Read the Docs build information Build id: 2503925 Project: icb-scanpy Version: 1.10.x Commit: 7ccf96d4b6ac10f0a718010578f725e3de2902f7 Date: 2024-09-24T17:19:45.359263Z State: finished Success: True [rtd-command-info] start-time: 2024-09-24T17:22:17.106335Z, end-time: 2024-09-24T17:22:18.644043Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-09-24T17:22:18.729798Z, end-time: 2024-09-24T17:22:19.981303Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/1.10.x:refs/remotes/origin/1.10.x From https://github.com/scverse/scanpy * [new branch] 1.10.x -> origin/1.10.x * [new tag] 1.10.2 -> 1.10.2 * [new tag] 1.10.3 -> 1.10.3 [rtd-command-info] start-time: 2024-09-24T17:22:20.148156Z, end-time: 2024-09-24T17:22:20.356827Z, duration: 0, exit-code: 0 git checkout --force origin/1.10.x Note: switching to 'origin/1.10.x'. 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 <new-branch-name> Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 7ccf96d Backport PR #3258 on branch 1.10.x (Add `SIM` checks) (#3259) [rtd-command-info] start-time: 2024-09-24T17:22:20.453549Z, end-time: 2024-09-24T17:22:20.549414Z, 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: 2024-09-24T17:22:20.718322Z, end-time: 2024-09-24T17:22:21.003047Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-09-24T17:22:21.091286Z, end-time: 2024-09-24T17:22:38.896118Z, duration: 17, 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/1.10.x/notebooks'... Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441' [rtd-command-info] start-time: 2024-09-24T17:22:38.999073Z, end-time: 2024-09-24T17:22:43.571686Z, duration: 4, 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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[new tag] 1.5.1 -> 1.5.1 * [new tag] 1.6.0 -> 1.6.0 * [new tag] 1.7.0rc1 -> 1.7.0rc1 * [new tag] 1.8.0 -> 1.8.0 * [new tag] 1.8.0.dev0 -> 1.8.0.dev0 * [new tag] 1.9.0 -> 1.9.0 * [new tag] 1.9.0.dev0 -> 1.9.0.dev0 Fetching submodule notebooks From https://github.com/scverse/scanpy-tutorials * branch 26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD [rtd-command-info] start-time: 2024-09-24T17:22:52.823866Z, end-time: 2024-09-24T17:22:53.553057Z, duration: 0, exit-code: 0 asdf global python 3.12.3 [rtd-command-info] start-time: 2024-09-24T17:22:54.779585Z, end-time: 2024-09-24T17:22:56.785058Z, duration: 2, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.3.final.0-64 in 865ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x, 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: 2024-09-24T17:22:56.882468Z, end-time: 2024-09-24T17:23:09.057562Z, 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/1.10.x/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 12.6 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.1.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 24.1 MB/s eta 0:00:00 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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, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 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: 2024-09-24T17:23:18.478581Z, end-time: 2024-09-24T17:25:02.533894Z, duration: 104, 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/1.10.x 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.dev11+g7ccf96d4) Downloading anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB) Collecting h5py>=3.1 (from scanpy==1.11.0.dev11+g7ccf96d4) Downloading h5py-3.11.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting joblib (from scanpy==1.11.0.dev11+g7ccf96d4) Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) Collecting legacy-api-wrap>=1.4 (from scanpy==1.11.0.dev11+g7ccf96d4) Downloading legacy_api_wrap-1.4-py3-none-any.whl.metadata 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psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (290 kB) Downloading 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 560.4 MB/s eta 0:00:00 Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) 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.dev11+g7ccf96d4-py3-none-any.whl size=2085612 sha256=d8674b9b2ec01c36c2b7091f79e3f6c4909c3a83abad9fde63205bb548a78de6 Stored in directory: /tmp/pip-ephem-wheel-cache-ckloekpu/wheels/03/32/8f/e2bb6e92096c0d3207d289273547e3ee951711c5aa24ae4c8f 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=34579 sha256=821137afa87c6d9d38945ba7f9a8506ceb98beffd5612fff417a3a6d2a74fad8 Stored in directory: /tmp/pip-ephem-wheel-cache-ckloekpu/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=8023 sha256=5603ea4384737b008be0011393fc0d238d2a94e1bbe19aa4089fdd45b319ad37 Stored in directory: /tmp/pip-ephem-wheel-cache-ckloekpu/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=2288955 sha256=71b1670eb21f655668a4f400874e8bea7e183b3015d0d7abf1450b3896e28390 Stored in directory: /tmp/pip-ephem-wheel-cache-ckloekpu/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e Successfully built scanpy sam-algorithm session-info hnswlib Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, distlib, array-api-compat, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, 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, 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, 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, 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, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb Successfully installed accessible-pygments-0.0.5 anndata-0.10.9 array-api-compat-1.8 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-3.0.