Read the Docs build information Build id: 2562517 Project: icb-scanpy Version: 3307 Commit: e406c3499b0bb13d111aa8baaa5aae664bc9645a Date: 2024-10-22T12:36:42.533197Z State: cancelled Success: False [rtd-command-info] start-time: 2024-10-22T12:36:43.933161Z, end-time: 2024-10-22T12:36:45.056755Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-10-22T12:36:45.137758Z, end-time: 2024-10-22T12:36:45.856909Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/3307/head:external-3307 From https://github.com/scverse/scanpy * [new ref] refs/pull/3307/head -> external-3307 [rtd-command-info] start-time: 2024-10-22T12:36:46.005377Z, end-time: 2024-10-22T12:36:46.133322Z, duration: 0, exit-code: 0 git checkout --force e406c3499b0bb13d111aa8baaa5aae664bc9645a Note: switching to 'e406c3499b0bb13d111aa8baaa5aae664bc9645a'. 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 e406c34 (chore): release note [rtd-command-info] start-time: 2024-10-22T12:36:46.221053Z, end-time: 2024-10-22T12:36:46.284199Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 submodules: include: all build: os: ubuntu-24.04 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: fail_on_warning: true # do not change or you will be fired configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - dev # for towncrier - leiden [rtd-command-info] start-time: 2024-10-22T12:36:46.436299Z, end-time: 2024-10-22T12:36:46.525960Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-10-22T12:36:46.614344Z, end-time: 2024-10-22T12:37:02.324143Z, duration: 15, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/notebooks'... Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441' [rtd-command-info] start-time: 2024-10-22T12:37:02.409101Z, end-time: 2024-10-22T12:37:05.600130Z, duration: 3, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 0.0 -> 0.0 * [new tag] 0.1 -> 0.1 * [new tag] 0.2 -> 0.2 * [new tag] 0.2.1 -> 0.2.1 * [new tag] 0.2.3 -> 0.2.3 * [new tag] 0.2.3.5 -> 0.2.3.5 * [new tag] 0.2.4 -> 0.2.4 * [new tag] 0.2.5 -> 0.2.5 * [new tag] 0.2.6 -> 0.2.6 * [new tag] 0.2.7 -> 0.2.7 * [new tag] 0.2.8 -> 0.2.8 * [new tag] 0.2.9 -> 0.2.9 * [new tag] 0.2.9.1 -> 0.2.9.1 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.4 -> 0.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.2.post1 -> 0.4.2.post1 * [new tag] 0.4.2.post2 -> 0.4.2.post2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 1.0 -> 1.0 * [new tag] 1.0.1 -> 1.0.1 * [new tag] 1.0.2 -> 1.0.2 * [new tag] 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2024-10-22T12:37:14.266784Z, end-time: 2024-10-22T12:37:26.712574Z, 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-scanpy/envs/3307/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.2-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 11.3 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3307/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.2.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 24.9 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: 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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-2024.8.30-py3-none-any.whl (167 kB) Downloading charset_normalizer-3.4.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 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 urllib3-2.2.3-py3-none-any.whl (126 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 Jinja2-3.1.4 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-24.1 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: 2024-10-22T12:37:33.168193Z, end-time: 2024-10-22T12:39:11.373303Z, duration: 98, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307 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): finished with status 'done' Collecting anndata>=0.8 (from scanpy==1.11.0.dev142+ge406c349) Downloading 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pure_eval-0.2.3-py3-none-any.whl (11 kB) Downloading tabulate-0.9.0-py3-none-any.whl (35 kB) Downloading tinycss2-1.3.0-py3-none-any.whl (22 kB) Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading greenlet-3.1.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (613 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 613.1/613.1 kB 465.1 MB/s eta 0:00:00 Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl (18 kB) Downloading pyarrow-17.0.0-cp312-cp312-manylinux_2_28_x86_64.whl (39.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.9/39.9 MB 271.0 MB/s eta 0:00:00 Downloading referencing-0.35.1-py3-none-any.whl (26 kB) Downloading rpds_py-0.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (357 kB) Downloading soupsieve-2.6-py3-none-any.whl (36 kB) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: scanpy, sam-algorithm, session-info, hnswlib Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.11.0.dev142+ge406c349-py3-none-any.whl size=2090069 sha256=02753684b347dab3a5b0ee733ecbde8a697e8f7280fabfe4146e0fa623eb6f8f Stored in directory: /tmp/pip-ephem-wheel-cache-slcn9iif/wheels/e6/07/e4/2d7a4084214a7d62a03004e1f24e1af9afeae1698385927ee6 Building wheel for sam-algorithm (setup.py): started Building wheel for sam-algorithm (setup.py): finished with status 'done' Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34578 sha256=d200d3986a9a1d639e009647df5704e96634214c143f9ad375e60b0b2c23dfea Stored in directory: /tmp/pip-ephem-wheel-cache-slcn9iif/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed Building wheel for