Read the Docs build information
Build id: 3962643
Project: icb-scanpy
Version: 3517
Commit: 9348f05472cc1921189d8249e2b940b5f52dfede
Date: 2026-04-26T13:31:27.832340Z
State: finished
Success: False


[rtd-command-info] start-time: 2026-04-26T13:31:28.570935Z, end-time: 2026-04-26T13:31:29.448927Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-04-26T13:31:29.537047Z, end-time: 2026-04-26T13:31:30.749196Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/3517/head:external-3517
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3517/head -> external-3517
 * [new tag]         1.11.0              -> 1.11.0
 * [new tag]         1.11.0rc1           -> 1.11.0rc1
 * [new tag]         1.11.0rc2           -> 1.11.0rc2

[rtd-command-info] start-time: 2026-04-26T13:31:31.415476Z, end-time: 2026-04-26T13:31:31.578391Z, duration: 0, exit-code: 0
git checkout --force 9348f05472cc1921189d8249e2b940b5f52dfede
Note: switching to '9348f05472cc1921189d8249e2b940b5f52dfede'.

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 9348f05 Update _anndata.py

[rtd-command-info] start-time: 2026-04-26T13:31:31.670599Z, end-time: 2026-04-26T13:31:31.707025Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
submodules:
  include: all
build:
  os: ubuntu-24.04
  tools:
    python: '3.13'
  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: 2026-04-26T13:31:31.837553Z, end-time: 2026-04-26T13:31:31.894021Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2026-04-26T13:31:31.987349Z, end-time: 2026-04-26T13:31:49.313995Z, 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/3517/notebooks'...
Submodule path 'notebooks': checked out '9f6926f87f052603916ee8f222965f654896e0c7'

[rtd-command-info] start-time: 2026-04-26T13:31:49.405964Z, end-time: 2026-04-26T13:31:51.956798Z, duration: 2, 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
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 * [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]           1.0.3       -> 1.0.3
 * [new tag]           1.0.4       -> 1.0.4
 * [new tag]           1.1         -> 1.1
 * [new tag]           1.10.0.dev0 -> 1.10.0.dev0
 * [new tag]           1.10.0rc1   -> 1.10.0rc1
 * [new tag]           1.12.0      -> 1.12.0
 * [new tag]           1.12.0rc1   -> 1.12.0rc1
 * [new tag]           1.1a1       -> 1.1a1
 * [new tag]           1.1a2       -> 1.1a2
 * [new tag]           1.2.0       -> 1.2.0
 * [new tag]           1.2.1       -> 1.2.1
 * [new tag]           1.2.2       -> 1.2.2
 * [new tag]           1.3         -> 1.3
 * [new tag]           1.3.1       -> 1.3.1
 * [new tag]           1.3.2       -> 1.3.2
 * [new tag]           1.3.3       -> 1.3.3
 * [new tag]           1.3.4       -> 1.3.4
 * [new tag]           1.3.5       -> 1.3.5
 * [new tag]           1.3.6       -> 1.3.6
 * [new tag]           1.3.7       -> 1.3.7
 * [new tag]           1.3.8       -> 1.3.8
 * [new tag]           1.4         -> 1.4
 * [new tag]           1.4.1       -> 1.4.1
 * [new tag]           1.4.2       -> 1.4.2
 * [new tag]           1.4.3       -> 1.4.3
 * [new tag]           1.4.4       -> 1.4.4
 * [new tag]           1.4.5       -> 1.4.5
 * [new tag]           1.4.5.1     -> 1.4.5.1
 * [new tag]           1.4.5.post1 -> 1.4.5.post1
 * [new tag]           1.4.5.post2 -> 1.4.5.post2
 * [new tag]           1.4.5.post3 -> 1.4.5.post3
 * [new tag]           1.4.6       -> 1.4.6
 * [new tag]           1.5.0       -> 1.5.0
 * [new tag]           1.5.0a1     -> 1.5.0a1
 * [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