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 debugpy-1.8.5 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 distlib-0.3.8 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.54.1 fsspec-2024.9.0 greenlet-3.1.1 h5py-3.11.0 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-8.27.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 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 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-3.3 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-10.4.0 platformdirs-4.3.6 pre-commit-3.8.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.1.4 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.dev11+g7ccf96d4 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 soupsieve-2.6 sphinx-autodoc-typehints-2.4.4 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.5 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.35 stack-data-0.6.3 statsmodels-0.14.3 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-0.12.1 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-20.26.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.20.2 [rtd-command-info] start-time: 2024-09-24T17:25:02.867685Z, end-time: 2024-09-24T17:25:55.019634Z, duration: 52, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true Loading template... Finding news fragments... Rendering news fragments... Matplotlib is building the font cache; this may take a moment. Writing to newsfile... Staging newsfile... Keeping the following files: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/release-notes/3206.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/release-notes/3243.bugfix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/release-notes/3244.bugfix.md Done! [rtd-command-info] start-time: 2024-09-24T17:25:55.726065Z, end-time: 2024-09-24T17:25:55.846802Z, 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") ########################################################################### # 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': "1.10.x", 'version_slug': "1.10.x", '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/"), ("1.10.x", "/en/1.10.x/"), ("1.9.x", "/en/1.9.x/"), ("1.8.x", "/en/1.8.x/"), ("1.7.x", "/en/1.7.x/"), ("1.6.x", "/en/1.6.x/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', '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': 'scanpy', 'github_version': '1.10.x', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '1.10.x', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '1.10.x', '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': '7ccf96d4', } # 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-scanpy/builds/2503925/' 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: 2024-09-24T17:25:56.017741Z, end-time: 2024-09-24T17:29:35.636527Z, duration: 219, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.0.2 loading translations [en]... done making output directory... done checking bibtex cache... out of date parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/references.bib... parsed 66 entries myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'dollarmath', 'colon_fence', 'html_image', 'deflist', 'html_admonition'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) myst-nb v1.1.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/_readthedocs/.jupyter_cache loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/en/stable//objects.inv ... loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest//objects.inv ... loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable//objects.inv ... loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler//objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable//objects.inv ... loading intersphinx inventory 'dask_ml' from https://ml.dask.org//objects.inv ... loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable//objects.inv ... intersphinx inventory has moved: https://anndata.readthedocs.io/en/stable//objects.inv -> https://anndata.readthedocs.io/en/stable/objects.inv loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable//objects.inv ... loading intersphinx inventory 'igraph' from https://python.igraph.org/en/stable/api//objects.inv ... intersphinx inventory has moved: https://bbknn.readthedocs.io/en/latest//objects.inv -> https://bbknn.readthedocs.io/en/latest/objects.inv loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest//objects.inv ... intersphinx inventory has moved: https://docs.dask.org/en/stable//objects.inv -> https://docs.dask.org/en/stable/objects.inv loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest//objects.inv ... intersphinx inventory has moved: https://ipython.readthedocs.io/en/stable//objects.inv -> https://ipython.readthedocs.io/en/stable/objects.inv intersphinx inventory has moved: https://python.igraph.org/en/stable/api//objects.inv -> https://python.igraph.org/en/stable/api/objects.inv loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable//objects.inv ... intersphinx inventory has moved: https://leidenalg.readthedocs.io/en/latest//objects.inv -> https://leidenalg.readthedocs.io/en/latest/objects.inv intersphinx inventory has moved: https://docs.h5py.org/en/stable//objects.inv -> https://docs.h5py.org/en/stable/objects.inv loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable//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 ... intersphinx inventory has moved: https://louvain-igraph.readthedocs.io/en/latest//objects.inv -> https://louvain-igraph.readthedocs.io/en/latest/objects.inv loading intersphinx inventory 'pynndescent' from https://pynndescent.readthedocs.io/en/latest//objects.inv ... loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest//objects.inv ... intersphinx inventory has moved: https://pynndescent.readthedocs.io/en/latest//objects.inv -> https://pynndescent.readthedocs.io/en/latest/objects.inv loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest//objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy//objects.inv ... loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org//objects.inv ... loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable//objects.inv ... intersphinx inventory has moved: https://docs.pytest.org/en/latest//objects.inv -> https://docs.pytest.org/en/latest/objects.inv intersphinx inventory has moved: https://rapids-singlecell.readthedocs.io/en/latest//objects.inv -> https://rapids-singlecell.readthedocs.io/en/latest/objects.inv [autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, api/queries.md, ..., tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/index.md, tutorials/spatial/integration-scanorama.ipynb, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.10.x/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 55 source files that are out of date updating environment: [new config] 311 added, 0 changed, 0 removed reading sources... [ 0%] api/classes reading sources... [ 1%] api/datasets reading sources... [ 1%] api/deprecated reading sources... [ 1%] api/experimental reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... 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[ 16%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.legend reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.savefig reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.show reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_totals reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.get_axes reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.getdoc reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.legend reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.make_figure reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.savefig reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.show reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes reading sources... [ 29%] api/generated/scanpy.pl.diffmap reading sources... [ 29%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 30%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 30%] api/generated/scanpy.pl.draw_graph WARNING: Package 'fa2-modified' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2-modified' (`pip install fa2-modified`). reading sources... [ 30%] api/generated/scanpy.pl.embedding reading sources... [ 31%] api/generated/scanpy.pl.embedding_density :65: (ERROR/3) no path specified :75: (ERROR/3) no path specified :82: (ERROR/3) no path specified reading sources... [ 31%] api/generated/scanpy.pl.filter_genes_dispersion reading sources... [ 31%] api/generated/scanpy.pl.highest_expr_genes reading sources... [ 32%] api/generated/scanpy.pl.highly_variable_genes reading sources... [ 32%] api/generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00<?, ?B/s] 48%|████▊ | 11.2M/23.5M [00:00<00:00, 118MB/s] 100%|██████████| 23.5M/23.5M [00:00<00:00, 143MB/s] reading sources... [ 32%] api/generated/scanpy.pl.paga_compare reading sources... [ 32%] api/generated/scanpy.pl.paga_path reading sources... [ 33%] api/generated/scanpy.pl.pca reading sources... [ 33%] api/generated/scanpy.pl.pca_loadings