Read the Docs build information Build id: 2611883 Project: icb-anndata Version: latest Commit: f4fd6a401696dcb449b9b85b2f642caae3c11d94 Date: 2024-11-13T12:26:59.872742Z State: finished Success: True [rtd-command-info] start-time: 2024-11-13T12:27:01.133197Z, end-time: 2024-11-13T12:27:01.696307Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2024-11-13T12:27:01.771636Z, end-time: 2024-11-13T12:27:02.892029Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 From https://github.com/scverse/anndata * [new tag] 0.10.0 -> 0.10.0 * [new tag] 0.10.0.dev0 -> 0.10.0.dev0 * [new tag] 0.10.0rc1 -> 0.10.0rc1 * [new tag] 0.10.1 -> 0.10.1 * [new tag] 0.10.2 -> 0.10.2 * [new tag] 0.10.3 -> 0.10.3 * [new tag] 0.10.4 -> 0.10.4 * [new tag] 0.10.5 -> 0.10.5 * [new tag] 0.10.5.post1 -> 0.10.5.post1 * [new tag] 0.10.6 -> 0.10.6 * [new tag] 0.10.7 -> 0.10.7 * [new tag] 0.10.8 -> 0.10.8 * [new tag] 0.10.9 -> 0.10.9 * [new tag] 0.11.0 -> 0.11.0 * [new tag] 0.11.0.dev0 -> 0.11.0.dev0 * [new tag] 0.11.0rc1 -> 0.11.0rc1 * [new tag] 0.11.0rc2 -> 0.11.0rc2 * [new tag] 0.11.0rc3 -> 0.11.0rc3 * [new tag] 0.11.1 -> 0.11.1 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.0.1 -> 0.3.0.1 * [new tag] 0.3.0.3 -> 0.3.0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.3.3 -> 0.3.3 * [new tag] 0.3.4 -> 0.3.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 0.5 -> 0.5 * [new tag] 0.5.1 -> 0.5.1 * [new tag] 0.5.10 -> 0.5.10 * [new tag] 0.5.2 -> 0.5.2 * [new tag] 0.5.3 -> 0.5.3 * [new tag] 0.5.4 -> 0.5.4 * [new tag] 0.5.5 -> 0.5.5 * [new tag] 0.5.6 -> 0.5.6 * [new tag] 0.5.7 -> 0.5.7 * [new tag] 0.5.8 -> 0.5.8 * [new tag] 0.5.9 -> 0.5.9 * [new tag] 0.6 -> 0.6 * [new tag] 0.6.1 -> 0.6.1 * [new tag] 0.6.10 -> 0.6.10 * [new tag] 0.6.11 -> 0.6.11 * [new tag] 0.6.12 -> 0.6.12 * [new tag] 0.6.13 -> 0.6.13 * [new tag] 0.6.14 -> 0.6.14 * [new tag] 0.6.15 -> 0.6.15 * [new tag] 0.6.16 -> 0.6.16 * [new tag] 0.6.17 -> 0.6.17 * [new tag] 0.6.18 -> 0.6.18 * [new tag] 0.6.19 -> 0.6.19 * [new tag] 0.6.2 -> 0.6.2 * [new tag] 0.6.20 -> 0.6.20 * [new tag] 0.6.21 -> 0.6.21 * [new tag] 0.6.22 -> 0.6.22 * [new tag] 0.6.22.post1 -> 0.6.22.post1 * [new tag] 0.6.22rc1 -> 0.6.22rc1 * [new tag] 0.6.3 -> 0.6.3 * [new tag] 0.6.4 -> 0.6.4 * [new tag] 0.6.5 -> 0.6.5 * [new tag] 0.6.6 -> 0.6.6 * [new tag] 0.6.7 -> 0.6.7 * [new tag] 0.6.8 -> 0.6.8 * [new tag] 0.6.9 -> 0.6.9 * [new tag] 0.7 -> 0.7 * [new tag] 0.7.1 -> 0.7.1 * [new tag] 0.7.2 -> 0.7.2 * [new tag] 0.7.2a1 -> 0.7.2a1 * [new tag] 0.7.3 -> 0.7.3 * [new tag] 0.7.4 -> 0.7.4 * [new tag] 0.7.5 -> 0.7.5 * [new tag] 0.7.6 -> 0.7.6 * [new tag] 0.7.7 -> 0.7.7 * [new tag] 0.7.8 -> 0.7.8 * [new tag] 0.7rc1 -> 0.7rc1 * [new tag] 0.7rc2 -> 0.7rc2 * [new tag] 0.8.0 -> 0.8.0 * [new tag] 0.8.0.dev0 -> 0.8.0.dev0 * [new tag] 0.8.0rc1 -> 0.8.0rc1 * [new tag] 0.9.0 -> 0.9.0 * [new tag] 0.9.0.dev0 -> 0.9.0.dev0 * [new tag] 0.9.0rc1 -> 0.9.0rc1 * [new tag] 0.9.1 -> 0.9.1 * [new tag] 0.9.2 -> 0.9.2 [rtd-command-info] start-time: 2024-11-13T12:27:02.964166Z, end-time: 2024-11-13T12:27:03.023728Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-20.04 tools: python: "3.12" jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true 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: 2024-11-13T12:27:03.149849Z, end-time: 2024-11-13T12:27:03.329967Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-11-13T12:27:03.395798Z, end-time: 2024-11-13T12:27:04.172029Z, 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: 2024-11-13T12:27:04.240796Z, end-time: 2024-11-13T12:27:05.216277Z, duration: 0, exit-code: 0 git fetch --unshallow || true [rtd-command-info] start-time: 2024-11-13T12:27:12.470772Z, end-time: 2024-11-13T12:27:12.857599Z, duration: 0, exit-code: 0 asdf global python 3.12.3 [rtd-command-info] start-time: 2024-11-13T12:27:13.302088Z, end-time: 2024-11-13T12:27:15.340574Z, duration: 2, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.3.final.0-64 in 867ms 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==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-11-13T12:27:15.415996Z, end-time: 2024-11-13T12:27:31.825191Z, duration: 16, 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/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.3.