Read the Docs build information Build id: 1370387 Project: icb-scanpy Version: 2454 Commit: 45ce12988f87948e5b1992ad3ba14313893b7f76 Date: 2023-03-23T11:12:15.402305Z State: finished Success: False [rtd-command-info] start-time: 2023-03-23T11:12:17.363844Z, end-time: 2023-03-23T11:12:20.012890Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2023-03-23T11:12:20.247388Z, end-time: 2023-03-23T11:12:20.962125Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2454/head:external-2454 From https://github.com/scverse/scanpy * [new ref] refs/pull/2454/head -> external-2454 [rtd-command-info] start-time: 2023-03-23T11:12:21.155481Z, end-time: 2023-03-23T11:12:21.242619Z, duration: 0, exit-code: 0 git checkout --force 45ce12988f87948e5b1992ad3ba14313893b7f76 Note: switching to '45ce12988f87948e5b1992ad3ba14313893b7f76'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 45ce1298 Removing Master Changes [rtd-command-info] start-time: 2023-03-23T11:12:21.487480Z, end-time: 2023-03-23T11:12:21.551940Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-03-23T11:12:26.766378Z, end-time: 2023-03-23T11:12:27.321813Z, duration: 0, exit-code: 0 asdf global python 3.9.15 [rtd-command-info] start-time: 2023-03-23T11:12:28.261458Z, end-time: 2023-03-23T11:12:29.612949Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.15.final.0-64 in 671ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454, 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==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2023-03-23T11:12:29.864092Z, end-time: 2023-03-23T11:12:42.774521Z, duration: 12, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-23.0.1-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages (57.4.0) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 57.4.0 Uninstalling setuptools-57.4.0: Successfully uninstalled setuptools-57.4.0 Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-23.0.1 setuptools-58.2.0 [rtd-command-info] start-time: 2023-03-23T11:12:42.965447Z, end-time: 2023-03-23T11:12:51.830420Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0 Collecting pillow Downloading Pillow-9.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 58.8 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 152.4 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting 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sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-9.4.0 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.15 [rtd-command-info] start-time: 2023-03-23T11:12:52.047262Z, end-time: 2023-03-23T11:14:08.227441Z, duration: 76, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing 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eta 0:00:00 Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages (from patsy->scanpy==1.10.0.dev32+g45ce1298) (1.16.0) Collecting pynndescent>=0.5 Downloading pynndescent-0.5.8.tar.gz (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 267.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting markdown-it-py<3.0.0,>=1.0.0 Downloading markdown_it_py-2.2.0-py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 190.8 MB/s eta 0:00:00 Collecting pyyaml Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 661.8/661.8 kB 270.4 MB/s eta 0:00:00 Collecting mdit-py-plugins~=0.3.4 Downloading mdit_py_plugins-0.3.5-py3-none-any.whl (52 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.1/52.1 kB 155.4 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wheels for collected packages: umap-learn, scanpy, session-info, pynndescent, python-igraph Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82830 sha256=8938ca7dd1905cf2dec2e2028cdc06beec81b17a1952d93ebb4421c59576f02f Stored in directory: /tmp/pip-ephem-wheel-cache-5x_rsedg/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9 Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.10.0.dev32+g45ce1298-py3-none-any.whl size=11486780 sha256=1537cc6bbe343026aeb0174cfb0f1275ad7b9f379d498a1757771ca56d0ef269 Stored in directory: /tmp/pip-ephem-wheel-cache-5x_rsedg/wheels/32/fa/c8/992af4c2e9aa75b5916b1b70067d1a3b65c703c4e9b44c75fa Building wheel for session-info (setup.py): started Building wheel for session-info (setup.py): finished with status 'done' Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8045 sha256=abc3dbe3e9d97a0638136112414ac0558fe80d31c2ca31cc8a4ff62fc4414ad7 Stored in directory: /tmp/pip-ephem-wheel-cache-5x_rsedg/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6 Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55511 sha256=2d54f88b06265f7be7dc3f3d3bbc2c324023508856a4d3786193b4e650844bf4 Stored in directory: /tmp/pip-ephem-wheel-cache-5x_rsedg/wheels/b9/89/cc/59ab91ef5b21dc2ab3635528d7d227f49dfc9169905dcb959d Building wheel for python-igraph (setup.py): started Building wheel for python-igraph (setup.py): finished with status 'done' Created wheel for python-igraph: filename=python_igraph-0.10.4-py3-none-any.whl size=9076 sha256=1c847f7fd7afc5c0fdd917f38f2912c8a338461cd585e062d7cc681f699c783c Stored in directory: /tmp/pip-ephem-wheel-cache-5x_rsedg/wheels/dc/07/ac/bff79052fd6222d1239b228cd24a47222f227c2350f9c4df01 Successfully built umap-learn scanpy session-info pynndescent python-igraph Installing collected packages: texttable, stdlib_list, pytz, zipp, tqdm, threadpoolctl, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, session-info, pyyaml, python-dateutil, pyparsing, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, Jinja2, igraph, fonttools, dunamai, docutils, cycler, scipy, python-igraph, patsy, pandas, numba, markdown-it-py, importlib-resources, importlib-metadata, h5py, get_version, contourpy, statsmodels, sphinx, scikit-learn, mdit-py-plugins, matplotlib, anndata, sphinxcontrib-jquery, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, myst-parser, umap-learn, sphinx-rtd-theme, scanpy Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed Jinja2-3.1.2 anndata-0.8.0 