Read the Docs build information
Build id: 4679178
Project: icb-scanpy
Version: 4487
Commit: 1e54c663f9a60fe50eac232584b834dccdd869b0
Date: 2026-11-05T13:26:49.540359Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-11-05T13:26:50.677545Z, end-time: 2026-11-05T13:26:53.285215Z, duration: 2, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-11-05T13:26:53.363944Z, end-time: 2026-11-05T13:26:54.870529Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/4487/head:external-4487
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/4487/head -> external-4487

[rtd-command-info] start-time: 2026-11-05T13:26:55.694232Z, end-time: 2026-11-05T13:26:56.065953Z, duration: 0, exit-code: 0
git checkout --force 1e54c663f9a60fe50eac232584b834dccdd869b0
Note: switching to '1e54c663f9a60fe50eac232584b834dccdd869b0'.

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 1e54c66 fix formatting

[rtd-command-info] start-time: 2026-11-05T13:26:56.138725Z, end-time: 2026-11-05T13:26:56.174932Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# https://docs.readthedocs.io/page/config-file/v2.html
version: 2
build:
  os: ubuntu-26.04
  tools:
    python: "3.14"
  jobs:
    post_checkout:
      # unshallow so version can be derived from tag
      - git fetch --unshallow || true
    create_environment:
      - asdf plugin add uv
      - asdf install uv latest
      - asdf global uv latest
    pre_build:
      # run towncrier to preview the next version’s release notes
      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true
    build:
      html:
        - uvx hatch -v env create docs
        - uvx hatch run docs:build -T
        - mv docs/_build $READTHEDOCS_OUTPUT

[rtd-command-info] start-time: 2026-11-05T13:26:56.268330Z, end-time: 2026-11-05T13:26:59.562091Z, duration: 3, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/scanpy
 * [new tag]           0.0         -> 0.0
 * [new tag]           0.1         -> 0.1
 * [new tag]           0.2         -> 0.2
 * [new tag]           0.2.1       -> 0.2.1
 * [new tag]           0.2.3       -> 0.2.3
 * [new tag]           0.2.3.5     -> 0.2.3.5
 * [new tag]           0.2.4       -> 0.2.4
 * [new tag]           0.2.5       -> 0.2.5
 * [new tag]           0.2.6       -> 0.2.6
 * [new tag]           0.2.7       -> 0.2.7
 * [new tag]           0.2.8       -> 0.2.8
 * [new tag]           0.2.9       -> 0.2.9
 * [new tag]           0.2.9.1     -> 0.2.9.1
 * [new tag]           0.3         -> 0.3
 * [new tag]           0.3.1       -> 0.3.1
 * [new tag]           0.3.2       -> 0.3.2
 * [new tag]           0.4         -> 0.4
 * [new tag]           0.4.1       -> 0.4.1
 * [new tag]           0.4.2       -> 0.4.2
 * [new tag]           0.4.2.post1 -> 0.4.2.post1
 * [new tag]           0.4.2.post2 -> 0.4.2.post2
 * [new tag]           0.4.3       -> 0.4.3
 * [new tag]           0.4.4       -> 0.4.4
 * [new tag]           1.0         -> 1.0
 * [new tag]           1.0.1       -> 1.0.1
 * [new tag]           1.0.2       -> 1.0.2
 * [new tag]           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]           1.11.0      -> 1.11.0
 * [new tag]           1.11.0rc1   -> 1.11.0rc1
 * [new tag]           1.11.0rc2   -> 1.11.0rc2
 * [new tag]           1.12.0      -> 1.12.0
 * [new tag]           1.12.0rc1   -> 1.12.0rc1
 * [new tag]           1.13.0a1    -> 1.13.0a1
 * [new tag]           1.13.0a2    -> 1.13.0a2
 * [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: 2026-11-05T13:27:03.941104Z, end-time: 2026-11-05T13:27:04.006849Z, duration: 0, exit-code: 0
asdf global python 3.14.6


[rtd-command-info] start-time: 2026-11-05T13:27:04.597559Z, end-time: 2026-11-05T13:27:05.866039Z, duration: 1, exit-code: 0
asdf plugin add uv
updating plugin repository...HEAD is now at 3715919 feat: add elp plugin (#1089)

[rtd-command-info] start-time: 2026-11-05T13:27:06.035554Z, end-time: 2026-11-05T13:27:07.006174Z, duration: 0, exit-code: 0
asdf install uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.7
* Downloading uv release 0.13.7...
uv 0.13.7 installation was successful!

