Read the Docs build information Build id: 1772030 Project: icb-anndata Version: latest Commit: 3dacb098cb7420ddb663ecaafe1c78d93b651f3f Date: 2023-10-10T15:27:04.720932Z State: finished Success: True [rtd-command-info] start-time: 2023-10-10T15:27:13.494437Z, end-time: 2023-10-10T15:27:14.085029Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2023-10-10T15:27:14.518543Z, end-time: 2023-10-10T15:27:15.772857Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/scverse/anndata * [new tag] 0.10.0 -> 0.10.0 * [new tag] 0.10.0rc1 -> 0.10.0rc1 * [new tag] 0.11.0.dev0 -> 0.11.0.dev0 [rtd-command-info] start-time: 2023-10-10T15:27:17.299239Z, end-time: 2023-10-10T15:27:17.378467Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 3dacb09 Fewer warnings (#1183) [rtd-command-info] start-time: 2023-10-10T15:27:17.808176Z, end-time: 2023-10-10T15:27:17.870315Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-10-10T15:27:20.330054Z, end-time: 2023-10-10T15:27:20.401197Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2023-10-10T15:27:20.845690Z, end-time: 2023-10-10T15:27:21.611445Z, duration: 0, exit-code: 0 git submodule update --init --force --recursive -- docs/tutorials/notebooks Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/tutorials/notebooks'... Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069' [rtd-command-info] start-time: 2023-10-10T15:27:22.068970Z, end-time: 2023-10-10T15:27:22.129471Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-20.04 tools: python: "3.11" sphinx: configuration: docs/conf.py fail_on_warning: true # do not change or you will be fired python: install: - method: pip path: . extra_requirements: - doc submodules: include: - "docs/tutorials/notebooks" recursive: true [rtd-command-info] start-time: 2023-10-10T15:27:31.447862Z, end-time: 2023-10-10T15:27:31.520286Z, duration: 0, exit-code: 0 asdf global python 3.11.4 [rtd-command-info] start-time: 2023-10-10T15:27:32.637381Z, end-time: 2023-10-10T15:27:33.568109Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.4.final.0-64 in 605ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2023-10-10T15:27:34.477135Z, end-time: 2023-10-10T15:27:43.737821Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (21.2.3) Collecting pip Downloading pip-23.2.1-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (57.4.0) 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Building wheel for anndata (pyproject.toml): started Building wheel for anndata (pyproject.toml): finished with status 'done' Created wheel for anndata: filename=anndata-0.11.0.dev7+g3dacb09-py3-none-any.whl size=118674 sha256=1054d0cf3cf880c76cd4a9984d67a54276942c65d1ff2d3b34702d5152795888 Stored in directory: /tmp/pip-ephem-wheel-cache-94767rjo/wheels/ac/78/17/d6beb4bb5885bedd4df2dd7b9cf80e3cd148368110ea659730 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=5033 sha256=43b604e93620c1347075b783cc460dbcce51b88816fd37cf913bfa744c260b36 Stored in directory: /tmp/pip-ephem-wheel-cache-94767rjo/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07 Successfully built anndata asciitree Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, asciitree, zipp, tzdata, typing-extensions, traitlets, tornado, tinycss2, soupsieve, six, rpds-py, pyzmq, pyyaml, pyparsing, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, kiwisolver, jupyterlab-pygments, fonttools, fasteners, docutils, defusedxml, decorator, cycler, attrs, array-api-compat, accessible-pygments, scipy, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib-metadata, h5py, contourpy, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, awkward, jsonschema, ipython, anndata, nbformat, nbclient, nbconvert, sphinx, pydata-sphinx-theme, sphinxext-opengraph, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-book-theme, sphinx-autodoc-typehints, scanpydoc, nbsphinx, myst-parser Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 Successfully installed accessible-pygments-0.0.4 anndata-0.11.0.dev7+g3dacb09 array-api-compat-1.4 asciitree-0.3.3 asttokens-2.4.0 attrs-23.1.0 awkward-2.4.5 awkward-cpp-24 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.1.0 contourpy-1.1.1 cycler-0.12.1 decorator-5.1.1 defusedxml-0.7.1 docutils-0.19 executing-2.0.0 fasteners-0.19 fastjsonschema-2.18.1 fonttools-4.43.1 h5py-3.10.0 importlib-metadata-6.8.0 ipython-8.16.1 jedi-0.19.1 jsonschema-4.19.1 jsonschema-specifications-2023.7.1 jupyter-client-8.3.1 jupyter-core-5.3.2 jupyterlab-pygments-0.2.2 kiwisolver-1.4.5 markdown-it-py-3.0.0 matplotlib-3.8.