Read the Docs build information Build id: 332770 Project: icb-anndata Version: stable Commit: e4581abc6297752b8954645b0fe08e0aee843b7f Date: 2020-05-18T21:11:06.180659Z State: finished Success: True [rtd-command-info] start-time: 2020-05-18T21:11:08.658698Z, end-time: 2020-05-18T21:11:09.757728Z, 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: 2020-05-18T21:11:10.117774Z, end-time: 2020-05-18T21:11:10.322893Z, duration: 0, exit-code: 0 git checkout --force origin/stable Note: checking out 'origin/stable'. 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 e4581ab Better Sphinx workaround (#309) [rtd-command-info] start-time: 2020-05-18T21:11:10.590496Z, end-time: 2020-05-18T21:11:10.787718Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-18T21:11:12.533754Z, end-time: 2020-05-18T21:11:16.573383Z, duration: 4, 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/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: 2020-05-18T21:11:16.764732Z, end-time: 2020-05-18T21:11:17.611818Z, 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/stable/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-18T21:11:17.817042Z, end-time: 2020-05-18T21:11:27.670102Z, 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 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-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 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=35b46b4c263cd0dc74728d7c97e12cc496734b9eee5887b4febe00744b63efac Stored in directory: /tmp/pip-ephem-wheel-cache-mrqyqh91/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=a86b69c4a380a88eecfb9e7cd89c10502e49229700ab9789cf0b03ace1e33475 Stored in directory: /tmp/pip-ephem-wheel-cache-mrqyqh91/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, pyparsing, six, packaging, pytz, babel, certifi, chardet, idna, urllib3, requests, sphinxcontrib-websupport, imagesize, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.4.0 Uninstalling setuptools-46.4.0: Successfully uninstalled setuptools-46.4.0 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: 2020-05-18T21:11:28.207158Z, end-time: 2020-05-18T21:13:32.445063Z, duration: 124, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requires.txt Collecting setuptools_scm Downloading setuptools_scm-3.5.0-py2.py3-none-any.whl (26 kB) Collecting importlib_metadata>=0.7 Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 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) 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-3.1.0-py3-none-any.whl (4.9 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (41.0.1) 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->-r docs/requires.txt (line 6)) (1.2.0) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.23.0) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.0.0) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.8.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (20.3) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Requirement already satisfied: Pygments>=2.0 in 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python-dateutil>=2.6.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) 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~=0.21->-r docs/requires.txt (line 12)) (2020.1) Collecting numpy>=1.13.3 Downloading numpy-1.18.4-cp36-cp36m-manylinux1_x86_64.whl (20.2 MB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from h5py->-r 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: idna<3,>=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->-r docs/requires.txt (line 6)) (2.9) 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/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.25.9) Requirement already satisfied: chardet<4,>=3.0.2 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->-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/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2020.4.5.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.4.7) Requirement already satisfied: MarkupSafe>=0.23 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->-r docs/requires.txt (line 6)) (1.1.1) 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=9d930230dbea9ab386b046b4ca8a3fce4f932c5c9917adc10e7440d0366b01f4 Stored in directory: /tmp/pip-ephem-wheel-cache-md6fr0hb/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=64927fc95810bd6f9c2480bcd8a825cf4cfa4c125b046668e453bea46fe3886e Stored in directory: /tmp/pip-ephem-wheel-cache-md6fr0hb/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=4748165 sha256=289a7556443e1c698f64e5dbdfa10b18dbc14513960700ff61a80454042de757 Stored in directory: /tmp/pip-ephem-wheel-cache-md6fr0hb/wheels/7f/c7/84/e71321ff27f7d3457f9482ebdef393961ac1df5005295f26ae Successfully built zarr asciitree numcodecs Installing collected packages: setuptools-scm, zipp, importlib-metadata, typing-extensions, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, sphinx-issues, python-dateutil, numpy, 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-1.6.0 monotonic-1.5 natsort-7.0.1 numcodecs-0.6.4 numpy-1.18.4 pandas-0.25.3 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 zarr-2.4.0 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-18T21:13:33.640004Z, end-time: 2020-05-18T21:13:33.859741Z, 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': "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/"), ("refpaths", "/en/refpaths/"), ], 'downloads': [ ("html", "//anndata.readthedocs.io/_/downloads/en/stable/htmlzip/"), ], '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': 'stable', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'stable', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'stable', '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': 'e4581abc', } 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: 2020-05-18T21:13:34.210837Z, end-time: 2020-05-18T21:13:43.579865Z, duration: 9, exit-code: 0 python sphinx-build -T -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, fileformat-prose.rst, index.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/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] 58 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... [ 12%] anndata.AnnData.copy reading sources... [ 13%] anndata.AnnData.filename reading sources... [ 15%] anndata.AnnData.is_view reading sources... [ 17%] anndata.AnnData.isbacked reading sources... [ 18%] anndata.AnnData.isview reading sources... [ 20%] anndata.AnnData.layers reading sources... [ 22%] anndata.AnnData.n_obs reading sources... [ 24%] anndata.AnnData.n_vars reading sources... [ 25%] anndata.AnnData.obs reading sources... [ 27%] anndata.AnnData.obs_keys reading sources... [ 29%] anndata.AnnData.obs_names reading sources... [ 31%] anndata.AnnData.obs_names_make_unique reading sources... [ 32%] anndata.AnnData.obs_vector reading sources... [ 34%] anndata.AnnData.obsm reading sources... [ 36%] anndata.AnnData.obsm_keys /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable" 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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) reading sources... [ 37%] anndata.AnnData.obsp reading sources... [ 39%] anndata.AnnData.raw reading sources... [ 41%] anndata.AnnData.rename_categories reading sources... [ 43%] anndata.AnnData.shape reading sources... [ 44%] anndata.AnnData.strings_to_categoricals reading sources... [ 46%] anndata.AnnData.to_df reading sources... [ 48%] anndata.AnnData.transpose reading sources... [ 50%] anndata.AnnData.uns reading sources... [ 51%] anndata.AnnData.uns_keys reading sources... [ 53%] anndata.AnnData.var reading sources... [ 55%] anndata.AnnData.var_keys reading sources... [ 56%] anndata.AnnData.var_names reading sources... [ 58%] anndata.AnnData.var_names_make_unique reading sources... [ 60%] anndata.AnnData.var_vector reading sources... [ 62%] anndata.AnnData.varm reading sources... [ 63%] anndata.AnnData.varm_keys reading sources... [ 65%] anndata.AnnData.varp reading sources... [ 67%] anndata.AnnData.write reading sources... [ 68%] anndata.AnnData.write_csvs reading sources... [ 70%] anndata.AnnData.write_h5ad reading sources... [ 72%] anndata.AnnData.write_loom reading sources... [ 74%] anndata.AnnData.write_zarr reading sources... [ 75%] anndata.read_csv reading sources... [ 77%] anndata.read_excel reading sources... [ 79%] anndata.read_h5ad reading sources... [ 81%] anndata.read_hdf reading sources... [ 82%] anndata.read_loom reading sources... [ 84%] anndata.read_mtx reading sources... [ 86%] anndata.read_text reading sources... [ 87%] anndata.read_umi_tools reading sources... [ 89%] anndata.read_zarr reading sources... [ 91%] api /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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... [ 12%] anndata.AnnData.copy writing output... [ 13%] anndata.AnnData.filename writing output... [ 15%] anndata.AnnData.is_view writing output... [ 17%] anndata.AnnData.isbacked writing output... [ 18%] anndata.AnnData.isview writing output... [ 20%] anndata.AnnData.layers writing output... [ 22%] anndata.AnnData.n_obs writing output... [ 24%] anndata.AnnData.n_vars writing output... [ 25%] anndata.AnnData.obs writing output... [ 27%] anndata.AnnData.obs_keys writing output... [ 29%] anndata.AnnData.obs_names writing output... [ 31%] anndata.AnnData.obs_names_make_unique writing output... [ 32%] anndata.AnnData.obs_vector writing output... [ 34%] anndata.AnnData.obsm writing output... [ 