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 40.6 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.5.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 135.9 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: 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MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.3 [rtd-command-info] start-time: 2024-11-13T12:27:42.901013Z, end-time: 2024-11-13T12:28:21.510052Z, duration: 38, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): 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wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading attrs-24.2.0-py3-none-any.whl (63 kB) Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl (18 kB) Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB) Downloading referencing-0.35.1-py3-none-any.whl (26 kB) Downloading rpds_py-0.21.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (364 kB) Downloading more_itertools-10.5.0-py3-none-any.whl (60 kB) Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl (860 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 860.6/860.6 kB 525.5 MB/s eta 0:00:00 Downloading tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (436 kB) Building wheels for collected packages: anndata, asciitree Building wheel for anndata (pyproject.toml): started Building wheel for anndata (pyproject.toml): finished with status 'done' Created wheel for anndata: filename=anndata-0.11.1.dev8+gf4fd6a40-py3-none-any.whl size=142063 sha256=a7853120f42ec4983f60b5e8163145be0cd8755ac193411e61fa335aa07effe1 Stored in directory: /tmp/pip-ephem-wheel-cache-3j686lt0/wheels/82/90/3c/52c0220902083d5ef2c53dee496364d2dd5a9cac08775f57a6 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=a07e7b7dadbca9b6bf4c8c5eec442db5e53a16e9f5b77705516268adaad8885a Stored in directory: /tmp/pip-ephem-wheel-cache-3j686lt0/wheels/a5/d7/98/f56ae733748cd0fa577172bda0e73e0b1f1793c98e09b9e458 Successfully built anndata asciitree Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, asciitree, tzdata, typing-extensions, traitlets, tornado, tinycss2, tabulate, soupsieve, six, ruamel.yaml.clib, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, msgpack, more-itertools, mistune, mdurl, jupyterlab-pygments, fsspec, filelock, fasteners, executing, defusedxml, decorator, click, bleach, attrs, array-api-compat, accessible-pygments, towncrier, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, html5lib, h5py, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-prompt, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, dict2css, awkward, autodocsumm, apeye-core, sphinx-book-theme, myst-parser, jsonschema, ipython, apeye, anndata, sphinx-toolbox, nbformat, nbclient, nbconvert, nbsphinx Successfully installed accessible-pygments-0.0.5 anndata-0.11.1.dev8+gf4fd6a40 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.9.1 asciitree-0.3.3 asttokens-2.4.1 attrs-24.2.0 autodocsumm-0.2.14 awkward-2.7.0 awkward-cpp-41 beautifulsoup4-4.12.3 bleach-6.2.0 cachecontrol-0.14.1 click-8.1.7 cssutils-2.11.1 decorator-5.1.1 defusedxml-0.7.1 dict2css-0.3.0.post1 domdf-python-tools-3.9.0 executing-2.1.0 fasteners-0.19 fastjsonschema-2.20.0 filelock-3.16.1 fsspec-2024.10.0 h5py-3.12.1 html5lib-1.1 ipython-8.29.0 jedi-0.19.