Read the Docs build information Build id: 285082 Project: icb-anndata Version: latest Commit: c09124375ac2828bc325081d5efe630a3ab87e82 Date: 2020-02-06T09:24:22.454670Z State: finished Success: False [rtd-command-info] start-time: 2020-02-06T09:24:24.536755Z, end-time: 2020-02-06T09:24:24.758172Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/anndata.git [rtd-command-info] start-time: 2020-02-06T09:24:24.819660Z, end-time: 2020-02-06T09:24:25.647746Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/theislab/anndata - [deleted] (none) -> origin/fix-obs-drop - [deleted] (none) -> origin/series-error e4581ab..c091243 master -> origin/master [rtd-command-info] start-time: 2020-02-06T09:24:26.027399Z, end-time: 2020-02-06T09:24:26.643234Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was e4581ab Better Sphinx workaround (#309) HEAD is now at c091243 Fix version type (#315) [rtd-command-info] start-time: 2020-02-06T09:24:26.715422Z, end-time: 2020-02-06T09:24:26.946619Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-02-06T09:24:28.170552Z, end-time: 2020-02-06T09:24:33.555801Z, duration: 5, exit-code: 0 python3.6 -mvirtualenv --no-site-packages Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-02-06T09:24:33.624890Z, end-time: 2020-02-06T09:24:34.663158Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (20.0.2) [rtd-command-info] start-time: 2020-02-06T09:24:35.106206Z, end-time: 2020-02-06T09:24:48.355567Z, duration: 13, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 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<1.1 Downloading readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting packaging Downloading packaging-20.1-py2.py3-none-any.whl (36 kB) Collecting requests>=2.0.0 Downloading requests-2.22.0-py2.py3-none-any.whl (57 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.6-py2.py3-none-any.whl (67 kB) Collecting idna<2.9,>=2.5 Downloading idna-2.8-py2.py3-none-any.whl (58 kB) Collecting chardet<3.1.0,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting certifi>=2017.4.17 Downloading certifi-2019.11.28-py2.py3-none-any.whl (156 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 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=23754 sha256=0aa28465fdee1b9ff2dfb25dd419164a17b6acdab26e6b32ea45d0eea9ac047e Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b 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=491058 sha256=41fffa4b9e56cfc57a9b683d8020a93915f675b27ec6547b2296876dc28facc8 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, sphinxcontrib-websupport, six, MarkupSafe, Jinja2, pyparsing, packaging, idna, chardet, urllib3, certifi, requests, pytz, babel, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 45.1.0 Uninstalling setuptools-45.1.0: Successfully uninstalled setuptools-45.1.0 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.2.0 mock-1.0.1 packaging-20.1 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.8 [rtd-command-info] start-time: 2020-02-06T09:24:48.428585Z, end-time: 2020-02-06T09:27:07.210612Z, duration: 138, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt Collecting setuptools_scm Downloading setuptools_scm-3.4.3-py2.py3-none-any.whl (26 kB) Collecting importlib_metadata>=0.7 Downloading importlib_metadata-1.5.0-py2.py3-none-any.whl (30 kB) Collecting typing_extensions Downloading typing_extensions-3.7.4.1-py3-none-any.whl (20 kB) Collecting sphinx>=2.0.1 Downloading Sphinx-2.3.1-py3-none-any.whl (2.7 MB) Collecting sphinx-autodoc-typehints Downloading sphinx_autodoc_typehints-1.10.3-py3-none-any.whl (8.4 kB) Collecting scanpydoc>=0.4.2 Downloading scanpydoc-0.4.5-py3-none-any.whl (23 kB) Collecting sphinx_issues Downloading sphinx_issues-1.2.0-py2.py3-none-any.whl (5.8 kB) Collecting pandas~=0.21 Downloading pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4 MB) Collecting scipy Downloading scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB) Collecting h5py Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB) Collecting natsort Downloading natsort-7.0.1-py3-none-any.whl (33 kB) Collecting zarr Downloading zarr-2.4.0.tar.gz (3.3 MB) Collecting zipp>=0.5 Downloading zipp-2.1.0-py3-none-any.whl (4.6 kB) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (0.14) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.2-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.3-py2.py3-none-any.whl (89 kB) Requirement already satisfied: packaging in 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docs/requires.txt (line 14)) (1.14.0) Collecting asciitree Downloading asciitree-0.3.3.tar.gz (4.0 kB) Collecting fasteners Downloading fasteners-0.15-py2.py3-none-any.whl (23 kB) Collecting numcodecs>=0.6.4 Downloading numcodecs-0.6.4.tar.gz (3.8 MB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.4.6) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.1.1) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.25.8) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.8) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2019.11.28) Collecting monotonic>=0.1 Downloading monotonic-1.5-py2.py3-none-any.whl (5.3 kB) Building wheels for collected packages: zarr, asciitree, numcodecs Building wheel for zarr (setup.py): started Building wheel for zarr (setup.py): finished with status 'done' Created wheel for zarr: filename=zarr-2.4.0-py3-none-any.whl size=127066 sha256=7be54055b7bae0fc558b760b2a7d1b3481ada3b0d2326597831928104da4882a Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/b3/3a/6e/c2cd6df1849363f3d56ba11e64368aa1ef3ac886f39c765e82 Building wheel for asciitree (setup.py): started Building wheel for asciitree (setup.py): finished with status 'done' Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5035 sha256=acef3b85a7d1a0ebc2bd4c31166e981e7ef67f76f6647b0c7f5fd975d020dff0 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/9d/b0/4a/2370154bc4a63b2ceec1670d3346840ff28bcbe49911f5df92 Building wheel for numcodecs (setup.py): started Building wheel for numcodecs (setup.py): still running... Building wheel for numcodecs (setup.py): finished with status 'done' Created wheel for numcodecs: filename=numcodecs-0.6.4-cp36-cp36m-linux_x86_64.whl size=4747130 sha256=2eade2cfd88fac82d10ae460393c6ff39fc6241b6a78dbefef8dd068310eed9f Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/7f/c7/84/e71321ff27f7d3457f9482ebdef393961ac1df5005295f26ae Successfully built zarr asciitree numcodecs Installing collected packages: setuptools-scm, zipp, importlib-metadata, typing-extensions, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, sphinx-issues, numpy, python-dateutil, pandas, scipy, h5py, natsort, asciitree, monotonic, fasteners, numcodecs, zarr Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed asciitree-0.3.3 fasteners-0.15 get-version-2.1 h5py-2.10.0 importlib-metadata-1.5.0 monotonic-1.5 natsort-7.0.1 numcodecs-0.6.4 numpy-1.18.1 pandas-0.25.3 python-dateutil-2.8.1 scanpydoc-0.4.5 scipy-1.4.1 setuptools-scm-3.4.3 sphinx-2.3.1 sphinx-autodoc-typehints-1.10.3 sphinx-issues-1.2.0 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 typing-extensions-3.7.4.1 zarr-2.4.0 zipp-2.1.0 [rtd-command-info] start-time: 2020-02-06T09:27:08.043697Z, end-time: 2020-02-06T09:27:08.303692Z, 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.insert(0, str(HERE.parent)) 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", # "plot_generator", # "plot_directive", "sphinx_autodoc_typehints", # needs to be after napoleon "sphinx_issues", # "ipython_directive", # "ipython_console_highlighting", "scanpydoc", ] # 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 app.add_stylesheet("css/custom.css") 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), ) 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 = "sphinx_rtd_theme" html_theme_options = dict(navigation_depth=2) 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_static_path = ["_static"] 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 # import importlib import sys import os.path from six import string_types 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://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("html", "//icb-anndata.