Read the Docs build information Build id: 325000 Project: icb-anndata Version: 342 Commit: f567a6edf99e8a119dce5603f94452a3443fd615 Date: 2020-05-01T14:55:54.928571Z State: finished Success: True [rtd-command-info] start-time: 2020-05-01T14:55:56.962070Z, end-time: 2020-05-01T14:55:58.067528Z, 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: 2020-05-01T14:55:58.239613Z, end-time: 2020-05-01T14:55:58.993380Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/342/head:external-342 From https://github.com/theislab/anndata * [new ref] refs/pull/342/head -> external-342 [rtd-command-info] start-time: 2020-05-01T14:55:59.546781Z, end-time: 2020-05-01T14:55:59.757770Z, duration: 0, exit-code: 0 git checkout --force f567a6edf99e8a119dce5603f94452a3443fd615 Note: checking out 'f567a6edf99e8a119dce5603f94452a3443fd615'. 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 f567a6e Make resolve_path work for layers and obsm/varm [rtd-command-info] start-time: 2020-05-01T14:55:59.926541Z, end-time: 2020-05-01T14:56:00.126491Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-01T14:56:01.521638Z, end-time: 2020-05-01T14:56:05.532294Z, 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/342/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-01T14:56:05.739449Z, end-time: 2020-05-01T14:56:06.578693Z, 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/342/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-01T14:56:06.679881Z, end-time: 2020-05-01T14:56:16.318911Z, 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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(510 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=63ada057ad19e37659629ce8a7f323c7863bbf83685795378613834275adac1d Stored in directory: /tmp/pip-ephem-wheel-cache-altcadj9/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=c9f20eecce70631fb8ed1c8da4192ed3adfc48a6e683a9151f97f8857d93d31e Stored in directory: /tmp/pip-ephem-wheel-cache-altcadj9/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, six, pyparsing, packaging, sphinxcontrib-websupport, MarkupSafe, Jinja2, snowballstemmer, certifi, chardet, urllib3, idna, requests, pytz, babel, 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: 2020-05-01T14:56:16.429168Z, end-time: 2020-05-01T14:56:31.422400Z, 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/342/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) 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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (3.0.4) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/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: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/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: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 8)) (2020.4.5.1) Installing collected packages: numpy, python-dateutil, pandas, scipy, h5py, natsort, zipp, importlib-metadata, setuptools-scm, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-jsmath, 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: 2020-05-01T14:56:32.463836Z, end-time: 2020-05-01T14:56:32.683044Z, 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", "anndata._core.ref_path.RefPath": "anndata.RefPath", "anndata._core.raw.Raw": "anndata.Raw", # Temporarily "anndata._core.sparse_dataset.SparseDataset": "scipy.sparse.spmatrix", "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': "342", 'version_slug': "342", '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': 'f567a6edf99e8a119dce5603f94452a3443fd615', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'f567a6edf99e8a119dce5603f94452a3443fd615', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'f567a6edf99e8a119dce5603f94452a3443fd615', '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': 'f567a6ed', } 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: 2020-05-01T14:56:32.800942Z, end-time: 2020-05-01T14:56:44.574045Z, duration: 11, exit-code: 0 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, fileformat-prose.rst, index.rst, internal-api.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.Raw.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.get_df.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.get_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.AnnData.is_view.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.Raw.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.Raw.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.Raw.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.Raw.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.dim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.get_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.parse.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.path.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342/docs/anndata.RefPath.raw_subpath.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] 82 added, 0 changed, 0 removed reading sources... [ 1%] anndata.AnnData reading sources... [ 2%] anndata.AnnData.T reading sources... [ 3%] anndata.AnnData.X reading sources... [ 4%] anndata.AnnData.chunk_X reading sources... [ 6%] anndata.AnnData.chunked_X reading sources... [ 7%] anndata.AnnData.concatenate reading sources... [ 8%] anndata.AnnData.copy reading sources... [ 9%] anndata.AnnData.filename reading sources... [ 10%] anndata.AnnData.get_df reading sources... [ 12%] anndata.AnnData.get_vector reading sources... [ 13%] anndata.AnnData.is_view reading sources... [ 14%] anndata.AnnData.isbacked reading sources... [ 15%] anndata.AnnData.layers reading sources... [ 17%] anndata.AnnData.n_obs reading sources... [ 18%] anndata.AnnData.n_vars reading sources... [ 19%] anndata.AnnData.obs reading sources... [ 20%] anndata.AnnData.obs_keys /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/342/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/342" 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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/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/342/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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