[rtd-command-info] start-time: 2026-04-26T13:31:57.021464Z, end-time: 2026-04-26T13:31:57.108799Z, duration: 0, exit-code: 0
asdf global python 3.13.3


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.3.final.0-64 in 372ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517, 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: 2026-04-26T13:31:58.364571Z, end-time: 2026-04-26T13:32:03.644236Z, duration: 5, 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/3517/lib/python3.13/site-packages (23.1)
Collecting pip
  Downloading pip-26.0.1-py3-none-any.whl (1.8 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages (67.6.1)
Collecting setuptools
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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: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-26.0.1 setuptools-82.0.1

[rtd-command-info] start-time: 2026-04-26T13:32:03.737624Z, end-time: 2026-04-26T13:32:08.719443Z, duration: 4, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
Collecting sphinx
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Collecting requests>=2.30.0 (from sphinx)
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Collecting roman-numerals>=1.0.0 (from sphinx)
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Collecting packaging>=23.0 (from sphinx)
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Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx)
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Collecting charset_normalizer<4,>=2 (from requests>=2.30.0->sphinx)
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Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
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Downloading pygments-2.20.0-py3-none-any.whl (1.2 MB)
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Downloading idna-3.13-py3-none-any.whl (68 kB)
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Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB)
Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.20.0 alabaster-1.0.0 babel-2.18.0 certifi-2026.4.22 charset_normalizer-3.4.7 docutils-0.22.4 idna-3.13 imagesize-2.0.0 packaging-26.2 requests-2.33.1 roman-numerals-4.1.0 snowballstemmer-3.0.1 sphinx-9.1.0 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 urllib3-2.6.3