[rtd-command-info] start-time: 2026-11-05T13:27:07.232474Z, end-time: 2026-11-05T13:27:07.332076Z, duration: 0, exit-code: 0
asdf global uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.7

[rtd-command-info] start-time: 2026-11-05T13:27:07.493389Z, end-time: 2026-11-05T13:27:07.530637Z, duration: 0, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true


[rtd-command-info] start-time: 2026-11-05T13:27:07.608897Z, end-time: 2026-11-05T13:27:15.433926Z, duration: 7, exit-code: 0
uvx hatch -v env create docs
Downloading uv (16.4MiB)
Downloading cryptography (4.5MiB)
Downloading virtualenv (5.4MiB)
Downloading pygments (1.2MiB)
 Downloaded pygments
 Downloaded cryptography
 Downloaded virtualenv
 Downloaded uv
Installed 43 packages in 17ms
No config file found, creating one with default settings now...
Success! Please see `hatch config`.
Creating environment: docs
Using CPython 3.14.6 interpreter at: /home/docs/.cache/uv/archive-v0/oC9sqaoJgHWxyNdw/bin/python
Creating virtual environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs
Installing project in development mode
Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs
Resolved 59 packages in 895ms
   Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487
Downloading matplotlib (10.4MiB)
Downloading pillow (6.8MiB)
Downloading fonttools (5.1MiB)
Downloading pydantic-core (2.2MiB)
Downloading networkx (2.0MiB)
Downloading scipy (33.7MiB)
Downloading kiwisolver (1.4MiB)
Downloading statsmodels (11.5MiB)
Downloading pandas (11.5MiB)
Downloading scikit-learn (8.7MiB)
Downloading numpy (15.9MiB)
Downloading llvmlite (56.9MiB)
Downloading numcodecs (1.4MiB)
Downloading h5py (5.2MiB)
Downloading numba (3.7MiB)
 Downloaded kiwisolver
 Downloaded numcodecs
 Downloaded networkx
 Downloaded pydantic-core
 Downloaded numba
 Downloaded fonttools
 Downloaded h5py
 Downloaded pillow
      Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487
 Downloaded scikit-learn
 Downloaded matplotlib
 Downloaded pandas
 Downloaded statsmodels
 Downloaded numpy
 Downloaded scipy
 Downloaded llvmlite
Prepared 55 packages in 960ms
Installed 59 packages in 88ms
 + anndata==0.13.4
 + annotated-types==0.8.0
 + array-api-compat==1.16.0
 + certifi==2026.10.23
 + charset-normalizer==3.5.2
 + cloudpickle==3.1.2
 + contourpy==1.4.0
 + cycler==0.12.1
 + donfig==0.8.1.post1
 + fast-array-utils==1.5.1
 + fonttools==4.68.0
 + formulaic==1.2.2
 + google-crc32c==1.9.0
 + h5py==3.16.0
 + idna==3.20
 + interface-meta==2.0.1
 + joblib==1.6.0
 + kiwisolver==1.5.1
 + legacy-api-wrap==1.5
 + llvmlite==0.50.0
 + matplotlib==3.11.2
 + msgspec==0.22.0
 + narwhals==2.28.0
 + natsort==8.4.0
 + networkx==3.7
 + numba==0.68.1
 + numcodecs==0.17.1
 + numpy==2.5.4
 + packaging==26.3
 + pandas==3.1.1
 + patsy==1.0.3
 + pillow==13.0.0
 + platformdirs==4.14.5
 + pooch==1.9.0
 + pydantic==2.14.3
 + pydantic-core==2.50.4
 + pydantic-settings==2.16.2
 + pynndescent==0.7.0
 + pyparsing==3.3.3
 + python-dateutil==4.0.0
 + python-dotenv==1.2.4
 + pyyaml==6.0.3
 + requests==2.34.2
 + scanpy==1.14.0.dev64+g1e54c663f (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487)
 + scikit-learn==1.9.1
 + scipy==1.18.1
 + scverse-misc==0.1.8
 + seaborn==0.13.2
 + session-info2==0.4.2
 + statsmodels==0.15.0
 + threadpoolctl==3.8.0
 + tqdm==4.70.1
 + typing-extensions==4.16.0
 + typing-inspection==0.4.5
 + tzdata==2026.6
 + umap-learn==0.5.12
 + urllib3==2.8.0
 + wrapt==2.5.2
 + zarr==3.4.2
Checking dependencies
Syncing dependencies
Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs
   Updating https://github.com/scverse/anndata.git (HEAD)
    Updated https://github.com/scverse/anndata.git (63e1117c58cd8bb428b1568878393c899f46c2b5)
Resolved 182 packages in 2.38s
   Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487
