):
       points = []
       dx = abs(x1 - x0)
       dy = abs(y1 - y0)
  -    sx = 1 if x0 < x1 else -1
  -    sy = 1 if y0 < y1 else -1
  -    err = dx - dy
  +    x, y = x0, y0
  +    sx = -1 if x0 > x1 else 1
  +    sy = -1 if y0 > y1 else 1
   
  -    while True:
  -        points.append((x0, y0))
  -        if x0 == x1 and y0 == y1:
  -            break
  -        e2 = 2 * err
  -        if e2 > -dy:
  -            err -= dy
  -            x0 += sx
  -        if e2 < dx:
  -            err += dx
  -            y0 += sy
  +    if dx > dy:
  +        err = dx / 2.0
  +        while x != x1:
  +            points.append((x, y))
  +            err -= dy
  +            if err < 0:
  +                y += sy
  +                err += dx
  +            x += sx
  +    else:
  +        err = dy / 2.0
  +        while y != y1:
  +            points.append((x, y))
  +            err -= dx
  +            if err < 0:
  +                x += sx
  +                err += dy
  +            y += sy
  +
  +    points.append((x, y))
       return points
  
  </patch>
golden_diff: diff --git a/Bio/_py3k/__init__.py b/Bio/_py3k/__init__.py
  --- a/Bio/_py3k/__init__.py
  +++ b/Bio/_py3k/__init__.py
  @@ -14,20 +14,7 @@
   # this file. This line tells flake8 to ignore it for quality assurance:
   # flake8: noqa
   
  -import sys
  -
  -import codecs
  -
  -
  -def _bytes_bytearray_to_str(s):
  -    """If s is bytes or bytearray, convert to a unicode string (PRIVATE)."""
  -    if isinstance(s, (bytes, bytearray)):
  -        return s.decode()
  -    return s
  -
  -
   import io
  -import locale
   
   # Python 3.4 onwards, the standard library wrappers should work:
   def _binary_to_string_handle(handle):
  @@ -54,9 +41,3 @@
       except AttributeError:
           pass
       return wrapped
  -
  -
  -# On Python 3 urllib, urllib2, and urlparse were merged:
  -from urllib.request import urlopen, Request, urlparse, urlcleanup
  -from urllib.parse import urlencode, quote
  -from urllib.error import URLError, HTTPError
  
