Read the Docs build information Build id: 1309407 Project: icb-scanpy Version: 2426 Commit: 0fcfa2994c40cb38ddf870277e59b098130ae73b Date: 2023-02-21T11:21:45.605173Z State: finished Success: False [rtd-command-info] start-time: 2023-02-21T11:21:47.311272Z, end-time: 2023-02-21T11:21:49.822021Z, 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: 2023-02-21T11:21:50.035331Z, end-time: 2023-02-21T11:21:50.716531Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2426/head:external-2426 From https://github.com/scverse/scanpy * [new ref] refs/pull/2426/head -> external-2426 [rtd-command-info] start-time: 2023-02-21T11:21:50.940515Z, end-time: 2023-02-21T11:21:51.144832Z, duration: 0, exit-code: 0 git checkout --force 0fcfa2994c40cb38ddf870277e59b098130ae73b Note: switching to '0fcfa2994c40cb38ddf870277e59b098130ae73b'. 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 0fcfa299 Nearest Neighbour sklearn [rtd-command-info] start-time: 2023-02-21T11:21:51.332098Z, end-time: 2023-02-21T11:21:51.408797Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-02-21T11:21:56.592816Z, end-time: 2023-02-21T11:21:56.701628Z, duration: 0, exit-code: 0 asdf global python 3.9.15 [rtd-command-info] start-time: 2023-02-21T11:21:57.193253Z, end-time: 2023-02-21T11:21:58.204162Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.15.final.0-64 in 663ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2426, 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: 2023-02-21T11:21:58.415466Z, end-time: 2023-02-21T11:22:09.985312Z, duration: 11, 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/2426/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/2426/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: 2023-02-21T11:22:10.189780Z, end-time: 2023-02-21T11:22:22.401181Z, duration: 12, 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 53.0 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 148.0 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting 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end-time: 2023-02-21T11:23:43.027703Z, duration: 80, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting tqdm Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 9.2 MB/s eta 0:00:00 Collecting scipy>=1.4 Downloading scipy-1.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 188.1 MB/s eta 0:00:00 Collecting 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/tmp/pip-ephem-wheel-cache-5ke0v5to/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+g0fcfa299-py3-none-any.whl size=11486274 sha256=be86778ce15c8fc2c28b021decc91716e420af1bae21bb0822420167ea29983c Stored in directory: /tmp/pip-ephem-wheel-cache-5ke0v5to/wheels/cd/f3/1c/4d3d9087ac7e3f02c6aab374433787e533d78b40121b332215 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=525e6d8f31ba1a5fcd03dfb4176c6e1175ea90f492b0b903f091f2c2bb407a2f Stored in directory: /tmp/pip-ephem-wheel-cache-5ke0v5to/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=02f625e3872c728130b03c9d76d26bc7ec20c245ddff0174bb9851871fdbd59f Stored in directory: /tmp/pip-ephem-wheel-cache-5ke0v5to/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=7cd1bf7c60b6c38e860278f73e8835c114fc338018e34a5203bebc5820bf7c18 Stored in directory: /tmp/pip-ephem-wheel-cache-5ke0v5to/wheels/dc/07/ac/bff79052fd6222d1239b228cd24a47222f227c2350f9c4df01 Successfully built umap-learn scanpy session-info pynndescent python-igraph Installing collected packages: texttable, stdlib_list, zipp, typing-extensions, 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, sphinxcontrib-jquery, 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, sphinx-rtd-theme, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, myst-parser, umap-learn, 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-4.38.0 get_version-3.5.4 h5py-3.8.0 igraph-0.10.4 importlib-metadata-6.0.0 importlib-resources-5.12.0 joblib-1.2.0 kiwisolver-1.4.4 llvmlite-0.39.1 markdown-it-py-2.1.0 matplotlib-3.7.0 mdit-py-plugins-0.3.4 mdurl-0.1.2 myst-parser-0.18.1 natsort-8.2.0 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 pyyaml-6.0 scanpy-1.10.0.dev32+g0fcfa299 scanpydoc-0.7.7 scikit-learn-1.2.1 scipy-1.10.1 seaborn-0.12.2 session-info-1.0.0 setuptools-67.3.3 sphinx-5.3.0 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-2.0.0 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-4.64.1 typing-extensions-4.5.0 umap-learn-0.5.3 zipp-3.14.0 [rtd-command-info] start-time: 2023-02-21T11:23:44.535612Z, end-time: 2023-02-21T11:23:44.610615Z, 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': "2426", 'version_slug': "2426", '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': '0fcfa2994c40cb38ddf870277e59b098130ae73b', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '0fcfa2994c40cb38ddf870277e59b098130ae73b', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '0fcfa2994c40cb38ddf870277e59b098130ae73b', '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': '0fcfa299', } # 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/2426' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1309407/' 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: 2023-02-21T11:23:44.890871Z, end-time: 2023-02-21T11:23:50.424466Z, duration: 5, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v5.3.0 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2426/lib/python3.9/site-packages/sphinx/config.py", line 350, in eval_config_file exec(code, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/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/2426/lib/python3.9/site-packages/sphinx/cmd/build.py", line 276, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2426/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/2426/lib/python3.9/site-packages/sphinx/config.py", line 172, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2426/lib/python3.9/site-packages/sphinx/config.py", line 363, 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/2426/lib/python3.9/site-packages/sphinx/config.py", line 350, in eval_config_file exec(code, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/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/2426/lib/python3.9/site-packages/sphinx/config.py", line 350, in eval_config_file exec(code, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/__init__.py", line 16, in from . import plotting as pl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/__init__.py", line 1, in from ._anndata import ( File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/scanpy/plotting/_anndata.py", line 28, in from . import _utils File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2426/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