36%] anndata.AnnData.obsm_keys writing output... [ 37%] anndata.AnnData.obsp writing output... [ 39%] anndata.AnnData.raw writing output... [ 41%] anndata.AnnData.rename_categories writing output... [ 43%] anndata.AnnData.shape writing output... [ 44%] anndata.AnnData.strings_to_categoricals writing output... [ 46%] anndata.AnnData.to_df writing output... [ 48%] anndata.AnnData.transpose writing output... [ 50%] anndata.AnnData.uns writing output... [ 51%] anndata.AnnData.uns_keys writing output... [ 53%] anndata.AnnData.var writing output... [ 55%] anndata.AnnData.var_keys writing output... [ 56%] anndata.AnnData.var_names writing output... [ 58%] anndata.AnnData.var_names_make_unique writing output... [ 60%] anndata.AnnData.var_vector writing output... [ 62%] anndata.AnnData.varm writing output... [ 63%] anndata.AnnData.varm_keys writing output... [ 65%] anndata.AnnData.varp writing output... [ 67%] anndata.AnnData.write writing output... [ 68%] anndata.AnnData.write_csvs writing output... [ 70%] anndata.AnnData.write_h5ad writing output... [ 72%] anndata.AnnData.write_loom writing output... [ 74%] anndata.AnnData.write_zarr writing output... [ 75%] anndata.read_csv writing output... [ 77%] anndata.read_excel writing output... [ 79%] anndata.read_h5ad writing output... [ 81%] anndata.read_hdf writing output... [ 82%] anndata.read_loom writing output... [ 84%] anndata.read_mtx writing output... [ 86%] anndata.read_text writing output... [ 87%] 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 generating indices... genindex py-modindexdone writing additional pages... searchdone copying static files... ... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) [rtd-command-info] start-time: 2020-05-18T21:13:43.775116Z, end-time: 2020-05-18T21:13:51.057102Z, duration: 7, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia 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, fileformat-prose.rst, index.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_h5ad.rst building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 58 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... [ 12%] anndata.AnnData.copy reading sources... [ 13%] anndata.AnnData.filename reading sources... [ 15%] anndata.AnnData.is_view reading sources... [ 17%] anndata.AnnData.isbacked reading sources... [ 18%] anndata.AnnData.isview reading sources... [ 20%] anndata.AnnData.layers reading sources... [ 22%] anndata.AnnData.n_obs reading sources... [ 24%] anndata.AnnData.n_vars reading sources... [ 25%] anndata.AnnData.obs reading sources... [ 27%] anndata.AnnData.obs_keys reading sources... [ 29%] anndata.AnnData.obs_names reading sources... [ 31%] anndata.AnnData.obs_names_make_unique reading sources... [ 32%] anndata.AnnData.obs_vector reading sources... [ 34%] anndata.AnnData.obsm reading sources... [ 36%] anndata.AnnData.obsm_keys /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable" 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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/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/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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[100%] release_notes looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... api anndata.AnnData anndata.AnnData.T anndata.AnnData.X anndata.AnnData.filename anndata.AnnData.is_view anndata.AnnData.isbacked anndata.AnnData.isview anndata.AnnData.layers anndata.AnnData.n_obs anndata.AnnData.n_vars anndata.AnnData.obs anndata.AnnData.obs_names anndata.AnnData.obsm anndata.AnnData.obsp anndata.AnnData.raw anndata.AnnData.shape anndata.AnnData.uns anndata.AnnData.var anndata.AnnData.var_names anndata.AnnData.varm anndata.AnnData.varp anndata.AnnData.chunk_X anndata.AnnData.chunked_X anndata.AnnData.concatenate anndata.AnnData.copy anndata.AnnData.obs_keys anndata.AnnData.obs_names_make_unique anndata.AnnData.obs_vector anndata.AnnData.obsm_keys anndata.AnnData.rename_categories anndata.AnnData.strings_to_categoricals anndata.AnnData.to_df anndata.AnnData.transpose anndata.AnnData.uns_keys anndata.AnnData.var_keys anndata.AnnData.var_names_make_unique anndata.AnnData.var_vector anndata.AnnData.varm_keys anndata.AnnData.write anndata.AnnData.write_csvs anndata.AnnData.write_h5ad anndata.AnnData.write_loom anndata.AnnData.write_zarr anndata.read_h5ad anndata.read_csv anndata.read_excel anndata.read_hdf anndata.read_loom anndata.read_mtx anndata.read_text anndata.read_umi_tools anndata.read_zarr fileformat-prose benchmarks references done writing... done writing additional files... done copying static files... ... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. 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