[rtd-command-info] start-time: 2026-04-26T13:32:08.823710Z, end-time: 2026-04-26T13:34:22.434269Z, duration: 133, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden]
Processing ./.
  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-plot @ git+https://github.com/scverse/anndata-plot.git (from scanpy==1.12.0.dev27+g9348f0547)
  Cloning https://github.com/scverse/anndata-plot.git to /tmp/pip-install-atalq3j_/anndata-plot_49709ec8cc584863b4eafbe8bd22eb79
  Running command git clone --filter=blob:none --quiet https://github.com/scverse/anndata-plot.git /tmp/pip-install-atalq3j_/anndata-plot_49709ec8cc584863b4eafbe8bd22eb79
  Resolved https://github.com/scverse/anndata-plot.git to commit cdc1692083d9537035de9c2cdd3959305481f3d1
  Installing build dependencies: started
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  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>=0.9 (from scanpy==1.12.0.dev27+g9348f0547)
  Downloading anndata-0.12.11-py3-none-any.whl.metadata (9.9 kB)
Collecting h5py>=3.8 (from scanpy==1.12.0.dev27+g9348f0547)
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Collecting joblib (from scanpy==1.12.0.dev27+g9348f0547)
  Downloading joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)
Collecting legacy-api-wrap>=1.4 (from scanpy==1.12.0.dev27+g9348f0547)
  Downloading legacy_api_wrap-1.5-py3-none-any.whl.metadata (2.2 kB)
Collecting matplotlib>=3.6 (from scanpy==1.12.0.dev27+g9348f0547)
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Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages (from scanpy==1.12.0.dev27+g9348f0547) (26.2)
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Collecting scikit-learn<1.6,>=1.1 (from scanpy==1.12.0.dev27+g9348f0547)
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Collecting scipy>=1.11 (from scanpy==1.12.0.dev27+g9348f0547)
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Collecting seaborn>=0.13 (from scanpy==1.12.0.dev27+g9348f0547)
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Collecting session-info2 (from scanpy==1.12.0.dev27+g9348f0547)
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Building wheels for collected packages: scanpy, anndata-plot, sam-algorithm, hnswlib
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.12.0.dev27+g9348f0547-py3-none-any.whl size=2096080 sha256=71492c952c7648a2b9211485fb87486183bcaf217f5d6f7e053335b040e168c8
  Stored in directory: /tmp/pip-ephem-wheel-cache-0hsv1a_1/wheels/53/51/26/7d7c5e376753294ae7e727b337e84069edca550a5bef543c92
  Building wheel for anndata-plot (pyproject.toml): started
  Building wheel for anndata-plot (pyproject.toml): finished with status 'done'
  Created wheel for anndata-plot: filename=anndata_plot-0.0.1-py3-none-any.whl size=5385 sha256=88a190dc5612f97fd4908c9e01e83e39eccd5951dff3c4d90eccfcb3ed92a228
  Stored in directory: /tmp/pip-ephem-wheel-cache-0hsv1a_1/wheels/c9/5d/7a/03a118b8f55fbb0fb25ef9029ed531a1940f857b629d60fdee
  Building wheel for sam-algorithm (pyproject.toml): started
  Building wheel for sam-algorithm (pyproject.toml): finished with status 'done'
  Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34665 sha256=8f4c53ff62b5cb48d96dd03c9db06d636d1e53e2fda977037a74b1beb2dbf523
  Stored in directory: /tmp/pip-ephem-wheel-cache-0hsv1a_1/wheels/b7/67/70/67ec89004e1dccab383c317142419fd53d7b55316b2fa46d24
  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-cp313-cp313-linux_x86_64.whl size=2601896 sha256=d28b262e4f60ec7782970c0d903dbc0903826f2366126f29dd0b041d21a1f979
  Stored in directory: /tmp/pip-ephem-wheel-cache-0hsv1a_1/wheels/35/04/88/b31765a4b9957705e18065db4657e61fc8da54f50e3ef0b67e
Successfully built scanpy anndata-plot sam-algorithm hnswlib
Installing collected packages: webencodings, trove-classifiers, texttable, sortedcontainers, pytz, pure-eval, ptyprocess, nvidia-cusparselt-cu13, multipledispatch, mpmath, fastjsonschema, distlib, cuda-toolkit, zipp, zict, xyzservices, wcwidth, vcs-versioning, uc-micro-py, tzdata, typing-extensions, triton, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tblib, tabulate, sympy, soupsieve, six, setuptools, session-info2, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, pyarrow, psutil, pluggy, platformdirs, pillow, pexpect, pathspec, parso, param, pandocfilters, nvidia-nvtx, nvidia-nvshmem-cu13, nvidia-nvjitlink, nvidia-nccl-cu13, nvidia-curand, nvidia-cufile, nvidia-cuda-runtime, nvidia-cuda-nvrtc, nvidia-cuda-cupti, nvidia-cublas, numpy, nodeenv, networkx, nest-asyncio, natsort, narwhals, msgpack, mistune, mdurl, markdown, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, ipython-pygments-lexers, igraph, identify, greenlet, google-crc32c, fsspec, fonttools, filelock, executing, docutils, dill, defusedxml, decorator, debugpy, cycler, cuda-pathfinder, comm, colorcet, cloudpickle, click, cfgv, bleach, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, sphinx, setuptools-scm, scverse-misc, scipy, referencing, pyviz-comms, python-discovery, python-dateutil, pyct, pybtex, prompt_toolkit, patsy, partd, nvidia-cusparse, nvidia-cufft, nvidia-cudnn-cu13, numcodecs, numba, matplotlib-inline, markdown-it-py, linkify-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, hatchling, h5py, donfig, cuda-bindings, contourpy, beautifulsoup4, zarr, virtualenv, sphinxext-opengraph, sphinx-tabs, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, sparse, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pandas, nvidia-cusolver, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, hatch-vcs, dask, bokeh, xarray, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, pynndescent, pre-commit, panel, myst-parser, jsonschema, ipykernel, distributed, dask-expr, anndata, umap-learn, torch, panel-material-ui, nbformat, holoviews, datashader, dask-glm, nbclient, hv-anndata, harmonypy, dask-ml, sam-algorithm, nbconvert, jupyter-cache, anndata-plot, scanpy, nbsphinx, myst-nb
  Attempting uninstall: setuptools
    Found existing installation: setuptools 82.0.1
    Uninstalling setuptools-82.0.1:
      Successfully uninstalled setuptools-82.0.1
  Attempting uninstall: docutils
    Found existing installation: docutils 0.22.4
    Uninstalling docutils-0.22.4:
      Successfully uninstalled docutils-0.22.4
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 9.1.0
    Uninstalling Sphinx-9.1.0:
      Successfully uninstalled Sphinx-9.1.0