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 more-itertools-10.5.0 msgpack-1.1.0 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 numcodecs-0.13.1 numpy-2.1.3 pandas-2.2.3 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 platformdirs-4.3.6 prompt-toolkit-3.0.48 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.0 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.21.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.12 scanpydoc-0.14.1 scipy-1.14.1 six-1.16.0 soupsieve-2.6 sphinx-autodoc-typehints-2.5.0 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-5.0.0 sphinx-jinja2-compat-0.3.0 sphinx-prompt-1.9.0 sphinx-tabs-3.4.5 sphinx-toolbox-3.8.1 sphinxext-opengraph-0.9.1 stack-data-0.6.3 tabulate-0.9.0 tinycss2-1.4.0 tornado-6.4.1 towncrier-24.8.0 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.2 wcwidth-0.2.13 webencodings-0.5.1 zarr-2.18.3 [rtd-command-info] start-time: 2024-11-13T12:28:21.722832Z, end-time: 2024-11-13T12:28:22.841004Z, duration: 1, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true Loading template... Finding news fragments... Rendering news fragments... Writing to newsfile... Staging newsfile... Keeping the following files: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/1743.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/1754.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/1725.bugfix.md Done! [rtd-command-info] start-time: 2024-11-13T12:28:22.933005Z, end-time: 2024-11-13T12:28:22.996221Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from functools import partial from importlib import metadata from pathlib import Path, PurePosixPath from typing import TYPE_CHECKING from docutils import nodes if TYPE_CHECKING: from sphinx.application import Sphinx HERE = Path(__file__).parent _extension_dir = HERE / "extensions" sys.path[:0] = [str(_extension_dir)] # -- General configuration ------------------------------------------------ # 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": "restructuredtext", ".md": "markdown"} master_doc = "index" default_role = "literal" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "tutorials/notebooks/*.rst", # exclude all 0.x.y.md files, but not index.md "release-notes/[!i]*.md", "news.md", # is `include`d into index.md ] 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", "sphinx_search.extension", "sphinxext.opengraph", "scanpydoc", # needs to be before linkcode "sphinx.ext.linkcode", "nbsphinx", "IPython.sphinxext.ipython_console_highlighting", "sphinx_toolbox.more_autodoc.autoprotocol", *(p.stem for p in _extension_dir.glob("*.py")), ] myst_enable_extensions = [ "html_image", # So README.md can be used on github and sphinx docs ] myst_heading_anchors = 3 # Generate the API documentation when building autosummary_generate = True autodoc_member_order = "bysource" issues_github_path = "scverse/anndata" rtd_links_prefix = PurePosixPath("src") # 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"] ], # TODO: sphinx’ builtin autodoc.typehints extension isn’t handled by `qualname_overrides` yet # https://github.com/theislab/scanpydoc/issues/140 ("py:class", "h5py._hl.group.Group"), ("py:class", "h5py._hl.dataset.Dataset"), # for experimental callback exports ("py:class", "anndata.compat.ZappyArray"), ("py:class", "anndata.compat.DaskArray"), ("py:class", "anndata.compat.CupyArray"), ("py:class", "anndata.compat.CupySparseMatrix"), ("py:class", "numpy.ma.core.MaskedArray"), ("py:class", "dask.array.core.Array"), ("py:class", "awkward.highlevel.Array"), ("py:class", "anndata._core.sparse_dataset.BaseCompressedSparseDataset"), ("py:obj", "numpy._typing._array_like._ScalarType_co"), # https://github.com/sphinx-doc/sphinx/issues/10974 ("py:class", "numpy.int64"), # https://github.com/tox-dev/sphinx-autodoc-typehints/issues/498 ("py:class", "types.EllipsisType"), ] def setup(app: Sphinx): app.add_generic_role("small", partial(nodes.inline, classes=["small"])) app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"])) 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://docs.xarray.dev/en/stable", None), dask=("https://docs.dask.