reading sources... [ 33%] api/generated/scanpy.pl.pca_overview reading sources... [ 34%] api/generated/scanpy.pl.pca_variance_ratio reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups_dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_heatmap WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True` reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_tracksplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_violin reading sources... [ 36%] api/generated/scanpy.pl.scrublet_score_distribution reading sources... [ 37%] api/generated/scanpy.pl.sim reading sources... [ 37%] api/generated/scanpy.pl.spatial reading sources... [ 37%] api/generated/scanpy.pl.tsne reading sources... [ 38%] api/generated/scanpy.pl.umap reading sources... [ 38%] api/generated/scanpy.pp.combat reading sources... [ 38%] api/generated/scanpy.pp.neighbors reading sources... [ 39%] api/generated/scanpy.pp.recipe_seurat reading sources... [ 39%] api/generated/scanpy.pp.recipe_weinreb17 reading sources... [ 39%] api/generated/scanpy.pp.recipe_zheng17 reading sources... [ 40%] api/generated/scanpy.pp.scrublet reading sources... [ 40%] api/generated/scanpy.pp.scrublet_simulate_doublets reading sources... [ 40%] api/get reading sources... [ 41%] api/index reading sources... [ 41%] api/metrics :17: (ERROR/3) no path specified reading sources... [ 41%] api/plotting :65: (ERROR/3) no path specified :75: (ERROR/3) no path specified :82: (ERROR/3) no path specified reading sources... [ 41%] api/preprocessing reading sources... [ 42%] api/queries reading sources... [ 42%] api/reading reading sources... [ 42%] api/settings reading sources... [ 43%] api/tools reading sources... [ 43%] basic_usage reading sources... [ 43%] community reading sources... [ 44%] contributors reading sources... [ 44%] dev/ci reading sources... [ 44%] dev/code reading sources... [ 45%] dev/documentation reading sources... [ 45%] dev/getting-set-up reading sources... [ 45%] dev/index reading sources... [ 46%] dev/release reading sources... [ 46%] dev/testing reading sources... 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[ 51%] external/tools reading sources... [ 52%] generated/scanpy.Neighbors reading sources... [ 52%] generated/scanpy.Neighbors.compute_eigen reading sources... [ 52%] generated/scanpy.Neighbors.compute_neighbors reading sources... [ 53%] generated/scanpy.Neighbors.compute_transitions reading sources... [ 53%] generated/scanpy.Neighbors.connectivities reading sources... [ 53%] generated/scanpy.Neighbors.distances reading sources... [ 54%] generated/scanpy.Neighbors.distances_dpt reading sources... [ 54%] generated/scanpy.Neighbors.eigen_basis reading sources... [ 54%] generated/scanpy.Neighbors.eigen_values reading sources... [ 55%] generated/scanpy.Neighbors.getdoc reading sources... [ 55%] generated/scanpy.Neighbors.rp_forest reading sources... [ 55%] generated/scanpy.Neighbors.to_igraph reading sources... [ 56%] generated/scanpy.Neighbors.transitions reading sources... [ 56%] generated/scanpy.Neighbors.transitions_sym reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.N_PCS reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.autosave reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.autoshow reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.cache_compression reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.cachedir reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.figdir reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_figs reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.logfile reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.logpath reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.max_memory reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.n_jobs reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.plot_suffix reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.set_figure_params reading sources... [ 62%] generated/scanpy._settings.ScanpyConfig.verbosity reading sources... [ 62%] generated/scanpy._settings.ScanpyConfig.writedir reading sources... [ 62%] generated/scanpy.datasets.blobs reading sources... [ 63%] generated/scanpy.datasets.ebi_expression_atlas reading sources... [ 63%] generated/scanpy.datasets.krumsiek11 reading sources... [ 63%] generated/scanpy.datasets.moignard15 reading sources... [ 64%] generated/scanpy.datasets.paul15 reading sources... [ 64%] generated/scanpy.datasets.pbmc3k reading sources... [ 64%] generated/scanpy.datasets.pbmc3k_processed reading sources... [ 65%] generated/scanpy.datasets.pbmc68k_reduced reading sources... [ 65%] generated/scanpy.datasets.toggleswitch reading sources... [ 65%] generated/scanpy.datasets.visium_sge reading sources... [ 66%] generated/scanpy.experimental.pp.highly_variable_genes reading sources... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals reading sources... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca reading sources... [ 67%] generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 67%] generated/scanpy.external.exporting.cellbrowser reading sources... [ 67%] generated/scanpy.external.exporting.spring_project reading sources... [ 68%] generated/scanpy.external.pl.phate reading sources... [ 68%] generated/scanpy.external.pl.sam reading sources... [ 68%] generated/scanpy.external.pl.trimap reading sources... [ 68%] generated/scanpy.external.pl.wishbone_marker_trajectory reading sources... [ 69%] generated/scanpy.external.pp.bbknn reading sources... [ 69%] generated/scanpy.external.pp.dca reading sources... [ 69%] generated/scanpy.external.pp.harmony_integrate reading sources... [ 70%] generated/scanpy.external.pp.hashsolo reading sources... [ 70%] generated/scanpy.external.pp.magic reading sources... [ 70%] generated/scanpy.external.pp.mnn_correct reading sources... [ 71%] generated/scanpy.external.pp.scanorama_integrate reading sources... [ 71%] generated/scanpy.get.aggregate reading sources... [ 71%] generated/scanpy.get.obs_df reading sources... [ 72%] generated/scanpy.get.rank_genes_groups_df reading sources... [ 72%] generated/scanpy.get.var_df reading sources... [ 72%] generated/scanpy.logging.print_header reading sources... [ 73%] generated/scanpy.logging.print_versions reading sources... [ 73%] generated/scanpy.metrics.confusion_matrix :17: (ERROR/3) no path specified reading sources... [ 73%] generated/scanpy.metrics.gearys_c reading sources... [ 74%] generated/scanpy.metrics.morans_i reading sources... [ 74%] generated/scanpy.pl.clustermap /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/anndata/_core/anndata.py:1754: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") reading sources... [ 74%] generated/scanpy.pl.dendrogram reading sources... [ 75%] generated/scanpy.pl.dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 75%] generated/scanpy.pl.heatmap reading sources... [ 75%] generated/scanpy.pl.matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 76%] generated/scanpy.pl.ranking reading sources... [ 76%] generated/scanpy.pl.scatter reading sources... [ 76%] generated/scanpy.pl.stacked_violin WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 77%] generated/scanpy.pl.tracksplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 77%] generated/scanpy.pl.violin reading sources... [ 77%] generated/scanpy.pp.calculate_qc_metrics 0%| | 0.00/5.58M [00:00<?, ?B/s] 0%| | 8.00k/5.58M [00:00<02:02, 47.6kB/s] 1%| | 32.0k/5.58M [00:00<00:56, 102kB/s] 2%|▏ | 96.0k/5.58M [00:00<00:25, 227kB/s] 4%|▎ | 208k/5.58M [00:00<00:14, 396kB/s] 8%|▊ | 432k/5.58M [00:00<00:07, 725kB/s] 16%|█▌ | 888k/5.58M [00:01<00:03, 1.38MB/s] 31%|███ | 1.73M/5.58M [00:01<00:01, 2.63MB/s] 58%|█████▊ | 3.26M/5.58M [00:01<00:00, 4.69MB/s] 86%|████████▌ | 4.79M/5.58M [00:01<00:00, 6.08MB/s] 100%|██████████| 5.58M/5.58M [00:01<00:00, 3.62MB/s] reading sources... [ 77%] generated/scanpy.pp.downsample_counts reading sources... [ 78%] generated/scanpy.pp.filter_cells reading sources... [ 78%] generated/scanpy.pp.filter_genes reading sources... [ 78%] generated/scanpy.pp.filter_genes_dispersion reading sources... [ 79%] generated/scanpy.pp.highly_variable_genes reading sources... [ 79%] generated/scanpy.pp.log1p reading sources... [ 79%] generated/scanpy.pp.normalize_per_cell reading sources... [ 80%] generated/scanpy.pp.normalize_total reading sources... [ 80%] generated/scanpy.pp.pca reading sources... [ 80%] generated/scanpy.pp.regress_out reading sources... [ 81%] generated/scanpy.pp.scale reading sources... [ 81%] generated/scanpy.pp.subsample reading sources... [ 81%] generated/scanpy.queries.biomart_annotations reading sources... [ 82%] generated/scanpy.queries.enrich reading sources... [ 82%] generated/scanpy.queries.gene_coordinates reading sources... [ 82%] generated/scanpy.queries.mitochondrial_genes reading sources... [ 83%] generated/scanpy.read reading sources... [ 83%] generated/scanpy.read_10x_h5 reading sources... [ 83%] generated/scanpy.read_10x_mtx reading sources... [ 84%] generated/scanpy.read_csv reading sources... [ 84%] generated/scanpy.read_excel reading sources... [ 84%] generated/scanpy.read_h5ad reading sources... [ 85%] generated/scanpy.read_hdf reading sources... [ 85%] generated/scanpy.read_loom reading sources... 