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prithviulm / qudi-core

A framework for modular measurement applications.
https://qudi-core-testing.readthedocs.io/en/latest/
GNU General Public License v3.0
0 stars 2 forks source link

[Bug] RTD build fails due to incomplete dependency specifications #1

Closed prithviulm closed 6 months ago

prithviulm commented 6 months ago

Version

Development

What is affected by the bug?

RTD reports the error Could not import extension IPython.sphinxext.ipython_directive (exception: No module named 'IPython') when building the docs. Locally building the docs using Make works in 26647177ab7597fd1f45bb22aeb8388a57256f91 (ignoring the numerous warnings and poor formatting but build is successful and the markdown files are parsed into html correctly). Need to fix the RTD build process to include installing the required and optional dependencies.

When does the bug occur?

On RTD when building the docs.

How do we replicate the issue?

Build the docs on RTD.

Expected behavior

Well the docs should build without problems!

Relevant log output

Read the Docs build information
Build id: 23433166
Project: qudi-core-testing
Version: latest
Commit: 26647177ab7597fd1f45bb22aeb8388a57256f91
Date: 2024-02-13T18:11:31.793254Z
State: finished
Success: False

[rtd-command-info] start-time: 2024-02-13T18:11:48.858372Z, end-time: 2024-02-13T18:11:49.414399Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/prithviulm/qudi-core.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-02-13T18:11:49.438116Z, end-time: 2024-02-13T18:11:49.842148Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main

[rtd-command-info] start-time: 2024-02-13T18:11:50.379656Z, end-time: 2024-02-13T18:11:50.506741Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 2664717 Added rtd config and edited files for myst syntax warnings. RTD site should work now, need to improve formatting and layout.

[rtd-command-info] start-time: 2024-02-13T18:11:50.552957Z, end-time: 2024-02-13T18:11:50.615385Z, duration: 0, exit-code: 0
git clean -d -f -f

[rtd-command-info] start-time: 2024-02-13T18:11:50.645422Z, end-time: 2024-02-13T18:11:50.710210Z, duration: 0, exit-code: 0
cat .readthedocs.yaml
# Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the OS, Python version and other tools you might need
build:
  os: ubuntu-22.04
  tools:
    python: "3.11"

# Build documentation in the "docs/" directory with Sphinx
sphinx:
  configuration: docs/conf.py
  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
  # builder: "dirhtml"
  # Fail on all warnings to avoid broken references
  # fail_on_warning: true

# Optional but recommended, declare the Python requirements required
# to build your documentation
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
# python:
#   install:
#     - requirements: docs/requirements.txt

[rtd-command-info] start-time: 2024-02-13T18:11:56.685061Z, end-time: 2024-02-13T18:11:56.766435Z, duration: 0, exit-code: 0
asdf global python 3.11.6

[rtd-command-info] start-time: 2024-02-13T18:11:57.147011Z, end-time: 2024-02-13T18:11:58.280359Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.6.final.0-64 in 786ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-02-13T18:11:58.330438Z, end-time: 2024-02-13T18:12:11.253433Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages (23.1)
Collecting pip
  Downloading pip-24.0-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 11.4 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages (67.6.1)
Collecting setuptools
  Downloading setuptools-69.1.0-py3-none-any.whl (819 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.3/819.3 kB 20.7 MB/s eta 0:00:00
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.0 setuptools-69.1.0