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", "anndata._types.ReadCallback": "anndata.experimental.ReadCallback", "anndata._types.WriteCallback": "anndata.experimental.WriteCallback", "anndata._types.Read": "anndata.experimental.Read", "anndata._types.Write": "anndata.experimental.Write", } autodoc_type_aliases = dict( NDArray=":data:`~numpy.typing.NDArray`", AxisStorable=":data:`~anndata.typing.AxisStorable`", **{ f"{v}variantRWAble": ":data:`~anndata.typing.RWAble`" for v in ["In", "Co", "Contra"] }, ) # -- 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 ---------------------------------------------- # The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search html_theme = "scanpydoc" html_theme_options = dict( use_repository_button=True, repository_url="https://github.com/scverse/anndata", repository_branch="main", navigation_with_keys=False, # https://github.com/pydata/pydata-sphinx-theme/issues/1492 ) 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", ) ] [rtd-command-info] start-time: 2024-11-13T12:28:23.058690Z, end-time: 2024-11-13T12:29:09.930534Z, duration: 46, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.3 loading translations [en]... done matplotlib is not installed, social cards will not be generated making output directory... done myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, 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 'h5py' from https://docs.h5py.org/en/latest/objects.inv ... loading intersphinx inventory 'hdf5plugin' from https://hdf5plugin.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'loompy' from https://linnarssonlab.org/loompy/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ... loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'xarray' from https://docs.xarray.dev/en/stable/objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/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, references.rst, release-notes/index.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.abc.CSCDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.abc.CSRDataset.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.io.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.read_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.sparse_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.settings.override.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.AxisStorable.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.Index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.RWAble.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.AnnCollection.iterate_axis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.to_adata.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 Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 19 source files that are out of date updating environment: [new config] 120 added, 0 changed, 0 removed reading sources... [ 1%] _key_contributors reading sources... [ 2%] api reading sources... [ 2%] benchmark-read-write /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/nbsphinx/__init__.py:1074: RuntimeWarning: You are using an unsupported version of pandoc (2.5). Your version must be at least (2.9.2) but less than (4.0.0). Refer to https://pandoc.org/installing.html. Continuing with doubts... nbconvert.utils.pandoc.check_pandoc_version() reading sources... [ 3%] benchmarks reading sources... [ 4%] concatenation reading sources... [ 5%] contributing reading sources... [ 6%] fileformat-prose reading sources... [ 7%] generated/anndata.AnnData reading sources... [ 8%] generated/anndata.AnnData.T reading sources... [ 8%] generated/anndata.AnnData.X reading sources... [ 9%] generated/anndata.AnnData.chunk_X reading sources... [ 