Successfully installed accessible-pygments-0.0.5 anndata-0.12.11 anndata-plot-0.0.1 array-api-compat-1.14.0 asttokens-3.0.1 attrs-26.1.0 beautifulsoup4-4.14.3 bleach-6.3.0 bokeh-3.9.0 cfgv-3.5.0 click-8.3.3 cloudpickle-3.1.2 colorcet-3.1.0 comm-0.2.3 contourpy-1.3.3 cuda-bindings-13.2.0 cuda-pathfinder-1.5.3 cuda-toolkit-13.0.2 cycler-0.12.1 dask-2024.7.1 dask-expr-1.1.9 dask-glm-0.4.0 dask-ml-2024.4.4 datashader-0.19.0 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 dill-0.4.1 distlib-0.4.0 distributed-2024.7.1 docutils-0.21.2 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 filelock-3.29.0 fonttools-4.62.1 fsspec-2026.3.0 google-crc32c-1.8.0 greenlet-3.4.0 h5py-3.16.0 harmonypy-0.2.0 hatch-vcs-0.5.0 hatchling-1.29.0 hnswlib-0.8.0 holoviews-1.23.0b4 hv-anndata-0.0.2 identify-2.6.19 igraph-1.0.0 importlib_metadata-9.0.0 ipykernel-7.2.0 ipython-9.13.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 joblib-1.5.3 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.8.0 jupyter-core-5.9.1 jupyterlab-pygments-0.3.0 kiwisolver-1.5.0 latexcodec-3.0.1 legacy-api-wrap-1.5 leidenalg-0.11.0 linkify-it-py-2.1.0 llvmlite-0.47.0 locket-1.0.0 markdown-3.10.2 markdown-it-py-4.0.0 matplotlib-3.10.9 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 mistune-3.2.0 mpmath-1.3.0 msgpack-1.1.2 multipledispatch-1.0.0 myst-nb-1.4.0 myst-parser-5.0.0 narwhals-2.20.0 natsort-8.4.0 nbclient-0.10.4 nbconvert-7.17.1 nbformat-5.10.4 nbsphinx-0.9.8 nest-asyncio-1.6.0 networkx-3.6.1 nodeenv-1.10.0 numba-0.65.1 numcodecs-0.16.5 numpy-2.4.4 nvidia-cublas-13.1.0.3 nvidia-cuda-cupti-13.0.85 nvidia-cuda-nvrtc-13.0.88 nvidia-cuda-runtime-13.0.96 nvidia-cudnn-cu13-9.19.0.56 nvidia-cufft-12.0.0.61 nvidia-cufile-1.15.1.6 nvidia-curand-10.4.0.35 nvidia-cusolver-12.0.4.66 nvidia-cusparse-12.6.3.3 nvidia-cusparselt-cu13-0.8.0 nvidia-nccl-cu13-2.28.9 nvidia-nvjitlink-13.0.88 nvidia-nvshmem-cu13-3.4.5 nvidia-nvtx-13.0.85 pandas-2.3.3 pandocfilters-1.5.1 panel-1.8.10 panel-material-ui-0.9.1 param-2.3.3 parso-0.8.6 partd-1.4.2 pathspec-1.1.0 patsy-1.0.2 pexpect-4.9.0 pillow-12.2.0 platformdirs-4.9.6 pluggy-1.6.0 pre-commit-4.6.0 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-24.0.0 pybtex-0.26.1 pybtex-docutils-1.0.3 pyct-0.6.0 pydata-sphinx-theme-0.16.1 pynndescent-0.6.0 pyparsing-3.3.2 python-dateutil-2.9.0.post0 python-discovery-1.2.2 pytz-2026.1.post1 pyviz-comms-3.0.6 pyyaml-6.0.3 pyzmq-27.1.0 readthedocs-sphinx-search-0.3.2 referencing-0.37.0 rpds-py-0.30.0 sam-algorithm-1.0.2 scanpy-1.12.0.dev27+g9348f0547 scanpydoc-0.17.1 scikit-learn-1.5.2 scipy-1.17.1 scverse-misc-0.0.4 seaborn-0.13.2 session-info2-0.4.1 setuptools-81.0.0 setuptools-scm-10.0.5 six-1.17.0 sortedcontainers-2.4.0 soupsieve-2.8.3 sparse-0.18.0 sphinx-8.1.3 sphinx-autodoc-typehints-3.0.1 sphinx-book-theme-1.2.0 sphinx-copybutton-0.5.2 sphinx-design-0.7.0 sphinx-tabs-3.5.0 sphinxcontrib-bibtex-2.6.5 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.49 stack_data-0.6.3 statsmodels-0.14.6 sympy-1.14.0 tabulate-0.10.0 tblib-3.2.2 texttable-1.7.0 threadpoolctl-3.6.0 tinycss2-1.4.0 toolz-1.1.0 torch-2.11.0 tornado-6.5.5 towncrier-25.8.0 tqdm-4.67.3 traitlets-5.14.3 triton-3.6.0 trove-classifiers-2026.1.14.14 typing-extensions-4.15.0 tzdata-2026.2 uc-micro-py-2.0.0 umap-learn-0.5.7 vcs-versioning-1.1.1 virtualenv-21.2.4 wcwidth-0.6.0 webencodings-0.5.1 xarray-2026.4.0 xyzservices-2026.3.0 zarr-3.1.6 zict-3.0.0 zipp-3.23.1

