prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Index Error updating from YT-3.4.0 to YT-3.5.1
  <!--To help us understand and resolve your issue, please fill out the form to
  the best of your ability.-->
  <!--You can feel free to delete the sections that do not apply.-->
  
  ### Bug report
  
  **Bug summary**
  
  Index error after yt upgrade 
  
  **Code for reproduction**
  
  <!--A minimum code snippet required to reproduce the bug, also minimizing the
  number of dependencies required.-->
  
  <!-- If you need to use a data file to trigger the issue you're having, consider
  using one of the datasets from the yt data hub (http://yt-project.org/data). If
  your issue cannot be triggered using a public dataset, you can use the yt
  curldrop (https://docs.hub.yt/services.html#curldrop) to share data
  files. Please include a link to the dataset in the issue if you use the
  curldrop.-->
  
  ```
  import yt
  from yt.units import kpc
  import matplotlib.pyplot as plt
  import numpy as np
  np.set_printoptions(threshold=1500)
  filename="/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_00018/info_00018.txt"
  ds=yt.load(filename)
  
  for i in sorted(ds.derived_field_list):
          print(i)
  ```
  
  **Actual outcome**
  
  <!--The output produced by the above code, which may be a screenshot, console
  output, etc.-->
  
  ```
  File "fields.py", line 10, in <module>
      for i in sorted(ds.derived_field_list):
    File "yt/data_objects/static_output.py", line 216, in ireq
      self.index
    File "yt/data_objects/static_output.py", line 509, in index
      self, dataset_type=self.dataset_type)
    File "yt/frontends/ramses/data_structures.py", line 236, in __init__
      super(RAMSESIndex, self).__init__(ds, dataset_type)
    File "yt/geometry/geometry_handler.py", line 50, in __init__
      self._setup_geometry()
    File "yt/geometry/oct_geometry_handler.py", line 25, in _setup_geometry
      self._initialize_oct_handler()
    File "yt/frontends/ramses/data_structures.py", line 245, in _initialize_oct_handler
      for i in cpu_list]
    File "yt/frontends/ramses/data_structures.py", line 245, in <listcomp>
      for i in cpu_list]
    File "yt/frontends/ramses/data_structures.py", line 82, in __init__
      self._read_amr_header()
    File "yt/frontends/ramses/data_structures.py", line 141, in _read_amr_header
      hvals.update(f.read_attrs(header))
    File "yt/utilities/cython_fortran_utils.pyx", line 223, in yt.utilities.cython_fortran_utils.FortranFile.read_attrs
  IndexError: index 0 is out of bounds for axis 0 with size 0
  ```
  
  **Expected outcome**
  
  has to print the fields in the data. Was working with yt 3.4.0
  
  **Version Information**
  <!--Please specify your platform and versions of the relevant libraries you are
  using:-->
    * Operating System: Mac
    * Python Version: 3.6
    * yt version: 3.5.1
    * Other Libraries (if applicable): 
  
  installed Anaconda separately and then did conda installation of YT using 'forge'
  <!--Please tell us how you installed yt and python e.g., from source,
  pip, conda. If you installed from conda, please specify which channel you used
  if not the default-->
  