10%] generated/anndata.AnnData.chunked_X reading sources... [ 11%] generated/anndata.AnnData.concatenate reading sources... [ 12%] generated/anndata.AnnData.copy reading sources... [ 12%] generated/anndata.AnnData.filename reading sources... [ 13%] generated/anndata.AnnData.is_view reading sources... [ 14%] generated/anndata.AnnData.isbacked reading sources... [ 15%] generated/anndata.AnnData.layers reading sources... [ 16%] generated/anndata.AnnData.n_obs reading sources... [ 17%] generated/anndata.AnnData.n_vars reading sources... [ 18%] generated/anndata.AnnData.obs reading sources... [ 18%] generated/anndata.AnnData.obs_keys reading sources... [ 19%] generated/anndata.AnnData.obs_names reading sources... [ 20%] generated/anndata.AnnData.obs_names_make_unique reading sources... [ 21%] generated/anndata.AnnData.obs_vector reading sources... [ 22%] generated/anndata.AnnData.obsm reading sources... [ 22%] generated/anndata.AnnData.obsm_keys reading sources... [ 23%] generated/anndata.AnnData.obsp reading sources... [ 24%] generated/anndata.AnnData.raw reading sources... [ 25%] generated/anndata.AnnData.rename_categories reading sources... [ 26%] generated/anndata.AnnData.shape reading sources... [ 27%] generated/anndata.AnnData.strings_to_categoricals reading sources... [ 28%] generated/anndata.AnnData.to_df reading sources... [ 28%] generated/anndata.AnnData.to_memory reading sources... [ 29%] generated/anndata.AnnData.transpose reading sources... [ 30%] generated/anndata.AnnData.uns reading sources... [ 31%] generated/anndata.AnnData.uns_keys reading sources... [ 32%] generated/anndata.AnnData.var reading sources... [ 32%] generated/anndata.AnnData.var_keys reading sources... [ 33%] generated/anndata.AnnData.var_names reading sources... [ 34%] generated/anndata.AnnData.var_names_make_unique reading sources... [ 35%] generated/anndata.AnnData.var_vector reading sources... [ 36%] generated/anndata.AnnData.varm reading sources... [ 37%] generated/anndata.AnnData.varm_keys reading sources... [ 38%] generated/anndata.AnnData.varp reading sources... [ 38%] generated/anndata.AnnData.write reading sources... [ 39%] generated/anndata.AnnData.write_csvs reading sources... [ 40%] generated/anndata.AnnData.write_h5ad reading sources... [ 41%] generated/anndata.AnnData.write_loom reading sources... [ 42%] generated/anndata.AnnData.write_zarr reading sources... [ 42%] generated/anndata.ImplicitModificationWarning reading sources... [ 43%] generated/anndata.abc.CSCDataset reading sources... [ 44%] generated/anndata.abc.CSCDataset.__getitem__ reading sources... [ 45%] generated/anndata.abc.CSCDataset.backend reading sources... [ 46%] generated/anndata.abc.CSCDataset.dtype reading sources... [ 47%] generated/anndata.abc.CSCDataset.format reading sources... [ 48%] generated/anndata.abc.CSCDataset.shape reading sources... [ 48%] generated/anndata.abc.CSCDataset.to_memory reading sources... [ 49%] generated/anndata.abc.CSRDataset reading sources... [ 50%] generated/anndata.abc.CSRDataset.__getitem__ reading sources... [ 51%] generated/anndata.abc.CSRDataset.backend reading sources... [ 52%] generated/anndata.abc.CSRDataset.dtype reading sources... [ 52%] generated/anndata.abc.CSRDataset.format reading sources... [ 53%] generated/anndata.abc.CSRDataset.shape reading sources... [ 54%] generated/anndata.abc.CSRDataset.to_memory reading sources... [ 55%] generated/anndata.concat reading sources... [ 56%] generated/anndata.experimental.AnnCollection reading sources... [ 57%] generated/anndata.experimental.AnnCollection.attrs_keys reading sources... [ 57%] generated/anndata.experimental.AnnCollection.convert reading sources... [ 58%] generated/anndata.experimental.AnnCollection.has_backed reading sources... [ 59%] generated/anndata.experimental.AnnCollection.iterate_axis reading sources... [ 