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': '/_', 'github_user': 'theislab', 'github_repo': 'anndata', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'c0912437', } 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") 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' [rtd-command-info] start-time: 2020-02-06T09:27:08.373047Z, end-time: 2020-02-06T09:27:22.306851Z, duration: 13, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v2.3.1 loading translations [en]... done making output directory... done loading intersphinx inventory from http://docs.h5py.org/en/latest/objects.inv... loading intersphinx inventory from https://linnarssonlab.org/loompy/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://zarr.readthedocs.io/en/stable/objects.inv... [autosummary] generating autosummary for: api.rst, benchmarks.rst, fileformat-prose.rst, index.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_h5ad.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 6 source files that are out of date updating environment: [new config] 59 added, 0 changed, 0 removed reading sources... [ 1%] anndata.AnnData reading sources... [ 3%] anndata.AnnData.T reading sources... [ 5%] anndata.AnnData.X reading sources... [ 6%] anndata.AnnData.chunk_X reading sources... [ 8%] anndata.AnnData.chunked_X reading sources... [ 10%] anndata.AnnData.concatenate reading sources... [ 11%] anndata.AnnData.copy reading sources... [ 13%] anndata.AnnData.filename reading sources... [ 15%] anndata.AnnData.is_view reading sources... [ 16%] anndata.AnnData.isbacked reading sources... [ 18%] anndata.AnnData.isview reading sources... [ 20%] anndata.AnnData.layers reading sources... [ 22%] anndata.AnnData.n_obs reading sources... [ 23%] anndata.AnnData.n_vars reading sources... [ 25%] anndata.AnnData.obs reading sources... [ 27%] anndata.AnnData.obs_keys reading sources... [ 28%] anndata.AnnData.obs_names reading sources... [ 30%] anndata.AnnData.obs_names_make_unique reading sources... [ 32%] anndata.AnnData.obs_vector reading sources... [ 33%] anndata.AnnData.obsm reading sources... [ 35%] anndata.AnnData.obsm_keys reading sources... [ 37%] anndata.AnnData.obsp reading sources... [ 38%] anndata.AnnData.raw reading sources... [ 40%] anndata.AnnData.rename_categories reading sources... [ 42%] anndata.AnnData.shape reading sources... [ 44%] anndata.AnnData.strings_to_categoricals reading sources... [ 45%] anndata.AnnData.to_df reading sources... [ 47%] anndata.AnnData.transpose reading sources... [ 49%] anndata.AnnData.uns reading sources... [ 50%] anndata.AnnData.uns_keys reading sources... [ 52%] anndata.AnnData.var reading sources... [ 54%] anndata.AnnData.var_keys reading sources... [ 55%] anndata.AnnData.var_names reading sources... [ 57%] anndata.AnnData.var_names_make_unique reading sources... [ 59%] anndata.AnnData.var_vector reading sources... [ 61%] anndata.AnnData.varm reading sources... [ 62%] anndata.AnnData.varm_keys reading sources... [ 64%] anndata.AnnData.varp reading sources... [ 66%] anndata.AnnData.write reading sources... [ 67%] anndata.AnnData.write_csvs reading sources... [ 69%] anndata.AnnData.write_h5ad reading sources... [ 71%] anndata.AnnData.write_loom reading sources... [ 72%] anndata.AnnData.write_zarr reading sources... [ 74%] anndata.ImplicitModificationWarning reading sources... [ 76%] anndata.read_csv reading sources... [ 77%] anndata.read_excel reading sources... [ 79%] anndata.read_h5ad reading sources... [ 81%] anndata.read_hdf reading sources... [ 83%] anndata.read_loom reading sources... [ 84%] anndata.read_mtx reading sources... [ 86%] anndata.read_text reading sources... [ 88%] anndata.read_umi_tools reading sources... [ 89%] anndata.read_zarr reading sources... [ 91%] api reading sources... [ 93%] benchmarks reading sources... [ 94%] fileformat-prose reading sources... [ 96%] index reading sources... [ 98%] references reading sources... [100%] release_notes looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 1%] anndata.AnnData writing output... [ 3%] anndata.AnnData.T writing output... [ 5%] anndata.AnnData.X writing output... [ 6%] anndata.AnnData.chunk_X writing output... [ 8%] anndata.AnnData.chunked_X writing output... [ 10%] anndata.AnnData.concatenate writing output... [ 11%] anndata.AnnData.copy writing output... [ 13%] anndata.AnnData.filename writing output... [ 