   Building anndata @ git+https://github.com/scverse/anndata.git@63e1117c58cd8bb428b1568878393c899f46c2b5
Downloading sphinx-design (2.1MiB)
Downloading jedi (4.7MiB)
Downloading pydata-sphinx-theme (3.1MiB)
Downloading bokeh (6.4MiB)
Downloading accessible-pygments (1.3MiB)
Downloading pyarrow (52.5MiB)
Downloading dask (1.4MiB)
Downloading debugpy (3.8MiB)
Downloading plotly (9.2MiB)
Downloading babel (9.7MiB)
Downloading sqlalchemy (4.4MiB)
Downloading igraph (5.4MiB)
Downloading leidenalg (2.6MiB)
Downloading panel (19.7MiB)
Downloading colour-science (8.6MiB)
Downloading scikit-image (13.1MiB)
Downloading sphinx (3.7MiB)
Downloading panel-material-ui (1.7MiB)
Downloading holoviews (5.7MiB)
 Downloaded dask
 Downloaded accessible-pygments
      Built anndata @ git+https://github.com/scverse/anndata.git@63e1117c58cd8bb428b1568878393c899f46c2b5
      Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487
 Downloaded panel-material-ui
 Downloaded sphinx-design
 Downloaded leidenalg
 Downloaded pydata-sphinx-theme
 Downloaded sphinx
 Downloaded debugpy
 Downloaded sqlalchemy
 Downloaded igraph
 Downloaded holoviews
 Downloaded bokeh
 Downloaded plotly
 Downloaded jedi
 Downloaded colour-science
 Downloaded babel
 Downloaded scikit-image
 Downloaded panel
 Downloaded pyarrow
Prepared 119 packages in 1.28s
Uninstalled 2 packages in 1ms
Installed 125 packages in 394ms
 + accessible-pygments==0.0.5
 + alabaster==1.0.0
 - anndata==0.13.4
 + anndata==0.14.0.dev91+g63e1117c5 (from git+https://github.com/scverse/anndata.git@63e1117c58cd8bb428b1568878393c899f46c2b5)
 + asttokens==3.0.2
 + attrs==26.1.0
 + babel==2.18.0
 + beautifulsoup4==4.15.0
 + bleach==6.4.0
 + bokeh==3.10.1
 + click==8.5.0
 + colorcet==3.2.1
 + colour-science==0.4.7
 + comm==0.2.3
 + dask==2026.8.0
 + dask-glm==0.4.0
 + dask-ml==2025.1.0
 + debugpy==1.8.22
 + defusedxml==0.7.1
 + distributed==2026.8.0
 + docutils==0.22.4
 + executing==2.3.0
 + fastjsonschema==2.22.3
 + fsspec==2026.9.0
 + holoviews==1.23.2
 + hv-anndata==0.1.2
 + igraph==1.0.0
 + illico==0.7.0
 + imageio==2.38.1
 + imagesize==2.0.1
 + importlib-metadata==10.1.0
 + ipykernel==7.4.0
 + ipython==9.18.1
 + ipython-pygments-lexers==1.1.1
 + jedi==0.20.1
 + jinja2==3.1.6
 + jsonschema==4.26.0
 + jsonschema-specifications==2025.9.1
 + jupyter-cache==1.0.1
 + jupyter-client==8.10.0
 + jupyter-core==5.9.1
 + jupyterlab-pygments==0.3.0
 + latexcodec==3.0.1
 + lazy-loader==0.6
 + leidenalg==0.12.0
 + linkify-it-py==2.2.0
 + locket==1.0.0
 + loguru==0.7.3
 + markdown==3.11.2
 + markdown-it-py==4.2.0
 + markupsafe==3.0.4
 + math-core==0.9.0
 + matplotlib-inline==0.2.2
 + mdit-py-plugins==0.6.1
 + mdurl==0.1.2
 + mistune==3.4.0
 + msgpack==1.2.4
 + multipledispatch==1.0.0
 + myst-nb==1.4.0
 + myst-parser==5.1.0
 + nbclient==0.11.0
 + nbconvert==7.17.2
 + nbformat==5.11.1
 + nbsphinx==0.9.8
 + nest-asyncio2==1.7.4
 + nh3==0.3.7
 + pandocfilters==1.5.1
 + panel==1.10.0
 + panel-material-ui==0.16.7
 + param==2.4.2
 + parso==0.8.7
 + partd==1.4.2
 + pexpect==4.9.0
 + plotly==7.1.0
 + prompt-toolkit==3.0.53
 + psutil==7.2.2
 + ptyprocess==0.7.0
 + pure-eval==0.2.4
 + pyarrow==26.0.1
 + pybtex==0.26.1
 + pybtex-docutils==1.0.3
 + pydata-sphinx-theme==0.24.0
 + pydocstring-rs==0.4.1
 + pygments==2.21.0
 + pyviz-comms==3.0.6
 + pyzmq==27.3.0
 + referencing==0.37.0
 + roman-numerals==4.1.0
 + rpds-py==2026.9.1
 ~ scanpy==1.14.0.dev64+g1e54c663f (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487)
 + scikit-image==0.26.0
 + scikit-misc==0.5.3
 + scverse-doc==0.4.0
 + snowballstemmer==3.1.1
 + sortedcontainers==2.4.0
 + soupsieve==4.0.1
 + sparse==0.19.3
 + sphinx==9.2.0
 + sphinx-autodoc-typehints==3.17.5
 + sphinx-copybutton==0.5.2
 + sphinx-design==0.7.0
 + sphinx-exec-jupyter==0.4.3
 + sphinx-issues==6.0.0
 + sphinxcontrib-applehelp==2.0.0
 + sphinxcontrib-bibtex==2.7.0
 + sphinxcontrib-devhelp==2.0.0
