Read the Docs build information Build id: 325397 Project: icb-anndata Version: 362 Commit: aac64da06c354c67f71015845fd8762bd3797e51 Date: 2020-05-02T09:38:11.287681Z State: finished Success: False [rtd-command-info] start-time: 2020-05-02T09:38:13.231665Z, end-time: 2020-05-02T09:38:14.323109Z, 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: 2020-05-02T09:38:14.426491Z, end-time: 2020-05-02T09:38:15.226810Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/362/head:external-362 From https://github.com/theislab/anndata * [new ref] refs/pull/362/head -> external-362 [rtd-command-info] start-time: 2020-05-02T09:38:15.642088Z, end-time: 2020-05-02T09:38:15.840612Z, duration: 0, exit-code: 0 git checkout --force aac64da06c354c67f71015845fd8762bd3797e51 Note: checking out 'aac64da06c354c67f71015845fd8762bd3797e51'. 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 aac64da deprecate chunk_X [rtd-command-info] start-time: 2020-05-02T09:38:15.948821Z, end-time: 2020-05-02T09:38:16.140794Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-02T09:38:17.399679Z, end-time: 2020-05-02T09:38:21.273787Z, duration: 3, exit-code: 0 python3.6 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-02T09:38:21.403066Z, end-time: 2020-05-02T09:38:22.215622Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-02T09:38:22.330244Z, end-time: 2020-05-02T09:38:31.707070Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 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idna-2.9-py2.py3-none-any.whl (58 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=ff03c5cbcd11e24732b9abb34cc5630e4608421b6eab422b4c0042a23dacf255 Stored in directory: /tmp/pip-ephem-wheel-cache-j4931m5o/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=a443d7f98c0b4cc93fe42c1f4b241aefe51d660044d7cd13331313c3c145b7d2 Stored in directory: /tmp/pip-ephem-wheel-cache-j4931m5o/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, sphinxcontrib-websupport, snowballstemmer, pytz, babel, MarkupSafe, Jinja2, urllib3, certifi, chardet, idna, requests, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-02T09:38:31.818134Z, end-time: 2020-05-02T09:38:46.154067Z, duration: 14, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requires.txt Collecting pandas>=0.23.0 Downloading pandas-1.0.3-cp36-cp36m-manylinux1_x86_64.whl (10.0 MB) Collecting numpy~=1.14 Downloading numpy-1.18.3-cp36-cp36m-manylinux1_x86_64.whl (20.2 MB) Collecting scipy~=1.0 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 importlib_metadata>=0.7 Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 7)) (20.3) Collecting setuptools_scm Downloading setuptools_scm-3.5.0-py2.py3-none-any.whl (26 kB) Collecting typing_extensions Downloading typing_extensions-3.7.4.2-py3-none-any.whl (22 kB) Collecting sphinx>=2.0.1 Downloading Sphinx-3.0.3-py3-none-any.whl (2.8 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) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from pandas>=0.23.0->-r docs/../requirements.txt (line 1)) (2020.1) Collecting python-dateutil>=2.6.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from h5py->-r docs/../requirements.txt (line 4)) (1.14.0) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from packaging->-r docs/../requirements.txt (line 7)) (2.4.7) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 8)) (0.14) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 8)) (41.0.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 8)) (2.8.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 8)) (2.11.2) Requirement already 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already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (2.9) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (2020.4.5.1) 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/362/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (1.25.9) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (3.0.4) Installing collected packages: python-dateutil, numpy, pandas, scipy, h5py, natsort, zipp, importlib-metadata, setuptools-scm, typing-extensions, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-serializinghtml, sphinxcontrib-htmlhelp, sphinxcontrib-qthelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, sphinx-issues Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed get-version-2.1 h5py-2.10.0 importlib-metadata-1.6.0 natsort-7.0.1 numpy-1.18.3 pandas-1.0.3 python-dateutil-2.8.1 scanpydoc-0.4.5 scipy-1.4.1 setuptools-scm-3.5.0 sphinx-3.0.3 sphinx-autodoc-typehints-1.10.3 sphinx-issues-1.2.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 typing-extensions-3.7.4.2 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-02T09:38:47.200942Z, end-time: 2020-05-02T09:38:47.416031Z, 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://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "362", 'version_slug': "362", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("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/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'anndata', 'github_version': 'aac64da06c354c67f71015845fd8762bd3797e51', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'aac64da06c354c67f71015845fd8762bd3797e51', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'aac64da06c354c67f71015845fd8762bd3797e51', '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': 'aac64da0', } 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") 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: 2020-05-02T09:38:47.576000Z, end-time: 2020-05-02T09:38:56.536947Z, duration: 8, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.0.3 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, concatenation.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/362/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.chunk_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/anndata.AnnData.write_h5ad.