15%] anndata.AnnData.is_view writing output... [ 16%] anndata.AnnData.isbacked writing output... [ 18%] anndata.AnnData.isview writing output... [ 20%] anndata.AnnData.layers writing output... [ 22%] anndata.AnnData.n_obs writing output... [ 23%] anndata.AnnData.n_vars writing output... [ 25%] anndata.AnnData.obs writing output... [ 27%] anndata.AnnData.obs_keys writing output... [ 28%] anndata.AnnData.obs_names writing output... [ 30%] anndata.AnnData.obs_names_make_unique writing output... [ 32%] anndata.AnnData.obs_vector writing output... [ 33%] anndata.AnnData.obsm writing output... [ 35%] anndata.AnnData.obsm_keys writing output... [ 37%] anndata.AnnData.obsp writing output... [ 38%] anndata.AnnData.raw writing output... [ 40%] anndata.AnnData.rename_categories writing output... [ 42%] anndata.AnnData.shape writing output... [ 44%] anndata.AnnData.strings_to_categoricals writing output... [ 45%] anndata.AnnData.to_df writing output... [ 47%] anndata.AnnData.transpose writing output... [ 49%] anndata.AnnData.uns writing output... [ 50%] anndata.AnnData.uns_keys writing output... [ 52%] anndata.AnnData.var writing output... [ 54%] anndata.AnnData.var_keys writing output... [ 55%] anndata.AnnData.var_names writing output... [ 57%] anndata.AnnData.var_names_make_unique writing output... [ 59%] anndata.AnnData.var_vector writing output... [ 61%] anndata.AnnData.varm writing output... [ 62%] anndata.AnnData.varm_keys writing output... [ 64%] anndata.AnnData.varp writing output... [ 66%] anndata.AnnData.write writing output... [ 67%] anndata.AnnData.write_csvs writing output... [ 69%] anndata.AnnData.write_h5ad writing output... [ 71%] anndata.AnnData.write_loom writing output... [ 72%] anndata.AnnData.write_zarr writing output... [ 74%] anndata.ImplicitModificationWarning writing output... [ 76%] anndata.read_csv writing output... [ 77%] anndata.read_excel writing output... [ 79%] anndata.read_h5ad writing output... [ 81%] anndata.read_hdf writing output... [ 83%] anndata.read_loom writing output... [ 84%] anndata.read_mtx writing output... [ 86%] anndata.read_text writing output... [ 88%] anndata.read_umi_tools writing output... [ 89%] anndata.read_zarr writing output... [ 91%] api writing output... [ 93%] benchmarks writing output... [ 94%] fileformat-prose writing output... [ 96%] index writing output... [ 98%] references writing output... [100%] release_notes /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest" is shallow and may cause errors warnings.warn('"{}" is shallow and may cause errors'.format(wd.path)) Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 276, in build_main app.build(args.force_all, filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 353, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_update len(to_build)) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 361, in build self.write(docnames, list(updated_docnames), method) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 535, in write self._write_serial(sorted(docnames)) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 545, in _write_serial self.write_doc(docname, doctree) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/contextlib.py", line 88, in __exit__ next(self.gen) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 219, in pending_warnings memhandler.flushTo(logger) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 184, in flushTo logger.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle self.callHandlers(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers hdlr.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle rv = self.filter(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter result = f.filter(record) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 404, in filter raise SphinxWarning(location + ":" + message) sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/_core/anndata.py:docstring of anndata.AnnData:68:py:attr reference target not found: pandas.DataFrame.iloc Warning, treated as error: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/_core/anndata.py:docstring of anndata.AnnData:68:py:attr reference target not found: pandas.DataFrame.iloc