verification_info: {"golden_diff": "diff --git a/Bio/_py3k/__init__.py b/Bio/_py3k/__init__.py\n--- a/Bio/_py3k/__init__.py\n+++ b/Bio/_py3k/__init__.py\n@@ -14,20 +14,7 @@\n # this file. This line tells flake8 to ignore it for quality assurance:\n # flake8: noqa\n \n-import sys\n-\n-import codecs\n-\n-\n-def _bytes_bytearray_to_str(s):\n-    \"\"\"If s is bytes or bytearray, convert to a unicode string (PRIVATE).\"\"\"\n-    if isinstance(s, (bytes, bytearray)):\n-        return s.decode()\n-    return s\n-\n-\n import io\n-import locale\n \n # Python 3.4 onwards, the standard library wrappers should work:\n def _binary_to_string_handle(handle):\n@@ -54,9 +41,3 @@\n     except AttributeError:\n         pass\n     return wrapped\n-\n-\n-# On Python 3 urllib, urllib2, and urlparse were merged:\n-from urllib.request import urlopen, Request, urlparse, urlcleanup\n-from urllib.parse import urlencode, quote\n-from urllib.error import URLError, HTTPError\n", "issue": "Remove use of Bio._py3k (Python 2 / 3 compatibility)\nAs of Biopython 1.76 (released December 2019), we are dropping Python 2 support and focusing on Python 3.6 or later. This means we no longer need our (internal) Python 2 vs 3 compatibility library ``Bio._py3k`` (which is a bit like the third party library ``six``).\r\n\r\nThis issue is suitable and specifically targeting first time contributors.\r\n\r\nThere are lots of cases:\r\n\r\n```\r\n$ grep _py3k Bio*/*.py Bio/*/*.py Bio/*/*/*.py\r\nBio/File.py:from Bio._py3k import basestring\r\nBio/MarkovModel.py:        from Bio._py3k import StringIO\r\nBio/Seq.py:from Bio._py3k import range\r\nBio/Seq.py:from Bio._py3k import basestring\r\n...\r\n```\r\n\r\nExample One\r\n------------\r\n\r\nTaking the first example, ``from Bio._py3k import basestring`` we see that this is defined under Python 3 as an alias of ``str``:\r\n\r\nhttps://github.com/biopython/biopython/blob/biopython-176/Bio/_py3k/__init__.py#L56\r\n\r\n```python\r\n    # Lots of our Python 2 code uses isinstance(x, basestring)\r\n    # which after 2to3 becomes isinstance(x, str)\r\n    basestring = str\r\n    unicode = str\r\n```\r\n\r\nTherefore the fix for ``Bio/File.py`` is to remove the ``from Bio._py3k import basestring`` line, and update where ``basestring`` was used to instead use ``str``, which in this case means editing one line:\r\n\r\n```python\r\nif isinstance(handleish, basestring):\r\n```\r\n\r\nwith:\r\n\r\n```python\r\nif isinstance(handleish, str):\r\n```\r\n\r\nExample Two\r\n------------\r\n\r\nTaking the second example, ``Bio/MarkovModel.py`` has ``from Bio._py3k import StringIO`` which we find on Python 3 can just be replaced with ``from io import StringIO``\r\n\r\nhttps://github.com/biopython/biopython/blob/biopython-176/Bio/_py3k/__init__.py#L130\r\n\r\nContributing\r\n-----------\r\n\r\nCould any newcomer wanting to work on this first comment on this issue saying which file(s) they are going to start with (e.g. ``Bio/File.py``, or ``BioSQL/``) to avoid duplication of effort.\r\n\r\n(*Update: The consensus was to switch to be function or constant instead, since they generally require the same technique/fix each time*)\r\n\r\nThen read https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst and setup ``flake8`` on your machine.\r\n\r\nThen make a pull request making the necessary changes so that those files no longer import from ``Bio._py3k``. Once that's done, you could pick some more to work on.\r\n\r\nEventually there will be nothing using ``Bio._py3k`` and that code itself can be removed, and this issue closed.\n", "before_files": [{"content": "# Copyright 2010-2018 by Peter Cock.  All rights reserved.\n#\n# This file is part of the Biopython distribution and governed by your\n# choice of the \"Biopython License Agreement\" or the \"BSD 3-Clause License\".\n# Please see the LICENSE file that should have been included as part of this\n# package.\n\"\"\"Python 3 compatibility tools (PRIVATE).\n\nOnce we drop support for Python 2, the whole of Bio._py3k will\ngo away.\n\"\"\"\n\n# From the point of view of pep8 and flake8, there are lots of issues with\n# this file. This line tells flake8 to ignore it for quality assurance:\n# flake8: noqa\n\nimport sys\n\nimport codecs\n\n\ndef _bytes_bytearray_to_str(s):\n    \"\"\"If s is bytes or bytearray, convert to a unicode string (PRIVATE).\"\"\"\n    if isinstance(s, (bytes, bytearray)):\n        return s.decode()\n    return s\n\n\nimport io\nimport locale\n\n# Python 3.4 onwards, the standard library wrappers should work:\ndef _binary_to_string_handle(handle):\n    \"\"\"Treat a binary (bytes) handle like a text (unicode) handle (PRIVATE).\"\"\"\n    try:\n        # If this is a network handle from urllib,\n        # the HTTP headers may tell us the encoding.\n        encoding = handle.headers.get_content_charset()\n    except AttributeError:\n        encoding = None\n    if encoding is None:\n        # The W3C recommendation is:\n        # When no explicit charset parameter is provided by the sender,\n        # media subtypes of the \"text\" type are defined to have a default\n        # charset value of \"ISO-8859-1\" when received via HTTP.\n        # \"ISO-8859-1\" is also known as 'latin-1'\n        # See the following for more detail:\n        # https://www.w3.org/Protocols/rfc2616/rfc2616-sec3.html#sec3.7.1\n        encoding = \"latin-1\"\n    wrapped = io.TextIOWrapper(io.BufferedReader(handle), encoding=encoding)\n    try:\n        # If wrapping an online handle, this is nice to have:\n        wrapped.url = handle.url\n    except AttributeError:\n        pass\n    return wrapped\n\n\n# On Python 3 urllib, urllib2, and urlparse were merged:\nfrom urllib.request import urlopen, Request, urlparse, urlcleanup\nfrom urllib.parse import urlencode, quote\nfrom urllib.error import URLError, HTTPError\n", "path": "Bio/_py3k/__init__.py"}]}