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[ 91%] generated/scanpy.tl.score_genes reading sources... [ 91%] generated/scanpy.tl.score_genes_cell_cycle reading sources... [ 91%] generated/scanpy.tl.sim reading sources... [ 92%] generated/scanpy.tl.tsne reading sources... [ 92%] generated/scanpy.tl.umap reading sources... [ 92%] how-to/index reading sources... [ 93%] how-to/knn-transformers reading sources... [ 93%] how-to/plotting-with-marsilea reading sources... [ 93%] index reading sources... [ 94%] installation reading sources... [ 94%] news reading sources... [ 94%] references reading sources... [ 95%] release-notes/index reading sources... [ 95%] tutorials/basics/clustering reading sources... [ 95%] tutorials/basics/clustering-2017 reading sources... [ 95%] tutorials/basics/index reading sources... [ 96%] tutorials/basics/integrating-data-using-ingest reading sources... [ 96%] tutorials/experimental/dask reading sources... [ 96%] tutorials/experimental/index reading sources... [ 97%] tutorials/experimental/pearson_residuals reading sources... [ 97%] tutorials/index reading sources... [ 97%] tutorials/plotting/advanced reading sources... [ 98%] tutorials/plotting/core reading sources... [ 98%] tutorials/plotting/index reading sources... [ 98%] tutorials/spatial/basic-analysis reading sources... [ 99%] tutorials/spatial/index reading sources... [ 99%] tutorials/spatial/integration-scanorama reading sources... [ 99%] tutorials/trajectories/index reading sources... [100%] tutorials/trajectories/paga-paul15 reading sources... [100%] usage-principles looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 0%] api/classes /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.css_files' is deprecated. Check CHANGES for Sphinx API modifications. if inject_css and theme_css not in app.builder.css_files: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: The str interface for _CascadingStyleSheet objects is deprecated. Use css.filename instead. if inject_css and theme_css not in app.builder.css_files: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:120: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications. hasattr(app.builder, 'script_files'), /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications. js_file not in app.builder.script_files, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead. js_file not in app.builder.script_files, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/sphinx_tabs/tabs.py:335: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead. if path.suffix == ".js" and path.as_posix() in context["script_files"]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.10.x/lib/python3.12/site-packages/sphinx_tabs/tabs.py:336: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead. context["script_files"].remove(path.as_posix()) writing output... [ 1%] api/datasets writing output... [ 1%] api/deprecated writing output... [ 1%] api/experimental writing output... [ 2%] api/generated/classes/scanpy.pl.DotPlot writing output... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT writing output... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE writing output... [ 8%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES writing output... [ 8%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT writing output... [ 8%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram writing output... [ 9%] api/generated/classes/scanpy.pl.DotPlot.add_totals writing output... [ 9%] api/generated/classes/scanpy.pl.DotPlot.get_axes writing output... [ 9%] api/generated/classes/scanpy.pl.DotPlot.getdoc writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.legend writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.make_figure writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.savefig writing output... 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[ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.legend writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.savefig writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.show writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.style writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES writing output... 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[ 29%] api/generated/scanpy.pl.dpt_groups_pseudotime writing output... [ 30%] api/generated/scanpy.pl.dpt_timeseries writing output... [ 30%] api/generated/scanpy.pl.draw_graph writing output... [ 30%] api/generated/scanpy.pl.embedding writing output... [ 31%] api/generated/scanpy.pl.embedding_density writing output... [ 31%] api/generated/scanpy.pl.filter_genes_dispersion writing output... [ 31%] api/generated/scanpy.pl.highest_expr_genes writing output... [ 32%] api/generated/scanpy.pl.highly_variable_genes writing output... [ 32%] api/generated/scanpy.pl.paga writing output... [ 32%] api/generated/scanpy.pl.paga_compare writing output... [ 32%] api/generated/scanpy.pl.paga_path writing output... [ 33%] api/generated/scanpy.pl.pca writing output... [ 33%] api/generated/scanpy.pl.pca_loadings writing output... [ 33%] api/generated/scanpy.pl.pca_overview writing output... [ 34%] api/generated/scanpy.pl.pca_variance_ratio writing output... 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