[rtd-command-info] start-time: 2026-04-26T13:34:22.624940Z, end-time: 2026-04-26T13:34:22.938711Z, duration: 0, 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/3517/docs/release-notes/3499.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/release-notes/3485.breaking.md
Done!

[rtd-command-info] start-time: 2026-04-26T13:34:23.032522Z, end-time: 2026-04-26T13:34:23.069375Z, duration: 0, exit-code: 0
cat docs/conf.py
"""Configuration for Scanpy’s Sphinx documentation."""

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}, scverse"
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),
    session_info2=("https://session-info2.readthedocs.io/en/stable/", None),
    squidpy=("https://squidpy.readthedocs.io/en/stable/", 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 = {
    "pathlib._local.Path": "pathlib.Path",
    "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"),
]

# 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")

[rtd-command-info] start-time: 2026-04-26T13:34:23.158407Z, end-time: 2026-04-26T13:56:51.727698Z, duration: 1348, exit-code: 1
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.1.3
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/_utils/__init__.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  from anndata import __version__ as anndata_version
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/__init__.py:24: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(anndata.__version__) >= Version("0.11.0rc2"):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/readwrite.py:15: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(anndata.__version__) >= Version("0.11.0rc2"):
Matplotlib is building the font cache; this may take a moment.
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/3517/docs/references.bib... parsed 66 entries
myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence', 'html_image', 'deflist', 'dollarmath', 'html_admonition', 'amsmath'}, 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 v1.4.0: 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, scroll_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/3517/_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 ...
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loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/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 ...
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loading intersphinx inventory 'pytest' from https://docs.pytest.org/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 ...
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loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ...
loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/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/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, 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/3517/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/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 52 source files that are out of date
updating environment: [new config] 309 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/neighbors/__init__.py:427: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if "X_diffmap" in adata.obsm_keys():
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
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`).
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/scatterplots.py:815: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_embedding_density.py:128: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:1546: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:1546: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):

