Read the Docs build information Build id: 677116 Project: icb-anndata Version: stable Commit: 0ec97410702f61b29acef80b6377d1232699fa94 Date: 2021-07-15T05:12:17.909200Z State: finished Success: False [rtd-command-info] start-time: 2021-07-15T05:12:19.324416Z, end-time: 2021-07-15T05:12:20.342324Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2021-07-15T05:12:20.465390Z, end-time: 2021-07-15T05:12:20.536403Z, duration: 0, exit-code: 0 git checkout --force 0ec97410702f61b29acef80b6377d1232699fa94 Note: checking out '0ec97410702f61b29acef80b6377d1232699fa94'. 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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 0ec9741 Release 0.7.6 (#549) [rtd-command-info] start-time: 2021-07-15T05:12:20.645368Z, end-time: 2021-07-15T05:12:20.711966Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-07-15T05:12:20.852805Z, end-time: 2021-07-15T05:12:20.916584Z, duration: 0, exit-code: 0 git rev-parse HEAD 0ec97410702f61b29acef80b6377d1232699fa94 [rtd-command-info] start-time: 2021-07-15T05:12:21.860434Z, end-time: 2021-07-15T05:12:37.582990Z, duration: 15, exit-code: 0 python3.6 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.6.12' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-07-15T05:12:37.712940Z, end-time: 2021-07-15T05:12:39.288071Z, duration: 1, 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/icb-anndata/envs/stable/lib/python3.6/site-packages (21.1.3) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (57.2.0) [rtd-command-info] start-time: 2021-07-15T05:12:39.399023Z, end-time: 2021-07-15T05:12:48.141865Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx<2) (57.2.0) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting packaging Downloading packaging-21.0-py3-none-any.whl (40 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp36-cp36m-manylinux2010_x86_64.whl (30 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB) Collecting idna<4,>=2.5 Downloading idna-3.2-py3-none-any.whl (59 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.2-py3-none-any.whl (35 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=537e6ad841c09fdbf7def00f2b92a499e8f884708dc820c6d01bbc7ef08cadca Stored in directory: /tmp/pip-ephem-wheel-cache-yl0roj85/wheels/98/4d/ec/1aa935d28cb63b7b16037fc990302a34244ac3b0601a4e0c00 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=f40278928715c0cd9b6d1b123e681e0b3dc683d4f0ac785e08596af725f7a213 Stored in directory: /tmp/pip-ephem-wheel-cache-yl0roj85/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.2 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.6 [rtd-command-info] start-time: 2021-07-15T05:12:48.250878Z, end-time: 2021-07-15T05:13:16.447358Z, duration: 28, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default. pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555. 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 wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting importlib_metadata>=0.7 Downloading importlib_metadata-4.6.1-py3-none-any.whl (17 kB) Collecting h5py Downloading h5py-3.1.0-cp36-cp36m-manylinux1_x86_64.whl (4.0 MB) Collecting natsort Downloading natsort-7.1.1-py3-none-any.whl (35 kB) Collecting numpy>=1.16.5 Downloading numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB) Requirement already satisfied: packaging>=20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from anndata==0.7.6) (21.0) Collecting scipy>1.4 Downloading scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl 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pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from packaging>=20->anndata==0.7.6) (2.4.7) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from pandas>=1.1.1->anndata==0.7.6) (2021.1) Collecting python-dateutil>=2.7.3 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas>=1.1.1->anndata==0.7.6) (1.16.0) Collecting get_version Downloading get_version-2.1-py3-none-any.whl (43 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->anndata==0.7.6) (3.0.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->anndata==0.7.6) (1.2.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->anndata==0.7.6) (57.2.0) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->anndata==0.7.6) (0.17.1) Requirement already satisfied: snowballstemmer>=1.1 in 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(from sphinx>=2.0.1->anndata==0.7.6) (2.9.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->anndata==0.7.6) (0.7.12) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->anndata==0.7.6) (2.0.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->anndata==0.7.6) (1.26.6) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->anndata==0.7.6) (2021.5.30) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->anndata==0.7.6) (3.2) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->anndata==0.7.6) (2.0.2) Collecting cached-property Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting docutils<0.18,>=0.14 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Building wheels for collected packages: anndata Building wheel for anndata (PEP 517): started Building wheel for anndata (PEP 517): finished with status 'done' Created wheel for anndata: filename=anndata-0.7.6-py3-none-any.whl size=127600 sha256=eb9e77ed5b908b41799d7cc4613b9158edeff99eac8c61b31083a57a063ba68f Stored in directory: /tmp/pip-ephem-wheel-cache-tofvx6hj/wheels/4d/29/49/d18764b9927c907616fd5fe1bddaf6f429d0ffb8eb95b6d97c Successfully built anndata Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, python-dateutil, numpy, docutils, cached-property, xlrd, sphinx, scipy, pandas, natsort, importlib-metadata, h5py, get-version, sphinx-rtd-theme, sphinx-issues, sphinx-autodoc-typehints, scanpydoc, anndata 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 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 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 anndata-0.7.6 cached-property-1.5.2 docutils-0.16 get-version-2.1 h5py-3.1.0 importlib-metadata-4.6.1 natsort-7.1.1 numpy-1.19.5 pandas-1.1.5 python-dateutil-2.8.2 scanpydoc-0.5.5 scipy-1.5.4 sphinx-4.1.1 sphinx-autodoc-typehints-1.12.0 sphinx-issues-1.2.