[rtd-command-info] start-time: 2024-02-13T18:12:11.296001Z, end-time: 2024-02-13T18:12:18.174514Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
Collecting sphinx
  Downloading sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB)
Collecting readthedocs-sphinx-ext
  Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting sphinxcontrib-applehelp (from sphinx)
  Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp (from sphinx)
  Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath (from sphinx)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx)
  Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx)
  Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-qthelp (from sphinx)
  Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB)
Collecting Jinja2>=3.0 (from sphinx)
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Collecting Pygments>=2.14 (from sphinx)
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Collecting docutils<0.21,>=0.18.1 (from sphinx)
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Collecting snowballstemmer>=2.0 (from sphinx)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
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Collecting babel>=2.9 (from sphinx)
  Downloading Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB)
Collecting alabaster<0.8,>=0.7 (from sphinx)
  Downloading alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB)
Collecting imagesize>=1.3 (from sphinx)
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting requests>=2.25.0 (from sphinx)
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting packaging>=21.0 (from sphinx)
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx)
  Downloading MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx)
  Downloading charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx)
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx)
  Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx)
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Downloading sphinx-7.2.6-py3-none-any.whl (3.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 66.3 MB/s eta 0:00:00
Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB)
Downloading alabaster-0.7.16-py3-none-any.whl (13 kB)
Downloading Babel-2.14.0-py3-none-any.whl (11.0 MB)
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Downloading docutils-0.20.1-py3-none-any.whl (572 kB)
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Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
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Downloading packaging-23.2-py3-none-any.whl (53 kB)
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Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
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Downloading requests-2.31.0-py3-none-any.whl (62 kB)
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Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB)
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Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB)
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Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB)
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Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB)
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Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB)
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Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
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Downloading MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB)
Downloading urllib3-2.2.0-py3-none-any.whl (120 kB)
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.0

[rtd-command-info] start-time: 2024-02-13T18:12:18.424377Z, end-time: 2024-02-13T18:12:18.489966Z, duration: 0, exit-code: 0
cat docs/conf.py
# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = 'qudi-core'
copyright = '2024, Ulm IQO'
author = 'Ulm IQO'

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

    # 'IPython.sphinxext.ipython_console_highlighting',
    # 'nbsphinx',
extensions = [
    'IPython.sphinxext.ipython_directive',
    'sphinx.ext.autodoc',
    'sphinx.ext.autosummary',
    'sphinx.ext.viewcode',
    'numpydoc',
    'myst_parser',
]

templates_path = ['_templates']
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']

autosummary_generate = True

# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = 'pydata_sphinx_theme'
# html_theme = 'sphinx_book_theme'
html_static_path = ['_static']

numpydoc_show_class_members = False
numpydoc_show_inherited_class_members = False
numpydoc_class_members_toctree = False

myst_heading_anchors = 4

###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################

#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.org/",
    'STATIC_URL': "https://assets.readthedocs.org/static/",
    'PRODUCTION_DOMAIN': "readthedocs.org",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'qudi-core-testing',
    'name': u'qudi-core-testing',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.org',
    'github_user': 'prithviulm',
    'proxied_api_host': '/_',
    'github_repo': 'qudi-core',
    'github_version': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-1',
    'commit': '26647177',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None

if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.org/projects/qudi-core-testing/builds/23433166/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2024-02-13T18:12:18.515092Z, end-time: 2024-02-13T18:12:19.082177Z, duration: 0, exit-code: 2
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages/sphinx/registry.py", line 447, in load_extension
    mod = import_module(extname)
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/.asdf/installs/python/3.11.6/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1126, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1126, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1140, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'IPython'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages/sphinx/cmd/build.py", line 293, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 233, in __init__
    self.setup_extension(extension)
  File "/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 406, in setup_extension
    self.registry.load_extension(self, extname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/qudi-core-testing/envs/latest/lib/python3.11/site-packages/sphinx/registry.py", line 450, in load_extension
    raise ExtensionError(__('Could not import extension %s') % extname,
sphinx.errors.ExtensionError: Could not import extension IPython.sphinxext.ipython_directive (exception: No module named 'IPython')

Extension error:
Could not import extension IPython.sphinxext.ipython_directive (exception: No module named 'IPython')

Additional Comments

Raw logs from RTD are pasted for reference.

Contact Details

No response

prithviulm commented 6 months ago

Fixed after 2d769a33be25d7b8fefd2d83afb87b183554d2b2. Added requirements-docs.txt and dropped python version to 3.10 for building docs. This is currently because th pinned version of pyside2==5.15.2.1 does not work on Python 3.11 and higher. Note that pyside2 and most other requirements are completely unnecessary as of now because we are just parsing the markdown files into html. See #3 for info.