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 41%|████▏     | 9.75M/23.5M [00:00<00:00, 102MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 176MB/s]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/neighbors/__init__.py:427: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if "X_diffmap" in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/paga.py:540: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  (c in adata.obs_keys() and adata.obs[c].dtype.name != "category")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/paga.py:540: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  (c in adata.obs_keys() and adata.obs[c].dtype.name != "category")
reading sources... [ 32%] api/generated/scanpy.pl.paga_compare
reading sources... [ 33%] api/generated/scanpy.pl.paga_path
reading sources... [ 33%] api/generated/scanpy.pl.pca
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 33%] api/generated/scanpy.pl.pca_loadings
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 34%] api/generated/scanpy.pl.pca_overview
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 34%] api/generated/scanpy.pl.pca_variance_ratio
reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_dotplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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... [ 36%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:1612: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if groupby not in adata.obs_keys() or adata.obs[groupby].dtype.name != "category":
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 37%] 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... [ 38%] api/generated/scanpy.pl.tsne
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 38%] api/generated/scanpy.pl.umap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 38%] api/generated/scanpy.pp.combat
reading sources... [ 39%] 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... [ 42%] api/preprocessing
reading sources... [ 42%] api/queries
reading sources... [ 42%] api/reading
reading sources... [ 43%] api/settings
reading sources... [ 43%] api/tools
reading sources... [ 43%] basic_usage
reading sources... [ 44%] community
reading sources... [ 44%] contributors
reading sources... [ 44%] dev/ci
reading sources... [ 45%] dev/code
reading sources... [ 45%] dev/documentation
reading sources... [ 45%] dev/getting-set-up
reading sources... [ 46%] dev/index
reading sources... [ 46%] dev/release
reading sources... [ 46%] dev/testing
reading sources... [ 47%] dev/versioning
reading sources... [ 47%] ecosystem
reading sources... [ 47%] external/exporting
reading sources... [ 48%] external/generated/scanpy.external.tl.cyclone
reading sources... [ 48%] external/generated/scanpy.external.tl.harmony_timeseries
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reading sources... [ 50%] external/generated/scanpy.external.tl.trimap
reading sources... [ 50%] external/generated/scanpy.external.tl.wishbone
reading sources... [ 51%] external/index
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reading sources... [ 73%] generated/scanpy.logging.print_versions
reading sources... [ 73%] generated/scanpy.metrics.confusion_matrix
:17: (ERROR/3) no path specified
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/metrics/_metrics.py:69: UserWarning: 'where' used without 'out', expect unitialized memory in output. If this is intentional, use out=None.
  mtx = np.divide(mtx, sums, where=sums != 0)
reading sources... [ 74%] 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/3517/lib/python3.13/site-packages/scanpy/readwrite.py:831: FutureWarning: The specified parameters ('first_column_names',) are no longer positional. Please specify them like `first_column_names=True`
  adata = read_text(filename, delimiter, first_column_names)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/anndata/_core/anndata.py:1878: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
reading sources... [ 75%] generated/scanpy.pl.dendrogram
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
reading sources... [ 75%] generated/scanpy.pl.dotplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
reading sources... [ 75%] generated/scanpy.pl.heatmap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
reading sources... [ 76%] generated/scanpy.pl.matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
reading sources... [ 76%] generated/scanpy.pl.ranking
reading sources... [ 76%] generated/scanpy.pl.scatter
reading sources... [ 77%] generated/scanpy.pl.stacked_violin
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):

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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/neighbors/__init__.py:427: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if "X_diffmap" in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_utils.py:40: UserWarning: You’re trying to run this on 32738 dimensions of `.X`, if you really want this, set `use_rep='X'`.
         Falling back to preprocessing with `sc.pp.pca` and default params.
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/preprocessing/_pca/__init__.py:245: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  Version(ad.__version__) < Version("0.9")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py:865: FutureWarning: In the future, the default backend for leiden will be igraph instead of leidenalg.