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  --- BEGIN FILES ---
  Path: `yt/frontends/ramses/definitions.py`
  Content:
  ```
  1 """
  2 Definitions for RAMSES files
  3 
  4 
  5 
  6 
  7 """
  8 
  9 #-----------------------------------------------------------------------------
  10 # Copyright (c) 2013, yt Development Team.
  11 #
  12 # Distributed under the terms of the Modified BSD License.
  13 #
  14 # The full license is in the file COPYING.txt, distributed with this software.
  15 #-----------------------------------------------------------------------------
  16 
  17 # These functions are RAMSES-specific
  18 from yt.config import ytcfg
  19 from yt.funcs import mylog
  20 import re
  21 
  22 def ramses_header(hvals):
  23     header = ( ('ncpu', 1, 'i'),
  24                ('ndim', 1, 'i'),
  25                ('nx', 3, 'i'),
  26                ('nlevelmax', 1, 'i'),
  27                ('ngridmax', 1, 'i'),
  28                ('nboundary', 1, 'i'),
  29                ('ngrid_current', 1, 'i'),
  30                ('boxlen', 1, 'd'),
  31                ('nout', 3, 'i')
  32               )
  33     yield header
  34     # TODO: REMOVE
  35     noutput, iout, ifout = hvals['nout']
  36     next_set = ( ('tout', noutput, 'd'),
  37                  ('aout', noutput, 'd'),
  38                  ('t', 1, 'd'),
  39                  ('dtold', hvals['nlevelmax'], 'd'),
  40                  ('dtnew', hvals['nlevelmax'], 'd'),
  41                  ('nstep',  2, 'i'),
  42                  ('stat', 3, 'd'),
  43                  ('cosm', 7, 'd'),
  44                  ('timing', 5, 'd'),
  45                  ('mass_sph', 1, 'd') )
  46     yield next_set
  47 
  48 field_aliases = {
  49     'standard_five':     ('Density',
  50                           'x-velocity',
  51                           'y-velocity',
  52                           'z-velocity',
  53                           'Pressure'),
  54     'standard_six':      ('Density',
  55                           'x-velocity',
  56                           'y-velocity',
  57                           'z-velocity',
  58                           'Pressure',
  59                           'Metallicity'),
  60 
  61 }
  62 
  63 ## Regular expressions used to parse file descriptors
  64 VERSION_RE = re.compile(r'# version: *(\d+)')
  65 # This will match comma-separated strings, discarding whitespaces
  66 # on the left hand side
  67 VAR_DESC_RE = re.compile(r'\s*([^\s]+),\s*([^\s]+),\s*([^\s]+)')
  68 
  69 
  70 ## Configure family mapping
  71 particle_families = {
  72     'DM': 1,
  73     'star': 2,
  74     'cloud': 3,
  75     'dust': 4,
  76     'star_tracer': -2,
  77     'cloud_tracer': -3,
  78     'dust_tracer': -4,
  79     'gas_tracer': 0
  80 }
  81 
  82 if ytcfg.has_section('ramses-families'):
  83     for key in particle_families.keys():
  84         val = ytcfg.getint('ramses-families', key, fallback=None)
  85         if val is not None:
  86             mylog.info('Changing family %s from %s to %s' % (key, particle_families[key], val))
  87             particle_families[key] = val
  88
  ```
  --- END FILES ---
  
  Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.
  
  Here is an example:
  
  ```diff
  diff --git a/examples/server_async.py b/examples/server_async.py
  --- a/examples/server_async.py
  +++ b/examples/server_async.py
  @@ -313,4 +313,4 @@
   
   
   if __name__ == "__main__":
  -    asyncio.run(run_async_server("."), debug=True)
  +    asyncio.run(run_async_server(), debug=True)
  diff --git a/examples/server_sync.py b/examples/server_sync.py
  --- a/examples/server_sync.py
  +++ b/examples/server_sync.py
  @@ -313,5 +313,5 @@
   
   
   if __name__ == "__main__":
  -    server = run_sync_server(".")
  +    server = run_sync_server()
       server.shutdown()
  
  ```
  
golden_diff: diff --git a/yt/frontends/ramses/definitions.py b/yt/frontends/ramses/definitions.py
  --- a/yt/frontends/ramses/definitions.py
  +++ b/yt/frontends/ramses/definitions.py
  @@ -42,7 +42,8 @@
                    ('stat', 3, 'd'),
                    ('cosm', 7, 'd'),
                    ('timing', 5, 'd'),
  -                 ('mass_sph', 1, 'd') )
  +                 ('mass_sph', 1, 'd', True)
  +                 )
       yield next_set
   