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 typing-extensions-3.10.0.0 xlrd-1.2.0 zipp-3.5.0 [rtd-command-info] start-time: 2021-07-15T05:13:17.211989Z, end-time: 2021-07-15T05:13:17.287741Z, duration: 0, exit-code: 0 git rev-parse HEAD 0ec97410702f61b29acef80b6377d1232699fa94 [rtd-command-info] start-time: 2021-07-15T05:13:17.523058Z, end-time: 2021-07-15T05:13:17.597348Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime from sphinx.application import Sphinx HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")] import anndata # noqa logger = logging.getLogger(__name__) for generated in HERE.glob("anndata.*.rst"): generated.unlink() # -- General configuration ------------------------------------------------ needs_sphinx = "1.7" # autosummary bugfix # General information project = "anndata" author = anndata.__author__ copyright = f"{datetime.now():%Y}, {author}." version = anndata.__version__.replace(".dirty", "") release = version # default settings templates_path = ["_templates"] source_suffix = ".rst" master_doc = "index" default_role = "literal" exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] pygments_style = "sphinx" extensions = [ "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx_autodoc_typehints", # needs to be after napoleon "scanpydoc", *[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 nitpicky = True # Report broken links suppress_warnings = ["ref.citation"] def work_around_issue_6785(): """See https://github.com/sphinx-doc/sphinx/issues/6785""" from docutils.parsers.rst import directives from sphinx.ext import autodoc from sphinx.domains.python import PyAttribute # check if the code changes on the sphinx side and we can remove this assert autodoc.PropertyDocumenter.directivetype == "method" autodoc.PropertyDocumenter.directivetype = "attribute" def get_signature_prefix(self, sig: str) -> str: # TODO: abstract attributes return "property " if "property" in self.options else "" PyAttribute.option_spec["property"] = directives.flag PyAttribute.get_signature_prefix = get_signature_prefix def setup(app: Sphinx): work_around_issue_6785() # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead. app.warningiserror = True intersphinx_mapping = dict( h5py=("http://docs.h5py.org/en/latest/", None), loompy=("https://linnarssonlab.org/loompy/", None), numpy=("https://docs.scipy.org/doc/numpy/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), python=("https://docs.python.org/3", None), scipy=("https://docs.scipy.org/doc/scipy/reference/", None), sklearn=("https://scikit-learn.org/stable/", None), zarr=("https://zarr.readthedocs.io/en/stable/", None), xarray=("http://xarray.pydata.org/en/stable/", None), ) qualname_overrides = { "anndata._core.anndata.AnnData": "anndata.AnnData", # Temporarily "anndata._core.raw.Raw": "anndata.AnnData", "anndata._core.views.ArrayView": "numpy.ndarray", **{ f"anndata._core.aligned_mapping.{cls}{kind}": "typing.Mapping" for cls in "Layers AxisArrays PairwiseArrays".split() for kind in ["", "View"] }, } # -- Options for HTML output ---------------------------------------------- html_theme = "scanpydoc" html_theme_options = dict(navigation_depth=4) html_context = dict( display_github=True, # Integrate GitHub github_user="theislab", # Username github_repo="anndata", # Repo name github_version="master", # Version conf_py_path="/docs/", # Path in the checkout to the docs root ) issues_github_path = "{github_user}/{github_repo}".format_map(html_context) html_show_sphinx = False # -- 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", ) ] ########################################################################### # 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. 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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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': "stable", 'version_slug': "stable", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("0.4.1", "/en/0.4.1/"), ("0.3", "/en/0.3/"), ("refpaths", "/en/refpaths/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://anndata.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'proxied_api_host': '/_', 'github_repo': 'anndata', 'github_version': '0ec97410702f61b29acef80b6377d1232699fa94', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '0ec97410702f61b29acef80b6377d1232699fa94', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '0ec97410702f61b29acef80b6377d1232699fa94', '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': '0ec97410', } # 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 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/677116/' 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: 2021-07-15T05:13:17.701895Z, end-time: 2021-07-15T05:13:19.153710Z, duration: 1, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.1.1 loading translations [en]... done making output directory... done Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/cmd/build.py", line 279, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/application.py", line 251, in __init__ self.config.setup(self) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/conf.py", line 86, in setup work_around_issue_6785() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/conf.py", line 74, in work_around_issue_6785 assert autodoc.PropertyDocumenter.directivetype == "method" AttributeError: type object 'PropertyDocumenter' has no attribute 'directivetype' Exception occurred: File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/conf.py", line 74, in work_around_issue_6785 assert autodoc.PropertyDocumenter.directivetype == "method" AttributeError: type object 'PropertyDocumenter' has no attribute 'directivetype' The full traceback has been saved in /tmp/sphinx-err-ig2ptn00.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at . Thanks!