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.8.0 nbconvert-7.9.2 nbformat-5.9.2 nbsphinx-0.9.3 numcodecs-0.12.0 numpy-1.26.0 pandas-2.1.1 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 pillow-10.0.1 platformdirs-3.11.0 prompt-toolkit-3.0.39 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.14.1 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 pyzmq-25.1.1 referencing-0.30.2 rpds-py-0.10.4 scanpydoc-0.9.5 scipy-1.11.3 six-1.16.0 soupsieve-2.5 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinx-issues-3.0.1 sphinxext-opengraph-0.8.2 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.3.3 traitlets-5.11.2 typing-extensions-4.8.0 tzdata-2023.3 wcwidth-0.2.8 webencodings-0.5.1 zarr-2.16.1 zipp-3.17.0 [rtd-command-info] start-time: 2023-10-10T15:28:39.343560Z, end-time: 2023-10-10T15:28:39.388307Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from importlib import metadata from pathlib import Path from typing import TYPE_CHECKING if TYPE_CHECKING: from sphinx.application import Sphinx HERE = Path(__file__).parent sys.path[:0] = [str(HERE / "extensions")] # -- General configuration ------------------------------------------------ needs_sphinx = "1.7" # autosummary bugfix # General information project = "anndata" author = f"{project} developers" copyright = f"{datetime.now():%Y}, {author}" release = version = metadata.version("anndata") # default settings templates_path = ["_templates"] html_static_path = ["_static"] source_suffix = [".rst", ".md"] master_doc = "index" default_role = "literal" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "tutorials/notebooks/*.rst", ] pygments_style = "sphinx" extensions = [ "myst_parser", "sphinx_copybutton", "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx_autodoc_typehints", # needs to be after napoleon "sphinx_issues", "sphinx_design", "sphinxext.opengraph", "scanpydoc", # needs to be before linkcode "sphinx.ext.linkcode", "nbsphinx", "IPython.sphinxext.ipython_console_highlighting", ] myst_enable_extensions = [ "html_image", # So README.md can be used on github and sphinx docs ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = "bysource" issues_github_path = "scverse/anndata" # 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")] typehints_defaults = "braces" todo_include_todos = False nitpicky = True # Report broken links nitpick_ignore = [ ("py:class", "scipy.sparse.base.spmatrix"), ("py:meth", "pandas.DataFrame.iloc"), ("py:meth", "pandas.DataFrame.loc"), ("py:class", "anndata._core.views.ArrayView"), ("py:class", "anndata._core.raw.Raw"), *[ ("py:class", f"anndata._core.aligned_mapping.{cls}{kind}") for cls in "Layers AxisArrays PairwiseArrays".split() for kind in ["", "View"] ], ] suppress_warnings = [ "ref.citation", "myst.header", # https://github.com/executablebooks/MyST-Parser/issues/262 ] def setup(app: Sphinx): # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead. app.warningiserror = True intersphinx_mapping = dict( h5py=("https://docs.h5py.org/en/latest/", None), hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest/", None), loompy=("https://linnarssonlab.org/loompy/", None), numpy=("https://numpy.org/doc/stable/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), python=("https://docs.python.org/3", None), scipy=("https://docs.scipy.org/doc/scipy/", None), sklearn=("https://scikit-learn.org/stable/", None), zarr=("https://zarr.readthedocs.io/en/stable/", None), xarray=("https://xarray.pydata.org/en/stable/", None), ) qualname_overrides = { "h5py._hl.group.Group": "h5py.Group", "h5py._hl.files.File": "h5py.File", "h5py._hl.dataset.Dataset": "h5py.Dataset", "anndata._core.anndata.AnnData": "anndata.AnnData", } # -- Social cards --------------------------------------------------------- ogp_site_url = "https://anndata.readthedocs.io/" ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg" # -- Options for HTML output ---------------------------------------------- html_theme = "sphinx_book_theme" html_theme_options = dict( use_repository_button=True, repository_url="https://github.com/scverse/anndata", repository_branch="main", ) html_logo = "_static/img/anndata_schema.svg" issues_github_path = "scverse/anndata" 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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("0.7.8", "/en/0.7.8/"), ("0.4.1", "/en/0.4.1/"), ("0.3", "/en/0.3/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'anndata', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '3dacb098', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1772030/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-10-10T15:28:39.937536Z, end-time: 2023-10-10T15:29:56.918215Z, duration: 76, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) loading intersphinx inventory from https://docs.h5py.org/en/latest/objects.inv... loading intersphinx inventory from https://hdf5plugin.