60%] generated/anndata.experimental.AnnCollection.lazy_attr reading sources... [ 61%] generated/anndata.experimental.AnnCollection.n_obs reading sources... [ 62%] generated/anndata.experimental.AnnCollection.n_vars reading sources... [ 62%] generated/anndata.experimental.AnnCollection.obs reading sources... [ 63%] generated/anndata.experimental.AnnCollection.obsm reading sources... [ 64%] generated/anndata.experimental.AnnCollection.shape reading sources... [ 65%] generated/anndata.experimental.AnnCollection.to_adata reading sources... [ 66%] generated/anndata.experimental.AnnLoader reading sources... [ 67%] generated/anndata.experimental.IOSpec reading sources... [ 68%] generated/anndata.experimental.IOSpec.encoding_type reading sources... [ 68%] generated/anndata.experimental.IOSpec.encoding_version reading sources... [ 69%] generated/anndata.experimental.Read reading sources... [ 70%] generated/anndata.experimental.ReadCallback reading sources... [ 71%] generated/anndata.experimental.StorageType reading sources... [ 72%] generated/anndata.experimental.Write reading sources... [ 72%] generated/anndata.experimental.WriteCallback reading sources... [ 73%] generated/anndata.experimental.concat_on_disk reading sources... [ 74%] generated/anndata.experimental.read_dispatched reading sources... [ 75%] generated/anndata.experimental.read_elem_as_dask reading sources... [ 76%] generated/anndata.experimental.write_dispatched reading sources... [ 77%] generated/anndata.io.read_csv reading sources... [ 78%] generated/anndata.io.read_elem reading sources... [ 78%] generated/anndata.io.read_excel reading sources... [ 79%] generated/anndata.io.read_h5ad reading sources... [ 80%] generated/anndata.io.read_hdf reading sources... [ 81%] generated/anndata.io.read_loom reading sources... [ 82%] generated/anndata.io.read_mtx reading sources... [ 82%] generated/anndata.io.read_text reading sources... [ 83%] generated/anndata.io.read_umi_tools reading sources... [ 84%] generated/anndata.io.read_zarr reading sources... [ 85%] generated/anndata.io.sparse_dataset reading sources... [ 86%] generated/anndata.io.write_elem reading sources... [ 87%] generated/anndata.settings reading sources... [ 88%] generated/anndata.settings.override reading sources... [ 88%] generated/anndata.typing.AxisStorable reading sources... [ 89%] generated/anndata.typing.Index reading sources... [ 90%] generated/anndata.typing.RWAble reading sources... [ 91%] index reading sources... [ 92%] interoperability reading sources... [ 92%] references reading sources... [ 93%] release-notes/index reading sources... [ 94%] tutorials/index reading sources... [ 95%] tutorials/notebooks/anncollection reading sources... [ 96%] tutorials/notebooks/anncollection-annloader reading sources... [ 97%] tutorials/notebooks/anndata_dask_array reading sources... [ 98%] tutorials/notebooks/annloader reading sources... [ 98%] tutorials/notebooks/awkward-arrays reading sources... [ 99%] tutorials/notebooks/getting-started reading sources... [100%] tutorials/notebooks/{read,write}_dispatched looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_csvs.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_csvs /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_loom.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_loom /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_zarr.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_zarr done preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/copybutton.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] _key_contributors writing output... [ 2%] api writing output... [ 2%] benchmark-read-write writing output... [ 3%] benchmarks writing output... [ 4%] concatenation writing output... [ 5%] contributing writing output... 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