 To achieve the future defaults please pass: flavor="igraph" and n_iterations=2.  directed must also be False to work with igraph's implementation.
  sc.tl.leiden(adata)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/neighbors/__init__.py:427: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if "X_diffmap" in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_utils.py:40: UserWarning: You’re trying to run this on 32738 dimensions of `.X`, if you really want this, set `use_rep='X'`.
         Falling back to preprocessing with `sc.pp.pca` and default params.
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/preprocessing/_pca/__init__.py:245: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  Version(ad.__version__) < Version("0.9")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/neighbors/__init__.py:427: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if "X_diffmap" in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_utils.py:40: UserWarning: You’re trying to run this on 32738 dimensions of `.X`, if you really want this, set `use_rep='X'`.
         Falling back to preprocessing with `sc.pp.pca` and default params.
  warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/preprocessing/_pca/__init__.py:245: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  Version(ad.__version__) < Version("0.9")
reading sources... [ 77%] generated/scanpy.pl.tracksplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:1612: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if groupby not in adata.obs_keys() or adata.obs[groupby].dtype.name != "category":
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_dendrogram.py:123: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in adata.obs_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:1612: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if groupby not in adata.obs_keys() or adata.obs[groupby].dtype.name != "category":
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_anndata.py:2105: FutureWarning: The method obs_keys is deprecated and will be removed in the future. Use obs instead of obs_keys. (e.g. `k in adata.obs` or `str(adata.obs.columns.tolist())`)
  if group not in list(adata.obs_keys()) + [adata.obs.index.name]:
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
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 78%] generated/scanpy.pp.calculate_qc_metrics
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
reading sources... [ 78%] generated/scanpy.pp.downsample_counts
reading sources... [ 78%] generated/scanpy.pp.filter_cells
reading sources... [ 79%] generated/scanpy.pp.filter_genes
reading sources... [ 79%] generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 79%] generated/scanpy.pp.highly_variable_genes
reading sources... [ 80%] generated/scanpy.pp.log1p
reading sources... [ 80%] generated/scanpy.pp.normalize_per_cell
reading sources... [ 80%] generated/scanpy.pp.normalize_total
reading sources... [ 81%] generated/scanpy.pp.pca
reading sources... [ 81%] generated/scanpy.pp.regress_out
reading sources... [ 81%] generated/scanpy.pp.sample
reading sources... [ 82%] generated/scanpy.pp.scale
reading sources... [ 82%] generated/scanpy.pp.subsample
reading sources... [ 82%] generated/scanpy.queries.biomart_annotations
reading sources... [ 83%] generated/scanpy.queries.enrich
reading sources... [ 83%] generated/scanpy.queries.gene_coordinates
reading sources... [ 83%] generated/scanpy.queries.mitochondrial_genes
reading sources... [ 83%] generated/scanpy.read
reading sources... [ 84%] generated/scanpy.read_10x_h5
reading sources... [ 84%] generated/scanpy.read_10x_mtx
reading sources... [ 84%] generated/scanpy.read_csv
reading sources... [ 85%] generated/scanpy.read_excel
reading sources... [ 85%] generated/scanpy.read_h5ad
reading sources... [ 85%] generated/scanpy.read_hdf
reading sources... [ 86%] generated/scanpy.read_loom
reading sources... [ 86%] generated/scanpy.read_mtx
reading sources... [ 86%] generated/scanpy.read_text
reading sources... [ 87%] generated/scanpy.read_umi_tools
reading sources... [ 87%] generated/scanpy.read_visium
reading sources... [ 87%] generated/scanpy.set_figure_params
reading sources... [ 88%] generated/scanpy.tl.dendrogram
reading sources... [ 88%] generated/scanpy.tl.diffmap
reading sources... [ 88%] generated/scanpy.tl.dpt
reading sources... [ 89%] generated/scanpy.tl.draw_graph
reading sources... [ 89%] generated/scanpy.tl.embedding_density
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/datasets/_utils.py:35: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(ad.__version__).release >= (0, 8):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/tools/_embedding_density.py:128: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:1546: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:1546: FutureWarning: The method obsm_keys is deprecated and will be removed in the future. Use obsm instead of obsm_keys. (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`)