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://linnarssonlab.org/loompy/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/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/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... loading intersphinx inventory from https://xarray.pydata.org/en/stable/objects.inv... intersphinx inventory has moved: https://xarray.pydata.org/en/stable/objects.inv -> https://docs.xarray.dev/en/stable/objects.inv [autosummary] generating autosummary for: _key_contributors.rst, api.md, benchmark-read-write.ipynb, benchmarks.md, concatenation.rst, contributing.md, fileformat-prose.md, index.md, interoperability.md, news.md, ..., release-notes/index.md, release-notes/release-latest.md, tutorials/index.md, tutorials/notebooks/anncollection-annloader.ipynb, tutorials/notebooks/anncollection.ipynb, tutorials/notebooks/anndata_dask_array.ipynb, tutorials/notebooks/annloader.ipynb, tutorials/notebooks/awkward-arrays.ipynb, tutorials/notebooks/getting-started.ipynb, tutorials/notebooks/{read,write}_dispatched.ipynb [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSCDataset.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.backend.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.format.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.name.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.to_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.CSRDataset.value.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.IOSpec.encoding_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.IOSpec.encoding_version.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 41 source files that are out of date updating environment: [new config] 137 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 1%] api reading sources... [ 2%] benchmark-read-write /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.5). Your version must be at least (2.14.2) but less than (4.0.0). Refer to https://pandoc.org/installing.html. Continuing with doubts... nbconvert.utils.pandoc.check_pandoc_version() reading sources... [ 2%] benchmarks reading sources... [ 3%] concatenation reading sources... [ 4%] contributing reading sources... [ 5%] fileformat-prose reading sources... [ 5%] generated/anndata.AnnData reading sources... [ 6%] generated/anndata.AnnData.T reading sources... [ 7%] generated/anndata.AnnData.X reading sources... [ 8%] generated/anndata.AnnData.chunk_X reading sources... [ 8%] generated/anndata.AnnData.chunked_X reading sources... [ 9%] generated/anndata.AnnData.concatenate reading sources... [ 10%] generated/anndata.AnnData.copy reading sources... [ 10%] generated/anndata.AnnData.filename reading sources... [ 11%] generated/anndata.AnnData.is_view reading sources... [ 12%] generated/anndata.AnnData.isbacked reading sources... [ 13%] generated/anndata.AnnData.layers reading sources... [ 13%] generated/anndata.AnnData.n_obs reading sources... [ 14%] generated/anndata.AnnData.n_vars reading sources... [ 15%] generated/anndata.AnnData.obs reading sources... [ 16%] generated/anndata.AnnData.obs_keys reading sources... [ 16%] generated/anndata.AnnData.obs_names reading sources... [ 17%] generated/anndata.AnnData.obs_names_make_unique reading sources... [ 18%] generated/anndata.AnnData.obs_vector reading sources... [ 18%] generated/anndata.AnnData.obsm reading sources... [ 19%] generated/anndata.AnnData.obsm_keys reading sources... [ 20%] generated/anndata.AnnData.obsp reading sources... [ 21%] generated/anndata.AnnData.raw reading sources... [ 21%] generated/anndata.AnnData.rename_categories reading sources... [ 22%] generated/anndata.AnnData.shape reading sources... [ 23%] generated/anndata.AnnData.strings_to_categoricals reading sources... [ 24%] generated/anndata.AnnData.to_df reading sources... [ 24%] generated/anndata.AnnData.to_memory reading sources... [ 25%] generated/anndata.AnnData.transpose reading sources... [ 26%] generated/anndata.AnnData.uns reading sources... [ 27%] generated/anndata.AnnData.uns_keys reading sources... [ 27%] generated/anndata.AnnData.var reading sources... [ 28%] generated/anndata.AnnData.var_keys reading sources... [ 29%] generated/anndata.AnnData.var_names reading sources... [ 29%] generated/anndata.AnnData.var_names_make_unique reading sources... [ 30%] generated/anndata.AnnData.var_vector reading sources... [ 31%] generated/anndata.AnnData.varm reading sources... [ 32%] generated/anndata.AnnData.varm_keys reading sources... [ 32%] generated/anndata.AnnData.varp reading sources... 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