session-info (setup.py): started Building wheel for session-info (setup.py): finished with status 'done' Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8024 sha256=66e0d3ef4188cd0caf203dbabb9b4679041901ad9e9dc7185efc6a1558846eeb Stored in directory: /tmp/pip-ephem-wheel-cache-slcn9iif/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d Building wheel for hnswlib (pyproject.toml): started Building wheel for hnswlib (pyproject.toml): finished with status 'done' Created wheel for hnswlib: filename=hnswlib-0.8.0-cp312-cp312-linux_x86_64.whl size=2288948 sha256=a6015e00a78c8ceeeb6bd2205e72ebdaf9962ebb4940526a104467b9da46368c Stored in directory: /tmp/pip-ephem-wheel-cache-slcn9iif/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e Successfully built scanpy sam-algorithm session-info hnswlib Installing collected packages: webencodings, wcwidth, texttable, sortedcontainers, pytz, pure-eval, ptyprocess, multipledispatch, fastjsonschema, distlib, array-api-compat, zipp, zict, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tblib, tabulate, stdlib_list, soupsieve, six, setuptools-scm, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nodeenv, networkx, nest-asyncio, natsort, msgpack, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, igraph, identify, greenlet, fsspec, fonttools, filelock, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, cfgv, attrs, accessible-pygments, virtualenv, towncrier, sqlalchemy, session-info, scipy, referencing, python-dateutil, pybtex, pyarrow, patsy, partd, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, sparse, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pre-commit, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, distributed, dask-expr, anndata, umap-learn, nbformat, ipykernel, dask-glm, scanpy, sam-algorithm, nbclient, dask-ml, nbconvert, jupyter-cache, nbsphinx, myst-nb Successfully installed accessible-pygments-0.0.5 anndata-0.10.9 array-api-compat-1.9 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.1.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.7.1 dask-expr-1.1.9 dask-glm-0.3.2 dask-ml-2024.4.4 debugpy-1.8.7 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.9 distlib-0.3.9 distributed-2024.7.1 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.54.1 fsspec-2024.10.0 greenlet-3.1.1 h5py-3.12.1 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.1 igraph-0.11.6 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.28.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-cache-1.0.0 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.7 latexcodec-3.0.0 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.43.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 msgpack-1.1.0 multipledispatch-1.0.0 myst-nb-1.1.2 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 nest-asyncio-1.6.0 networkx-3.4.2 nodeenv-1.9.1 numba-0.60.0 numpy-2.0.2 pandas-2.2.3 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-11.0.0 platformdirs-4.3.6 pre-commit-4.0.1 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-17.0.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.2.0 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-0.20.0 sam-algorithm-1.0.2 scanpy-1.11.0.dev142+ge406c349 scanpydoc-0.14.1 scikit-learn-1.5.2 scipy-1.14.1 seaborn-0.13.2 session-info-1.0.0 setuptools-scm-8.1.0 six-1.16.0 sortedcontainers-2.4.0 soupsieve-2.6 sparse-0.15.4 sphinx-autodoc-typehints-2.5.0 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.7 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.36 stack-data-0.6.3 statsmodels-0.14.4 stdlib_list-0.11.0 tabulate-0.9.0 tblib-3.0.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-1.0.0 tornado-6.4.1 towncrier-24.8.0 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.2 umap-learn-0.5.6 virtualenv-20.27.0 wcwidth-0.2.13 webencodings-0.5.1 zict-3.0.0 zipp-3.20.2 [rtd-command-info] start-time: 2024-10-22T12:39:11.733259Z, end-time: 2024-10-22T12:39:17.826740Z, duration: 6, 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-scanpy/checkouts/3307/docs/release-notes/3267.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3264.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3206.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3155.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3307.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3263.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3180.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/2921.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3184.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3286.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3243.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3296.feature.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3244.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3283.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3307/docs/release-notes/3299.bugfix.md Done! [rtd-command-info] start-time: 2024-10-22T12:39:17.909163Z, end-time: 2024-10-22T12:39:17.976958Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from functools import partial from pathlib import Path, PurePosixPath from typing import TYPE_CHECKING import matplotlib # noqa from docutils import nodes from packaging.version import Version # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use("agg") HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")] import scanpy # noqa if TYPE_CHECKING: from sphinx.application import Sphinx # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = "4.0" # Nicer param docs suppress_warnings = [ "myst.header", # https://github.com/executablebooks/MyST-Parser/issues/262 ] # General information project = "Scanpy" author = "Scanpy development team" repository_url = "https://github.com/scverse/scanpy" copyright = f"{datetime.now():%Y}, the Scanpy development team" version = scanpy.