 + sphinxcontrib-htmlhelp==2.1.0
 + sphinxcontrib-jsmath==2.0.0
 + sphinxcontrib-qthelp==2.0.0
 + sphinxcontrib-serializinghtml==2.0.0
 + sphinxext-opengraph==0.13.0
 + sqlalchemy==2.1.8
 + stack-data==0.6.3
 + tabulate==0.10.0
 + tblib==3.2.2
 + texttable==1.7.2
 + tifffile==2026.10.15
 + tinycss2==1.5.1
 + toolz==1.2.0
 + tornado==6.6
 + traitlets==5.16.1
 + wcwidth==0.9.4
 + webencodings==0.6.1
 + xyzservices==2026.9.1
 + zict==3.0.0
 + zipp==4.1.2

[rtd-command-info] start-time: 2026-11-05T13:27:15.514107Z, end-time: 2026-11-05T13:33:12.384224Z, duration: 356, exit-code: 0
uvx hatch run docs:build -T
Running Sphinx v9.2.0
loading translations [en]... done
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'dollarmath', 'deflist', 'html_image', 'colon_fence', '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, strikethrough_single_tilde=False, colon_fence_exact_match=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='cache', execution_cache_path='', execution_excludepatterns=['tutorials/*', 'tutorials/*/*', 'tutorials/*/*/*', 'how-to/*', 'how-to/*/*', 'how-to/*/*/*'], execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=True, 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/4487/docs/_build/.jupyter_cache
[autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.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
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:699: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  return getattr(mod, name_parts[-1]), mod, modname
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.Preset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.Verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.datasets.moignard15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/external/generated/scanpy.external.tl.wishbone.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.pp.ScaleResult.std.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.pp.ScrubletResult.doublet_score.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.pp.ScrubletResult.predicted_doublet.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.CellCycleResult.g2m_score.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.CellCycleResult.phase.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.CellCycleResult.s_score.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.DptResult.groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.DptResult.order.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.DptResult.order_indices.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.tl.DptResult.pseudotime.rst
loading intersphinx inventory 'anndata' from https://anndata.scverse.org/en/stable/objects.inv ...
loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'cellrank' from https://cellrank.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'cellbrowser' from https://cellbrowser.readthedocs.io/en/master/objects.inv ...
loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler/objects.inv ...
loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/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 'decoupler' from https://decoupler.scverse.org/en/stable/objects.inv ...
loading intersphinx inventory 'dynamo' from https://dynamo-release.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'fast_array_utils' from https://fast-array-utils.scverse.org/en/stable/objects.inv ...
loading intersphinx inventory 'flit' from https://flit.pypa.io/en/stable/objects.inv ...
loading intersphinx inventory 'glasbey' from https://glasbey.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
loading intersphinx inventory 'holoviews' from https://holoviews.org/objects.inv ...
loading intersphinx inventory 'hv_anndata' from https://hv-anndata.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.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 ...