contourpy-1.0.7 cycler-0.11.0 docutils-0.18.1 dunamai-1.16.0 fonttools-4.39.2 get_version-3.5.4 h5py-3.8.0 igraph-0.10.4 importlib-metadata-6.1.0 importlib-resources-5.12.0 joblib-1.2.0 kiwisolver-1.4.4 llvmlite-0.39.1 markdown-it-py-2.2.0 matplotlib-3.7.1 mdit-py-plugins-0.3.5 mdurl-0.1.2 myst-parser-1.0.0 natsort-8.3.1 networkx-3.0 numba-0.56.4 numpy-1.23.5 pandas-1.5.3 patsy-0.5.3 pynndescent-0.5.8 pyparsing-3.0.9 python-dateutil-2.8.2 python-igraph-0.10.4 pytz-2022.7.1 pyyaml-6.0 scanpy-1.10.0.dev32+g45ce1298 scanpydoc-0.7.8 scikit-learn-1.2.2 scipy-1.10.1 seaborn-0.12.2 session-info-1.0.0 setuptools-67.6.0 sphinx-6.1.3 sphinx-autodoc-typehints-1.22 sphinx-rtd-theme-1.2.0 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.13.5 stdlib_list-0.8.0 texttable-1.6.7 threadpoolctl-3.1.0 tqdm-4.65.0 umap-learn-0.5.3 zipp-3.15.0 [rtd-command-info] start-time: 2023-03-23T11:14:09.899089Z, end-time: 2023-03-23T11:14:09.959981Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa from packaging.version import parse as parse_version # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '2.0' # Nicer param docs suppress_warnings = [ 'ref.citation', 'myst.header', # https://github.com/executablebooks/MyST-Parser/issues/262 ] # General information project = 'Scanpy' author = 'Scanpy development team' copyright = f'{datetime.now():%Y}, the Scanpy development team.' version = scanpy.__version__.replace('.dirty', '') # Bumping the version updates all docs, so don't do that if parse_version(version).is_devrelease: parsed = parse_version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # default settings templates_path = ['_templates'] master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'myst_parser', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', # 'scanpydoc', # scanpydoc.elegant_typehints causes full doc rebuilds 'scanpydoc.rtd_github_links', 'scanpydoc.theme', 'scanpydoc.definition_list_typed_field', 'scanpydoc.autosummary_generate_imported', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images typehints_defaults = 'braces' scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('https://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/stable/', None), networkx=('https://networkx.org/documentation/stable/', None), numpy=('https://numpy.org/doc/stable/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), pytest=('https://docs.pytest.org/en/latest/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'scanpydoc' html_theme_options = dict( navigation_depth=4, logo_only=True, docsearch_index='scanpy', docsearch_key='fa4304eb95d2134997e3729553a674b2', ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.warningiserror = on_rtd # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", # If the docs are built with an old version of numpy, this will make it work: "numpy.random.RandomState": "numpy.random.mtrand.RandomState", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", "pandas.core.series.Series": "pandas.Series", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.plotting._utils._AxesSubplot'), ('py:class', 'scanpy._utils.Empty'), ('py:class', 'numpy.random.mtrand.RandomState'), # Will work once scipy 1.8 is released ('py:class', 'scipy.sparse.base.spmatrix'), ('py:class', 'scipy.sparse.csr.csr_matrix'), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root ########################################################################### # 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "2454", 'version_slug': "2454", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy.readthedocs.io/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': '45ce12988f87948e5b1992ad3ba14313893b7f76', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '45ce12988f87948e5b1992ad3ba14313893b7f76', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '45ce12988f87948e5b1992ad3ba14313893b7f76', '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-17997319-2', 'commit': '45ce1298', } # 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(): html_context.update(context) 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 'external' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'https://github.com/scverse/scanpy/pull/2454' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1370387/' 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: 2023-03-23T11:14:10.212101Z, end-time: 2023-03-23T11:14:56.231490Z, duration: 46, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.1.3 Matplotlib is building the font cache; this may take a moment. Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/config.py", line 351, in eval_config_file exec(code, namespace) # NoQA: S102 File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_utils.py", line 35, in class _AxesSubplot(Axes, axes.SubplotBase, ABC): TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/cmd/build.py", line 279, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/application.py", line 202, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/config.py", line 173, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/config.py", line 364, in eval_config_file raise ConfigError(msg % traceback.format_exc()) from exc sphinx.errors.ConfigError: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/config.py", line 351, in eval_config_file exec(code, namespace) # NoQA: S102 File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_utils.py", line 35, in class _AxesSubplot(Axes, axes.SubplotBase, ABC): TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases Configuration error: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2454/lib/python3.9/site-packages/sphinx/config.py", line 351, in eval_config_file exec(code, namespace) # NoQA: S102 File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2454/scanpy/plotting/_utils.py", line 35, in class _AxesSubplot(Axes, axes.SubplotBase, ABC): TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases