prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  CI: Problem with `gen_cli.py`
  see: https://app.circleci.com/pipelines/github/mne-tools/mne-bids/4785/workflows/21ad6804-1cc2-42dd-9133-f24de2ea3db5/jobs/6923
  
  ```
  Traceback (most recent call last):
    File "/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/events.py", line 94, in emit
      results.append(listener.handler(self.app, *args))
    File "/home/circleci/project/doc/sphinxext/gen_cli.py", line 84, in generate_cli_rst
      output[0], output[2] = output[2], output[0]
  IndexError: list index out of range
  
  The above exception was the direct cause of the following exception:
  
  Traceback (most recent call last):
    File "/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/cmd/build.py", line 276, in build_main
      app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
    File "/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/application.py", line 262, in __init__
      self._init_builder()
    File "/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/application.py", line 335, in _init_builder
      self.events.emit('builder-inited')
    File "/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/events.py", line 105, in emit
      raise ExtensionError(__("Handler %r for event %r threw an exception") %
  sphinx.errors.ExtensionError: Handler <function generate_cli_rst at 0x7fe9bf90c160> for event 'builder-inited' threw an exception (exception: list index out of range)
  ```
  
  https://github.com/mne-tools/mne-bids/blob/46b0a5300ed5c17ca93b8bbf1d9542069597ef62/doc/sphinxext/gen_cli.py#L1
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  --- BEGIN FILES ---
  Path: `doc/sphinxext/gen_cli.py`
  Content:
  ```
  1 """Custom sphinx extension to generate docs for the command line interface.
  2 
  3 Inspired by MNE-Python's `gen_commands.py`
  4 see: github.com/mne-tools/mne-python/blob/main/doc/sphinxext/gen_commands.py
  5 """
  6 # Authors: Eric Larson <larson.eric.d@gmail.com>
  7 #          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
  8 #          Stefan Appelhoff <stefan.appelhoff@mailbox.org>
  9 #
  10 # License: BSD-3-Clause
  11 import os
  12 import glob
  13 from os import path as op
  14 import subprocess
  15 import sys
  16 
  17 import sphinx.util
  18 from mne.utils import run_subprocess, _replace_md5
  19 
  20 
  21 def setup(app):
  22     """Set up the app."""
  23     app.connect('builder-inited', generate_cli_rst)
  24 
  25 
  26 # Header markings go:
  27 # 1. =/= : Page title
  28 # 2. =   : Command name
  29 # 3. -/- : Command description
  30 # 4. -   : Command sections (Examples, Notes)
  31 
  32 header = """\
  33 :orphan:
  34 
  35 .. _python_cli:
  36 
  37 =====================================
  38 MNE-BIDS Command Line Interface (CLI)
  39 =====================================
  40 
  41 Here we list the MNE-BIDS tools that you can use from the command line.
  42 
  43 """
  44 
  45 command_rst = """
  46 
  47 .. _gen_%s:
  48 
  49 %s
  50 %s
  51 
  52 .. rst-class:: callout
  53 
  54 %s
  55 
  56 """
  57 
  58 
  59 def generate_cli_rst(app=None):
  60     """Generate the command line interface docs."""
  61     out_dir = op.abspath(op.join(op.dirname(__file__), '..', 'generated'))
  62     if not op.isdir(out_dir):
  63         os.mkdir(out_dir)
  64     out_fname = op.join(out_dir, 'cli.rst.new')
  65 
  66     cli_path = op.abspath(
  67         op.join(os.path.dirname(__file__), '..', '..', 'mne_bids', 'commands'))
  68     fnames = sorted([
  69         op.basename(fname)
  70         for fname in glob.glob(op.join(cli_path, 'mne_bids*.py'))])
  71     iterator = sphinx.util.status_iterator(
  72         fnames, 'generating MNE-BIDS cli help ... ', length=len(fnames))
  73     with open(out_fname, 'w', encoding='utf-8') as f:
  74         f.write(header)
  75         for fname in iterator:
  76             cmd_name = fname[:-3]
  77             run_name = op.join(cli_path, fname)
  78             output, _ = run_subprocess([sys.executable, run_name, '--help'],
  79                                        stdout=subprocess.PIPE,
  80                                        stderr=subprocess.PIPE, verbose=False)
  81             output = output.splitlines()
  82 
  83             # Swap usage and title lines
  84             output[0], output[2] = output[2], output[0]
  85 
  86             # Add header marking
  87             for idx in (1, 0):
  88                 output.insert(idx, '-' * len(output[0]))
  89 
  90             # Add code styling for the "Usage: " line
  91             for li, line in enumerate(output):
  92                 if line.startswith('Usage: mne_bids '):
  93                     output[li] = 'Usage: ``%s``' % line[7:]
  94                     break
  95 
  96             # Turn "Options:" into field list
  97             if 'Options:' in output:
  98                 ii = output.index('Options:')
  99                 output[ii] = 'Options'
  100                 output.insert(ii + 1, '-------')
  101                 output.insert(ii + 2, '')
  102                 output.insert(ii + 3, '.. rst-class:: field-list cmd-list')
  103                 output.insert(ii + 4, '')
  104             output = '\n'.join(output)
  105             f.write(command_rst % (cmd_name,
  106                                    cmd_name.replace('mne_bids_', 'mne_bids '),
  107                                    '=' * len(cmd_name),
  108                                    output))
  109     _replace_md5(out_fname)
  110     print('[Done]')
  111 
  112 
  113 # This is useful for testing/iterating to see what the result looks like
  114 if __name__ == '__main__':
  115     generate_cli_rst()
  116
  ```
  --- 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/doc/sphinxext/gen_cli.py b/doc/sphinxext/gen_cli.py
  --- a/doc/sphinxext/gen_cli.py
  +++ b/doc/sphinxext/gen_cli.py
  @@ -76,8 +76,7 @@
               cmd_name = fname[:-3]
               run_name = op.join(cli_path, fname)
               output, _ = run_subprocess([sys.executable, run_name, '--help'],
  -                                       stdout=subprocess.PIPE,
  -                                       stderr=subprocess.PIPE, verbose=False)
  +                                       verbose=False)
               output = output.splitlines()
   
               # Swap usage and title lines
  
verification_info: {"golden_diff": "diff --git a/doc/sphinxext/gen_cli.py b/doc/sphinxext/gen_cli.py\n--- a/doc/sphinxext/gen_cli.py\n+++ b/doc/sphinxext/gen_cli.py\n@@ -76,8 +76,7 @@\n             cmd_name = fname[:-3]\n             run_name = op.join(cli_path, fname)\n             output, _ = run_subprocess([sys.executable, run_name, '--help'],\n-                                       stdout=subprocess.PIPE,\n-                                       stderr=subprocess.PIPE, verbose=False)\n+                                       verbose=False)\n             output = output.splitlines()\n \n             # Swap usage and title lines\n", "issue": "CI: Problem with `gen_cli.py`\nsee: https://app.circleci.com/pipelines/github/mne-tools/mne-bids/4785/workflows/21ad6804-1cc2-42dd-9133-f24de2ea3db5/jobs/6923\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/events.py\", line 94, in emit\r\n    results.append(listener.handler(self.app, *args))\r\n  File \"/home/circleci/project/doc/sphinxext/gen_cli.py\", line 84, in generate_cli_rst\r\n    output[0], output[2] = output[2], output[0]\r\nIndexError: list index out of range\r\n\r\nThe above exception was the direct cause of the following exception:\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/cmd/build.py\", line 276, in build_main\r\n    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,\r\n  File \"/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/application.py\", line 262, in __init__\r\n    self._init_builder()\r\n  File \"/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/application.py\", line 335, in _init_builder\r\n    self.events.emit('builder-inited')\r\n  File \"/home/circleci/mne_bids_env/lib/python3.9/site-packages/sphinx/events.py\", line 105, in emit\r\n    raise ExtensionError(__(\"Handler %r for event %r threw an exception\") %\r\nsphinx.errors.ExtensionError: Handler <function generate_cli_rst at 0x7fe9bf90c160> for event 'builder-inited' threw an exception (exception: list index out of range)\r\n```\r\n\r\nhttps://github.com/mne-tools/mne-bids/blob/46b0a5300ed5c17ca93b8bbf1d9542069597ef62/doc/sphinxext/gen_cli.py#L1\n", "before_files": [{"content": "\"\"\"Custom sphinx extension to generate docs for the command line interface.\n\nInspired by MNE-Python's `gen_commands.py`\nsee: github.com/mne-tools/mne-python/blob/main/doc/sphinxext/gen_commands.py\n\"\"\"\n# Authors: Eric Larson <larson.eric.d@gmail.com>\n#          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>\n#          Stefan Appelhoff <stefan.appelhoff@mailbox.org>\n#\n# License: BSD-3-Clause\nimport os\nimport glob\nfrom os import path as op\nimport subprocess\nimport sys\n\nimport sphinx.util\nfrom mne.utils import run_subprocess, _replace_md5\n\n\ndef setup(app):\n    \"\"\"Set up the app.\"\"\"\n    app.connect('builder-inited', generate_cli_rst)\n\n\n# Header markings go:\n# 1. =/= : Page title\n# 2. =   : Command name\n# 3. -/- : Command description\n# 4. -   : Command sections (Examples, Notes)\n\nheader = \"\"\"\\\n:orphan:\n\n.. _python_cli:\n\n=====================================\nMNE-BIDS Command Line Interface (CLI)\n=====================================\n\nHere we list the MNE-BIDS tools that you can use from the command line.\n\n\"\"\"\n\ncommand_rst = \"\"\"\n\n.. _gen_%s:\n\n%s\n%s\n\n.. rst-class:: callout\n\n%s\n\n\"\"\"\n\n\ndef generate_cli_rst(app=None):\n    \"\"\"Generate the command line interface docs.\"\"\"\n    out_dir = op.abspath(op.join(op.dirname(__file__), '..', 'generated'))\n    if not op.isdir(out_dir):\n        os.mkdir(out_dir)\n    out_fname = op.join(out_dir, 'cli.rst.new')\n\n    cli_path = op.abspath(\n        op.join(os.path.dirname(__file__), '..', '..', 'mne_bids', 'commands'))\n    fnames = sorted([\n        op.basename(fname)\n        for fname in glob.glob(op.join(cli_path, 'mne_bids*.py'))])\n    iterator = sphinx.util.status_iterator(\n        fnames, 'generating MNE-BIDS cli help ... ', length=len(fnames))\n    with open(out_fname, 'w', encoding='utf-8') as f:\n        f.write(header)\n        for fname in iterator:\n            cmd_name = fname[:-3]\n            run_name = op.join(cli_path, fname)\n            output, _ = run_subprocess([sys.executable, run_name, '--help'],\n                                       stdout=subprocess.PIPE,\n                                       stderr=subprocess.PIPE, verbose=False)\n            output = output.splitlines()\n\n            # Swap usage and title lines\n            output[0], output[2] = output[2], output[0]\n\n            # Add header marking\n            for idx in (1, 0):\n                output.insert(idx, '-' * len(output[0]))\n\n            # Add code styling for the \"Usage: \" line\n            for li, line in enumerate(output):\n                if line.startswith('Usage: mne_bids '):\n                    output[li] = 'Usage: ``%s``' % line[7:]\n                    break\n\n            # Turn \"Options:\" into field list\n            if 'Options:' in output:\n                ii = output.index('Options:')\n                output[ii] = 'Options'\n                output.insert(ii + 1, '-------')\n                output.insert(ii + 2, '')\n                output.insert(ii + 3, '.. rst-class:: field-list cmd-list')\n                output.insert(ii + 4, '')\n            output = '\\n'.join(output)\n            f.write(command_rst % (cmd_name,\n                                   cmd_name.replace('mne_bids_', 'mne_bids '),\n                                   '=' * len(cmd_name),\n                                   output))\n    _replace_md5(out_fname)\n    print('[Done]')\n\n\n# This is useful for testing/iterating to see what the result looks like\nif __name__ == '__main__':\n    generate_cli_rst()\n", "path": "doc/sphinxext/gen_cli.py"}], "after_files": [{"content": "\"\"\"Custom sphinx extension to generate docs for the command line interface.\n\nInspired by MNE-Python's `gen_commands.py`\nsee: github.com/mne-tools/mne-python/blob/main/doc/sphinxext/gen_commands.py\n\"\"\"\n# Authors: Eric Larson <larson.eric.d@gmail.com>\n#          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>\n#          Stefan Appelhoff <stefan.appelhoff@mailbox.org>\n#\n# License: BSD-3-Clause\nimport os\nimport glob\nfrom os import path as op\nimport subprocess\nimport sys\n\nimport sphinx.util\nfrom mne.utils import run_subprocess, _replace_md5\n\n\ndef setup(app):\n    \"\"\"Set up the app.\"\"\"\n    app.connect('builder-inited', generate_cli_rst)\n\n\n# Header markings go:\n# 1. =/= : Page title\n# 2. =   : Command name\n# 3. -/- : Command description\n# 4. -   : Command sections (Examples, Notes)\n\nheader = \"\"\"\\\n:orphan:\n\n.. _python_cli:\n\n=====================================\nMNE-BIDS Command Line Interface (CLI)\n=====================================\n\nHere we list the MNE-BIDS tools that you can use from the command line.\n\n\"\"\"\n\ncommand_rst = \"\"\"\n\n.. _gen_%s:\n\n%s\n%s\n\n.. rst-class:: callout\n\n%s\n\n\"\"\"\n\n\ndef generate_cli_rst(app=None):\n    \"\"\"Generate the command line interface docs.\"\"\"\n    out_dir = op.abspath(op.join(op.dirname(__file__), '..', 'generated'))\n    if not op.isdir(out_dir):\n        os.mkdir(out_dir)\n    out_fname = op.join(out_dir, 'cli.rst.new')\n\n    cli_path = op.abspath(\n        op.join(os.path.dirname(__file__), '..', '..', 'mne_bids', 'commands'))\n    fnames = sorted([\n        op.basename(fname)\n        for fname in glob.glob(op.join(cli_path, 'mne_bids*.py'))])\n    iterator = sphinx.util.status_iterator(\n        fnames, 'generating MNE-BIDS cli help ... ', length=len(fnames))\n    with open(out_fname, 'w', encoding='utf-8') as f:\n        f.write(header)\n        for fname in iterator:\n            cmd_name = fname[:-3]\n            run_name = op.join(cli_path, fname)\n            output, _ = run_subprocess([sys.executable, run_name, '--help'],\n                                       verbose=False)\n            output = output.splitlines()\n\n            # Swap usage and title lines\n            output[0], output[2] = output[2], output[0]\n\n            # Add header marking\n            for idx in (1, 0):\n                output.insert(idx, '-' * len(output[0]))\n\n            # Add code styling for the \"Usage: \" line\n            for li, line in enumerate(output):\n                if line.startswith('Usage: mne_bids '):\n                    output[li] = 'Usage: ``%s``' % line[7:]\n                    break\n\n            # Turn \"Options:\" into field list\n            if 'Options:' in output:\n                ii = output.index('Options:')\n                output[ii] = 'Options'\n                output.insert(ii + 1, '-------')\n                output.insert(ii + 2, '')\n                output.insert(ii + 3, '.. rst-class:: field-list cmd-list')\n                output.insert(ii + 4, '')\n            output = '\\n'.join(output)\n            f.write(command_rst % (cmd_name,\n                                   cmd_name.replace('mne_bids_', 'mne_bids '),\n                                   '=' * len(cmd_name),\n                                   output))\n    _replace_md5(out_fname)\n    print('[Done]')\n\n\n# This is useful for testing/iterating to see what the result looks like\nif __name__ == '__main__':\n    generate_cli_rst()\n", "path": "doc/sphinxext/gen_cli.py"}]}