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 'marsilea' from https://marsilea.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv ...
loading intersphinx inventory 'mudata' from https://mudata.scverse.org/stable/objects.inv ...
loading intersphinx inventory 'napoleon' from https://sphinxcontrib-napoleon.readthedocs.io/en/latest/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 'palantir' from https://palantir.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ...
loading intersphinx inventory 'phate' from https://phate.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'pydeseq2' from https://pydeseq2.readthedocs.io/en/stable/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 ...
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.scverse.org/en/stable/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'scverse_misc' from https://scverse-misc.readthedocs.io/stable/objects.inv ...
loading intersphinx inventory 'scverse_tutorials' from https://scverse-tutorials.readthedocs.io/en/latest/objects.inv ...
intersphinx inventory has moved: https://docs.rapids.ai/api/cuml/stable/objects.inv -> https://docs.nvidia.com/cuml/latest/objects.inv
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 'spatialdata' from https://spatialdata.scverse.org/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 ...
loading intersphinx inventory 'towncrier' from https://towncrier.readthedocs.io/en/stable/objects.inv ...
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/references.bib... parsed 82 entries
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 53 source files that are out of date
updating environment: [new config] 314 added, 0 changed, 0 removed
reading sources... [  0%] api/classes
reading sources... [  1%] api/datasets
reading sources... [  1%] api/deprecated
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:699: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  return getattr(mod, name_parts[-1]), mod, modname
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/sphinx/util/inspect.py:459: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  return getattr(obj, name, *defargs)
reading sources... [  1%] api/experimental
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.legend
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.style
reading sources... [  7%] api/generated/classes/scanpy.pl.MatrixPlot
/tmp/tmpg7sn9351/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpg7sn9351/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executed notebook in 17.26 seconds [mystnb]
/tmp/tmpg7sn9351/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Cached executed notebook: ID=1 [mystnb]
reading sources... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
reading sources... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
reading sources... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
reading sources... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
reading sources... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.style
/tmp/tmpb22jyoi_/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpb22jyoi_/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executed notebook in 0.66 seconds [mystnb]
/tmp/tmpb22jyoi_/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Cached executed notebook: ID=2 [mystnb]
reading sources... [ 10%] api/generated/classes/scanpy.pl.StackedViolin
reading sources... [ 10%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
reading sources... [ 10%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.style
reading sources... [ 15%] api/generated/scanpy.Neighbors
reading sources... [ 15%] api/generated/scanpy.Neighbors.compute_eigen
reading sources... [ 16%] api/generated/scanpy.Neighbors.compute_neighbors
reading sources... [ 16%] api/generated/scanpy.Neighbors.compute_transitions
reading sources... [ 16%] api/generated/scanpy.Neighbors.connectivities
reading sources... [ 17%] api/generated/scanpy.Neighbors.distances
reading sources... [ 17%] api/generated/scanpy.Neighbors.distances_dpt
reading sources... [ 17%] api/generated/scanpy.Neighbors.eigen_basis
reading sources... [ 18%] api/generated/scanpy.Neighbors.eigen_values
reading sources... [ 18%] api/generated/scanpy.Neighbors.rp_forest
reading sources... [ 18%] api/generated/scanpy.Neighbors.to_igraph
reading sources... [ 18%] api/generated/scanpy.Neighbors.transitions
reading sources... [ 19%] api/generated/scanpy.Neighbors.transitions_sym
reading sources... [ 19%] api/generated/scanpy.Preset
reading sources... [ 19%] api/generated/scanpy.Preset.calculate_qc_metrics
reading sources... [ 20%] api/generated/scanpy.Preset.check
reading sources... [ 20%] api/generated/scanpy.Preset.diffmap
reading sources... [ 20%] api/generated/scanpy.Preset.draw_graph
reading sources... [ 21%] api/generated/scanpy.Preset.highly_variable_genes
reading sources... [ 21%] api/generated/scanpy.Preset.leiden
