Read the Docs build information Build id: 2727083 Project: icb-anndata Version: latest Commit: a8c62e8b7ffaac41553056a823ddff662fffd42c Date: 2025-01-10T15:37:26.665232Z State: finished Success: False [rtd-command-info] start-time: 2025-01-10T15:37:27.924882Z, end-time: 2025-01-10T15:37:28.533039Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2025-01-10T15:37:28.600566Z, end-time: 2025-01-10T15:37:29.568006Z, duration: 0, 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] 0.11.0 -> 0.11.0 * [new tag] 0.11.0rc3 -> 0.11.0rc3 [rtd-command-info] start-time: 2025-01-10T15:37:29.709118Z, end-time: 2025-01-10T15:37:29.791064Z, 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 a8c62e8 (fix): remove `loompy` xfail (#1820) [rtd-command-info] start-time: 2025-01-10T15:37:29.865221Z, end-time: 2025-01-10T15:37:29.924135Z, 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: 2025-01-10T15:37:30.063820Z, end-time: 2025-01-10T15:37:30.145487Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2025-01-10T15:37:30.214919Z, end-time: 2025-01-10T15:37:31.017388Z, 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: 2025-01-10T15:37:31.081998Z, end-time: 2025-01-10T15:37:32.539983Z, duration: 1, exit-code: 0 git fetch --unshallow || true 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] 0.11.0.dev0 -> 0.11.0.dev0 * [new tag] 0.11.0rc1 -> 0.11.0rc1 * [new tag] 0.11.0rc2 -> 0.11.0rc2 * [new tag] 0.3 -> 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 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setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-01-10T15:37:40.677823Z, end-time: 2025-01-10T15:37:52.933539Z, duration: 12, 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 42.8 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-75.8.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 75.3 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: 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sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) Downloading certifi-2024.12.14-py3-none-any.whl (164 kB) Downloading charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (145 kB) Downloading idna-3.10-py3-none-any.whl (70 kB) Downloading MarkupSafe-3.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Downloading urllib3-2.3.0-py3-none-any.whl (128 kB) Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.5 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.16.0 certifi-2024.12.14 charset-normalizer-3.4.1 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 urllib3-2.3.0 [rtd-command-info] start-time: 2025-01-10T15:38:01.119001Z, end-time: 2025-01-10T15:38:40.252491Z, duration: 39, 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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for anndata (pyproject.toml): finished with status 'done' Created wheel for anndata: filename=anndata-0.11.1.dev34+ga8c62e8-py3-none-any.whl size=143745 sha256=f61debfc06cff2da8412eb71b4e97c5f85193dbab2528de5fdc918bd113d8b68 Stored in directory: /tmp/pip-ephem-wheel-cache-1verq8hg/wheels/82/90/3c/52c0220902083d5ef2c53dee496364d2dd5a9cac08775f57a6 Successfully built anndata Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, 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, legacy-api-wrap, jupyterlab-pygments, fsspec, filelock, executing, defusedxml, decorator, crc32c, click, bleach, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, html5lib, h5py, donfig, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, awkward-cpp, 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, ipython, dict2css, awkward, autodocsumm, apeye-core, zarr, sphinx-book-theme, myst-parser, jsonschema, apeye, anndata, sphinx-toolbox, nbformat, nbclient, nbconvert, nbsphinx Successfully installed accessible-pygments-0.0.5 anndata-0.11.1.dev34+ga8c62e8 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.10.0 asttokens-3.0.0 attrs-24.3.0 autodocsumm-0.2.14 awkward-2.7.2 awkward-cpp-43 beautifulsoup4-4.12.3 bleach-6.2.0 cachecontrol-0.14.2 click-8.1.8 crc32c-2.7.1 cssutils-2.11.1 decorator-5.1.1 defusedxml-0.7.1 dict2css-0.3.0.post1 domdf-python-tools-3.9.0 donfig-0.8.1.post1 executing-2.1.0 fastjsonschema-2.21.1 filelock-3.16.1 fsspec-2024.12.0 h5py-3.12.1 html5lib-1.1 ipython-8.31.0 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 legacy-api-wrap-1.4.1 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.1.0 more-itertools-10.5.0 msgpack-1.1.0 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.2 nbconvert-7.16.5 nbformat-5.10.4 nbsphinx-0.9.6 numcodecs-0.14.1 numpy-2.2.1 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-0.16.1 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-0.22.3 ruamel.yaml-0.18.10 ruamel.yaml.clib-0.2.12 scanpydoc-0.14.1 scipy-1.15.0 six-1.17.0 soupsieve-2.6 sphinx-autodoc-typehints-3.0.0 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-6.4.2 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-3.0.0 [rtd-command-info] start-time: 2025-01-10T15:38:40.454402Z, end-time: 2025-01-10T15:38:40.521469Z, duration: 0, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true [rtd-command-info] start-time: 2025-01-10T15:38:40.591314Z, end-time: 2025-01-10T15:38:40.655104Z, 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" autodoc_mock_imports = ["torch"] # autodoc_default_flags = ['members'] issues_github_path = "scverse/anndata" rtd_links_prefix = PurePosixPath("src") 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: 2025-01-10T15:38:40.725076Z, end-time: 2025-01-10T15:38:44.180992Z, duration: 3, exit-code: 2 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 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/generate.py", line 556, in generate_autosummary_docs name, obj, parent, modname = import_by_name(entry.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/__init__.py", line 667, in import_by_name raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions) sphinx.ext.autosummary.ImportExceptionGroup: no module named anndata.AnnData During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/events.py", line 404, in emit results.append(listener.handler(self.app, *args)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/__init__.py", line 834, in process_generate_options generate_autosummary_docs(genfiles, suffix=suffix, base_path=app.srcdir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/generate.py", line 561, in generate_autosummary_docs name, obj, parent, modname = import_ivar_by_name(entry.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/__init__.py", line 724, in import_ivar_by_name real_name, obj, parent, modname = import_by_name(name, prefixes) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/ext/autosummary/__init__.py", line 667, in import_by_name raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions) sphinx.ext.autosummary.ImportExceptionGroup: no module named anndata The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/cmd/build.py", line 496, in build_main app = Sphinx( ^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/application.py", line 295, in __init__ self._init_builder() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/application.py", line 369, in _init_builder self.events.emit('builder-inited') File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.12/site-packages/sphinx/events.py", line 415, in emit raise ExtensionError( sphinx.errors.ExtensionError: Handler for event 'builder-inited' threw an exception (exception: no module named anndata) Extension error (sphinx.ext.autosummary): Handler for event 'builder-inited' threw an exception (exception: no module named anndata)