  if f"X_{basis}" not in adata.obsm_keys():
reading sources... [ 89%] generated/scanpy.tl.filter_rank_genes_groups
reading sources... [ 90%] generated/scanpy.tl.ingest
reading sources... [ 90%] generated/scanpy.tl.leiden
reading sources... [ 90%] generated/scanpy.tl.louvain
reading sources... [ 91%] generated/scanpy.tl.marker_gene_overlap
reading sources... [ 91%] generated/scanpy.tl.paga
reading sources... [ 91%] generated/scanpy.tl.rank_genes_groups
reading sources... [ 92%] generated/scanpy.tl.score_genes
reading sources... [ 92%] generated/scanpy.tl.score_genes_cell_cycle
reading sources... [ 92%] generated/scanpy.tl.sim
reading sources... [ 93%] generated/scanpy.tl.tsne
reading sources... [ 93%] generated/scanpy.tl.umap
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:143: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
    ~~~~^^^^^^^^^^
  File "<string>", line 4, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 88, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py", line 868, in stacked_violin
    return hv.Scatter(adata, "obsm.X_umap.0", ["obsm.X_umap.1", "obs.leiden"]).opts(
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/selection.py", line 24, in __init__
    super().__init__(*args, **kwargs)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/chart.py", line 62, in __init__
    super().__init__(data, **params)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/__init__.py", line 366, in __init__
    initialized = Interface.initialize(
        type(self), data, kdims, vdims, datatype=kwargs.get("datatype")
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/interface.py", line 288, in initialize
    raise DataError(error)
holoviews.core.data.interface.DataError: None of the available storage backends were able to support the supplied data format. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:154: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
    ~~~~^^^^^^^^^^
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 88, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py", line 868, in stacked_violin
    return hv.Scatter(adata, "obsm.X_umap.0", ["obsm.X_umap.1", "obs.leiden"]).opts(
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/selection.py", line 24, in __init__
    super().__init__(*args, **kwargs)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/chart.py", line 62, in __init__
    super().__init__(data, **params)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/__init__.py", line 366, in __init__
    initialized = Interface.initialize(
        type(self), data, kdims, vdims, datatype=kwargs.get("datatype")
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/interface.py", line 288, in initialize
    raise DataError(error)
holoviews.core.data.interface.DataError: None of the available storage backends were able to support the supplied data format. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:162: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
    ~~~~^^^^^^^^^^
  File "<string>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 88, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/scanpy/plotting/_stacked_violin.py", line 868, in stacked_violin
    return hv.Scatter(adata, "obsm.X_umap.0", ["obsm.X_umap.1", "obs.leiden"]).opts(
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/selection.py", line 24, in __init__
    super().__init__(*args, **kwargs)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/element/chart.py", line 62, in __init__
    super().__init__(data, **params)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/__init__.py", line 366, in __init__
    initialized = Interface.initialize(
        type(self), data, kdims, vdims, datatype=kwargs.get("datatype")
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3517/lib/python3.13/site-packages/holoviews/core/data/interface.py", line 288, in initialize
    raise DataError(error)
holoviews.core.data.interface.DataError: None of the available storage backends were able to support the supplied data format. [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/external/generated/scanpy.external.tl.palantir.rst: document is referenced in multiple toctrees: ['external/tools', 'external/tools'], selecting: external/tools <- external/generated/scanpy.external.tl.palantir
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
done
preparing documents... done
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copying static files: done
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copying extra files: done
copying assets: done
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dumping search index in English (code: en)... done
dumping object inventory... done
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3517/_readthedocs/html/_static/js/rtd_search_config.js
build finished with problems, 46 warnings (with warnings treated as errors).