__version__.replace(".dirty", "") # Bumping the version updates all docs, so don't do that if Version(version).is_devrelease: parsed = Version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # Bibliography settings bibtex_bibfiles = ["references.bib"] bibtex_reference_style = "author_year" # default settings templates_path = ["_templates"] master_doc = "index" default_role = "literal" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", # exclude all 0.x.y.md files, but not index.md "release-notes/[!i]*.md", ] extensions = [ "myst_nb", "sphinx_copybutton", "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx.ext.extlinks", "sphinxcontrib.bibtex", "matplotlib.sphinxext.plot_directive", "sphinx_autodoc_typehints", # needs to be after napoleon "git_ref", # needs to be before scanpydoc.rtd_github_links "scanpydoc", # needs to be before sphinx.ext.linkcode "sphinx.ext.linkcode", "sphinx_design", "sphinx_tabs.tabs", "sphinx_search.extension", "sphinxext.opengraph", *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}], ] # 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 api_dir = HERE / "api" # function_images myst_enable_extensions = [ "amsmath", "colon_fence", "deflist", "dollarmath", "html_image", "html_admonition", ] myst_url_schemes = ("http", "https", "mailto", "ftp") myst_heading_anchors = 3 nb_output_stderr = "remove" nb_execution_mode = "off" nb_merge_streams = True ogp_site_url = "https://scanpy.readthedocs.io/en/stable/" ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg" typehints_defaults = "braces" pygments_style = "default" pygments_dark_style = "native" intersphinx_mapping = dict( anndata=("https://anndata.readthedocs.io/en/stable/", None), bbknn=("https://bbknn.readthedocs.io/en/latest/", None), cuml=("https://docs.rapids.ai/api/cuml/stable/", None), cycler=("https://matplotlib.org/cycler/", None), dask=("https://docs.dask.org/en/stable/", None), dask_ml=("https://ml.dask.org/", None), h5py=("https://docs.h5py.org/en/stable/", None), ipython=("https://ipython.readthedocs.io/en/stable/", None), igraph=("https://python.igraph.org/en/stable/api/", None), leidenalg=("https://leidenalg.readthedocs.io/en/latest/", None), louvain=("https://louvain-igraph.readthedocs.io/en/latest/", None), matplotlib=("https://matplotlib.org/stable/", None), networkx=("https://networkx.org/documentation/stable/", None), numpy=("https://numpy.org/doc/stable/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None), pytest=("https://docs.pytest.org/en/latest/", None), python=("https://docs.python.org/3", None), rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None), scipy=("https://docs.scipy.org/doc/scipy/", None), seaborn=("https://seaborn.pydata.org/", None), sklearn=("https://scikit-learn.org/stable/", None), ) # -- Options for HTML output ---------------------------------------------- # The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search html_theme = "scanpydoc" html_theme_options = { "repository_url": repository_url, "use_repository_button": True, } html_static_path = ["_static"] html_show_sphinx = False html_logo = "_static/img/Scanpy_Logo_BrightFG.svg" html_title = "scanpy" def setup(app: Sphinx): """App setup hook.""" app.add_generic_role("small", partial(nodes.inline, classes=["small"])) app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"])) app.add_config_value( "recommonmark_config", { "auto_toc_tree_section": "Contents", "enable_auto_toc_tree": True, "enable_math": True, "enable_inline_math": False, "enable_eval_rst": True, }, True, # noqa: FBT003 ) # -- 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", ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.metrics.DistanceMetric", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", "pandas.core.series.Series": "pandas.Series", "numpy.bool_": "numpy.bool", # Since numpy 2, numpy.bool is the canonical dtype } nitpick_ignore = [ # Technical issues ("py:class", "numpy.int64"), # documented as “attribute” ("py:class", "numpy._typing._dtype_like._SupportsDType"), ("py:class", "numpy._typing._dtype_like._DTypeDict"), # Will probably be documented ("py:class", "scanpy._settings.Verbosity"), ("py:class", "scanpy.neighbors.OnFlySymMatrix"), ("py:class", "scanpy.plotting._baseplot_class.BasePlot"), # Currently undocumented # https://github.com/mwaskom/seaborn/issues/1810 ("py:class", "seaborn.matrix.ClusterGrid"), ("py:class", "samalg.SAM"), # Won’t be documented ("py:class", "scanpy.plotting._utils._AxesSubplot"), ("py:class", "scanpy._utils.Empty"), ("py:class", "numpy.random.mtrand.RandomState"), ("py:class", "scanpy.neighbors._types.KnnTransformerLike"), # Will work once scipy 1.8 is released ("py:class", "scipy.sparse.base.spmatrix"), ("py:class", "scipy.sparse.csr.csr_matrix"), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root # link config extlinks = { "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"), "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"), } rtd_links_prefix = PurePosixPath("src")