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 7 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_obs 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.layers reading sources... [ 20%] anndata.AnnData.n_obs reading sources... [ 22%] anndata.AnnData.n_vars reading sources... [ 23%] anndata.AnnData.obs reading sources... [ 25%] anndata.AnnData.obs_keys reading sources... [ 27%] anndata.AnnData.obs_names reading sources... [ 28%] anndata.AnnData.obs_names_make_unique reading sources... [ 30%] anndata.AnnData.obs_vector reading sources... [ 32%] anndata.AnnData.obsm reading sources... [ 33%] anndata.AnnData.obsm_keys reading sources... [ 35%] anndata.AnnData.obsp reading sources... [ 37%] anndata.AnnData.raw reading sources... [ 38%] anndata.AnnData.rename_categories /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362" is shallow and may cause errors warnings.warn('"{}" is shallow and may cause errors'.format(wd.path)) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/deprecation.py:52: RemovedInSphinx40Warning: sphinx.builders.html.DirectoryHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. return getattr(self._module, name) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/readthedocs_ext/readthedocs.py:14: RemovedInSphinx40Warning: sphinx.builders.html.SingleFileHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. from sphinx.builders.html import (DirectoryHTMLBuilder, SingleFileHTMLBuilder, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/362/docs/conf.py:93: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet("css/custom.css") /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) reading sources... [ 40%] anndata.AnnData.shape reading sources... [ 42%] anndata.AnnData.strings_to_categoricals reading sources... [ 44%] anndata.AnnData.to_df reading sources... [ 45%] anndata.AnnData.transpose reading sources... [ 47%] anndata.AnnData.uns reading sources... [ 49%] anndata.AnnData.uns_keys reading sources... [ 50%] anndata.AnnData.var reading sources... [ 52%] anndata.AnnData.var_keys reading sources... [ 54%] anndata.AnnData.var_names reading sources... [ 55%] anndata.AnnData.var_names_make_unique reading sources... [ 57%] anndata.AnnData.var_vector reading sources... [ 59%] anndata.AnnData.varm reading sources... [ 61%] anndata.AnnData.varm_keys reading sources... [ 62%] anndata.AnnData.varp reading sources... [ 64%] anndata.AnnData.write reading sources... [ 66%] anndata.AnnData.write_csvs reading sources... [ 67%] anndata.AnnData.write_h5ad reading sources... [ 69%] anndata.AnnData.write_loom reading sources... [ 71%] anndata.AnnData.write_zarr reading sources... [ 72%] anndata.ImplicitModificationWarning reading sources... [ 74%] anndata.read_csv reading sources... [ 76%] anndata.read_excel reading sources... [ 77%] anndata.read_h5ad reading sources... [ 79%] anndata.read_hdf reading sources... [ 81%] anndata.read_loom reading sources... [ 83%] anndata.read_mtx reading sources... [ 84%] anndata.read_text reading sources... [ 86%] anndata.read_umi_tools reading sources... [ 88%] anndata.read_zarr reading sources... [ 89%] api reading sources... [ 91%] benchmarks reading sources... [ 93%] concatenation 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_obs 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.layers writing output... [ 20%] anndata.AnnData.n_obs writing output... [ 22%] anndata.AnnData.n_vars writing output... [ 23%] anndata.AnnData.obs writing output... [ 25%] anndata.AnnData.obs_keys writing output... [ 27%] anndata.AnnData.obs_names writing output... [ 28%] anndata.AnnData.obs_names_make_unique writing output... [ 30%] anndata.AnnData.obs_vector writing output... [ 32%] anndata.AnnData.obsm writing output... [ 33%] anndata.AnnData.obsm_keys writing output... [ 35%] anndata.AnnData.obsp writing output... [ 37%] anndata.AnnData.raw writing output... [ 38%] anndata.AnnData.rename_categories writing output... [ 40%] anndata.AnnData.shape writing output... [ 42%] anndata.AnnData.strings_to_categoricals writing output... [ 44%] anndata.AnnData.to_df writing output... [ 45%] anndata.AnnData.transpose writing output... [ 47%] anndata.AnnData.uns writing output... [ 49%] anndata.AnnData.uns_keys writing output... [ 50%] anndata.AnnData.var writing output... [ 52%] anndata.AnnData.var_keys writing output... [ 54%] anndata.AnnData.var_names writing output... [ 55%] anndata.AnnData.var_names_make_unique writing output... [ 57%] anndata.AnnData.var_vector writing output... [ 59%] anndata.AnnData.varm writing output... [ 61%] anndata.AnnData.varm_keys writing output... [ 62%] anndata.AnnData.varp writing output... [ 64%] anndata.AnnData.write writing output... [ 66%] anndata.AnnData.write_csvs writing output... [ 67%] anndata.AnnData.write_h5ad writing output... [ 69%] anndata.AnnData.write_loom writing output... [ 71%] anndata.AnnData.write_zarr writing output... [ 72%] anndata.ImplicitModificationWarning writing output... [ 74%] anndata.read_csv writing output... [ 76%] anndata.read_excel writing output... [ 77%] anndata.read_h5ad writing output... [ 79%] anndata.read_hdf writing output... [ 81%] anndata.read_loom writing output... [ 83%] anndata.read_mtx writing output... [ 84%] anndata.read_text writing output... [ 86%] anndata.read_umi_tools writing output... [ 88%] anndata.read_zarr writing output... [ 89%] api writing output... [ 91%] benchmarks writing output... [ 93%] concatenation 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/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/cmd/build.py", line 280, in build_main app.build(args.force_all, filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/application.py", line 348, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/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/362/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/362/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/362/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/362/lib/python3.6/site-packages/sphinx/util/logging.py", line 213, in pending_warnings memhandler.flushTo(logger) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/362/lib/python3.6/site-packages/sphinx/util/logging.py", line 178, 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/362/lib/python3.6/site-packages/sphinx/util/logging.py", line 415, in filter raise SphinxWarning(location + ":" + str(message)) sphinx.errors.SphinxWarning: release_notes.rst:100:py:func reference target not found: anndata.AnnData.chunk_X Warning, treated as error: release_notes.rst:100:py:func reference target not found: anndata.AnnData.chunk_X