   field_aliases = {
  
verification_info: {"golden_diff": "diff --git a/yt/frontends/ramses/definitions.py b/yt/frontends/ramses/definitions.py\n--- a/yt/frontends/ramses/definitions.py\n+++ b/yt/frontends/ramses/definitions.py\n@@ -42,7 +42,8 @@\n                  ('stat', 3, 'd'),\n                  ('cosm', 7, 'd'),\n                  ('timing', 5, 'd'),\n-                 ('mass_sph', 1, 'd') )\n+                 ('mass_sph', 1, 'd', True)\n+                 )\n     yield next_set\n \n field_aliases = {\n", "issue": "Index Error updating from YT-3.4.0 to YT-3.5.1\n<!--To help us understand and resolve your issue, please fill out the form to\r\nthe best of your ability.-->\r\n<!--You can feel free to delete the sections that do not apply.-->\r\n\r\n### Bug report\r\n\r\n**Bug summary**\r\n\r\nIndex error after yt upgrade \r\n\r\n**Code for reproduction**\r\n\r\n<!--A minimum code snippet required to reproduce the bug, also minimizing the\r\nnumber of dependencies required.-->\r\n\r\n<!-- If you need to use a data file to trigger the issue you're having, consider\r\nusing one of the datasets from the yt data hub (http://yt-project.org/data). If\r\nyour issue cannot be triggered using a public dataset, you can use the yt\r\ncurldrop (https://docs.hub.yt/services.html#curldrop) to share data\r\nfiles. Please include a link to the dataset in the issue if you use the\r\ncurldrop.-->\r\n\r\n```\r\nimport yt\r\nfrom yt.units import kpc\r\nimport matplotlib.pyplot as plt\r\nimport numpy as np\r\nnp.set_printoptions(threshold=1500)\r\nfilename=\"/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_00018/info_00018.txt\"\r\nds=yt.load(filename)\r\n\r\nfor i in sorted(ds.derived_field_list):\r\n        print(i)\r\n```\r\n\r\n**Actual outcome**\r\n\r\n<!--The output produced by the above code, which may be a screenshot, console\r\noutput, etc.-->\r\n\r\n```\r\nFile \"fields.py\", line 10, in <module>\r\n    for i in sorted(ds.derived_field_list):\r\n  File \"yt/data_objects/static_output.py\", line 216, in ireq\r\n    self.index\r\n  File \"yt/data_objects/static_output.py\", line 509, in index\r\n    self, dataset_type=self.dataset_type)\r\n  File \"yt/frontends/ramses/data_structures.py\", line 236, in __init__\r\n    super(RAMSESIndex, self).__init__(ds, dataset_type)\r\n  File \"yt/geometry/geometry_handler.py\", line 50, in __init__\r\n    self._setup_geometry()\r\n  File \"yt/geometry/oct_geometry_handler.py\", line 25, in _setup_geometry\r\n    self._initialize_oct_handler()\r\n  File \"yt/frontends/ramses/data_structures.py\", line 245, in _initialize_oct_handler\r\n    for i in cpu_list]\r\n  File \"yt/frontends/ramses/data_structures.py\", line 245, in <listcomp>\r\n    for i in cpu_list]\r\n  File \"yt/frontends/ramses/data_structures.py\", line 82, in __init__\r\n    self._read_amr_header()\r\n  File \"yt/frontends/ramses/data_structures.py\", line 141, in _read_amr_header\r\n    hvals.update(f.read_attrs(header))\r\n  File \"yt/utilities/cython_fortran_utils.pyx\", line 223, in yt.utilities.cython_fortran_utils.FortranFile.read_attrs\r\nIndexError: index 0 is out of bounds for axis 0 with size 0\r\n```\r\n\r\n**Expected outcome**\r\n\r\nhas to print the fields in the data. Was working with yt 3.4.0\r\n\r\n**Version Information**\r\n<!--Please specify your platform and versions of the relevant libraries you are\r\nusing:-->\r\n  * Operating System: Mac\r\n  * Python Version: 3.6\r\n  * yt version: 3.5.1\r\n  * Other Libraries (if applicable): \r\n\r\ninstalled Anaconda separately and then did conda installation of YT using 'forge'\r\n<!--Please tell us how you installed yt and python e.g., from source,\r\npip, conda. If you installed from conda, please specify which channel you used\r\nif not the default-->\r\n\n", "before_files": [{"content": "\"\"\"\nDefinitions for RAMSES files\n\n\n\n\n\"\"\"\n\n#-----------------------------------------------------------------------------\n# Copyright (c) 2013, yt Development Team.\n#\n# Distributed under the terms of the Modified BSD License.\n#\n# The full license is in the file COPYING.txt, distributed with this software.\n#-----------------------------------------------------------------------------\n\n# These functions are RAMSES-specific\nfrom yt.config import ytcfg\nfrom yt.funcs import mylog\nimport re\n\ndef ramses_header(hvals):\n    header = ( ('ncpu', 1, 'i'),\n               ('ndim', 1, 'i'),\n               ('nx', 3, 'i'),\n               ('nlevelmax', 1, 'i'),\n               ('ngridmax', 1, 'i'),\n               ('nboundary', 1, 'i'),\n               ('ngrid_current', 1, 'i'),\n               ('boxlen', 1, 'd'),\n               ('nout', 3, 'i')\n              )\n    yield header\n    # TODO: REMOVE\n    noutput, iout, ifout = hvals['nout']\n    next_set = ( ('tout', noutput, 'd'),\n                 ('aout', noutput, 'd'),\n                 ('t', 1, 'd'),\n                 ('dtold', hvals['nlevelmax'], 'd'),\n                 ('dtnew', hvals['nlevelmax'], 'd'),\n                 ('nstep',  2, 'i'),\n                 ('stat', 3, 'd'),\n                 ('cosm', 7, 'd'),\n                 ('timing', 5, 'd'),\n                 ('mass_sph', 1, 'd') )\n    yield next_set\n\nfield_aliases = {\n    'standard_five':     ('Density',\n                          'x-velocity',\n                          'y-velocity',\n                          'z-velocity',\n                          'Pressure'),\n    'standard_six':      ('Density',\n                          'x-velocity',\n                          'y-velocity',\n                          'z-velocity',\n                          'Pressure',\n                          'Metallicity'),\n\n}\n\n## Regular expressions used to parse file descriptors\nVERSION_RE = re.compile(r'# version: *(\\d+)')\n# This will match comma-separated strings, discarding whitespaces\n# on the left hand side\nVAR_DESC_RE = re.compile(r'\\s*([^\\s]+),\\s*([^\\s]+),\\s*([^\\s]+)')\n\n\n## Configure family mapping\nparticle_families = {\n    'DM': 1,\n    'star': 2,\n    'cloud': 3,\n    'dust': 4,\n    'star_tracer': -2,\n    'cloud_tracer': -3,\n    'dust_tracer': -4,\n    'gas_tracer': 0\n}\n\nif ytcfg.has_section('ramses-families'):\n    for key in particle_families.keys():\n        val = ytcfg.getint('ramses-families', key, fallback=None)\n        if val is not None:\n            mylog.info('Changing family %s from %s to %s' % (key, particle_families[key], val))\n            particle_families[key] = val\n", "path": "yt/frontends/ramses/definitions.py"}], "after_files": [{"content": "\"\"\"\nDefinitions for RAMSES files\n\n\n\n\n\"\"\"\n\n#-----------------------------------------------------------------------------\n# Copyright (c) 2013, yt Development Team.\n#\n# Distributed under the terms of the Modified BSD License.\n#\n# The full license is in the file COPYING.txt, distributed with this software.\n#-----------------------------------------------------------------------------\n\n# These functions are RAMSES-specific\nfrom yt.config import ytcfg\nfrom yt.funcs import mylog\nimport re\n\ndef ramses_header(hvals):\n    header = ( ('ncpu', 1, 'i'),\n               ('ndim', 1, 'i'),\n               ('nx', 3, 'i'),\n               ('nlevelmax', 1, 'i'),\n               ('ngridmax', 1, 'i'),\n               ('nboundary', 1, 'i'),\n               ('ngrid_current', 1, 'i'),\n               ('boxlen', 1, 'd'),\n               ('nout', 3, 'i')\n              )\n    yield header\n    # TODO: REMOVE\n    noutput, iout, ifout = hvals['nout']\n    next_set = ( ('tout', noutput, 'd'),\n                 ('aout', noutput, 'd'),\n                 ('t', 1, 'd'),\n                 ('dtold', hvals['nlevelmax'], 'd'),\n                 ('dtnew', hvals['nlevelmax'], 'd'),\n                 ('nstep',  2, 'i'),\n                 ('stat', 3, 'd'),\n                 ('cosm', 7, 'd'),\n                 ('timing', 5, 'd'),\n                 ('mass_sph', 1, 'd', True)\n                 )\n    yield next_set\n\nfield_aliases = {\n    'standard_five':     ('Density',\n                          'x-velocity',\n                          'y-velocity',\n                          'z-velocity',\n                          'Pressure'),\n    'standard_six':      ('Density',\n                          'x-velocity',\n                          'y-velocity',\n                          'z-velocity',\n                          'Pressure',\n                          'Metallicity'),\n\n}\n\n## Regular expressions used to parse file descriptors\nVERSION_RE = re.compile(r'# version: *(\\d+)')\n# This will match comma-separated strings, discarding whitespaces\n# on the left hand side\nVAR_DESC_RE = re.compile(r'\\s*([^\\s]+),\\s*([^\\s]+),\\s*([^\\s]+)')\n\n\n## Configure family mapping\nparticle_families = {\n    'DM': 1,\n    'star': 2,\n    'cloud': 3,\n    'dust': 4,\n    'star_tracer': -2,\n    'cloud_tracer': -3,\n    'dust_tracer': -4,\n    'gas_tracer': 0\n}\n\nif ytcfg.has_section('ramses-families'):\n    for key in particle_families.keys():\n        val = ytcfg.getint('ramses-families', key, fallback=None)\n        if val is not None:\n            mylog.info('Changing family %s from %s to %s' % (key, particle_families[key], val))\n            particle_families[key] = val\n", "path": "yt/frontends/ramses/definitions.py"}]}