reading sources... [ 21%] api/generated/scanpy.Preset.override
reading sources... [ 22%] api/generated/scanpy.Preset.pca
reading sources... [ 22%] api/generated/scanpy.Preset.rank_genes_groups
reading sources... [ 22%] api/generated/scanpy.Preset.scale
reading sources... [ 23%] api/generated/scanpy.Preset.score_genes
reading sources... [ 23%] api/generated/scanpy.Preset.tsne
reading sources... [ 23%] api/generated/scanpy.Preset.umap
reading sources... [ 24%] api/generated/scanpy.Verbosity
reading sources... [ 24%] api/generated/scanpy.Verbosity.debug
reading sources... [ 24%] api/generated/scanpy.Verbosity.error
reading sources... [ 25%] api/generated/scanpy.Verbosity.hint
reading sources... [ 25%] api/generated/scanpy.Verbosity.info
reading sources... [ 25%] api/generated/scanpy.Verbosity.level
reading sources... [ 25%] api/generated/scanpy.Verbosity.warning
reading sources... [ 26%] api/generated/scanpy.datasets.blobs
reading sources... [ 26%] api/generated/scanpy.datasets.ebi_expression_atlas
reading sources... [ 26%] api/generated/scanpy.datasets.krumsiek11
reading sources... [ 27%] api/generated/scanpy.datasets.moignard15
reading sources... [ 27%] api/generated/scanpy.datasets.paul15
reading sources... [ 27%] api/generated/scanpy.datasets.pbmc3k
reading sources... [ 28%] api/generated/scanpy.datasets.pbmc3k_processed
reading sources... [ 28%] api/generated/scanpy.datasets.pbmc68k_reduced
reading sources... [ 28%] api/generated/scanpy.datasets.toggleswitch
reading sources... [ 29%] api/generated/scanpy.datasets.visium_sge
reading sources... [ 29%] api/generated/scanpy.experimental.pp.highly_variable_genes
reading sources... [ 29%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals
reading sources... [ 30%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
reading sources... [ 30%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals
reading sources... [ 30%] api/generated/scanpy.get.aggregate
reading sources... [ 31%] api/generated/scanpy.get.obs_df
reading sources... [ 31%] api/generated/scanpy.get.pca
/tmp/tmp7s3elmq8/api/generated/scanpy.get.pca-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp7s3elmq8/api/generated/scanpy.get.pca-exec-1.ipynb: Executed notebook in 0.57 seconds [mystnb]
/tmp/tmp7s3elmq8/api/generated/scanpy.get.pca-exec-1.ipynb: Cached executed notebook: ID=3 [mystnb]
reading sources... [ 31%] api/generated/scanpy.get.rank_genes_groups_df
reading sources... [ 32%] api/generated/scanpy.get.var_df
reading sources... [ 32%] api/generated/scanpy.io.read
reading sources... [ 32%] api/generated/scanpy.io.read_10x_h5
reading sources... [ 32%] api/generated/scanpy.io.read_10x_mtx
reading sources... [ 33%] api/generated/scanpy.io.read_csv
reading sources... [ 33%] api/generated/scanpy.io.read_excel
reading sources... [ 33%] api/generated/scanpy.io.read_h5ad
reading sources... [ 34%] api/generated/scanpy.io.read_hdf
reading sources... [ 34%] api/generated/scanpy.io.read_mtx
reading sources... [ 34%] api/generated/scanpy.io.read_text
reading sources... [ 35%] api/generated/scanpy.io.read_umi_tools
reading sources... [ 35%] api/generated/scanpy.io.write
reading sources... [ 35%] api/generated/scanpy.logging.print_header
reading sources... [ 36%] api/generated/scanpy.logging.print_versions
reading sources... [ 36%] api/generated/scanpy.metrics.confusion_matrix
/tmp/tmpo_6bav8j/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpo_6bav8j/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Executed notebook in 0.89 seconds [mystnb]
/tmp/tmpo_6bav8j/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Cached executed notebook: ID=4 [mystnb]
reading sources... [ 36%] api/generated/scanpy.metrics.gearys_c
reading sources... [ 37%] api/generated/scanpy.metrics.modularity
reading sources... [ 37%] api/generated/scanpy.metrics.morans_i
reading sources... [ 37%] api/generated/scanpy.pl.clustermap
/tmp/tmpi0ao7vb0/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpi0ao7vb0/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executed notebook in 1.43 seconds [mystnb]
/tmp/tmpi0ao7vb0/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Cached executed notebook: ID=5 [mystnb]
reading sources... [ 38%] api/generated/scanpy.pl.correlation_matrix
/tmp/tmp3_klh3u6/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp3_klh3u6/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executed notebook in 0.71 seconds [mystnb]
/tmp/tmp3_klh3u6/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Cached executed notebook: ID=6 [mystnb]
reading sources... [ 38%] api/generated/scanpy.pl.dendrogram
/tmp/tmpad1dukox/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpad1dukox/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Executed notebook in 0.65 seconds [mystnb]
/tmp/tmpad1dukox/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Cached executed notebook: ID=7 [mystnb]
reading sources... [ 38%] api/generated/scanpy.pl.diffmap
/tmp/tmps31wwt7u/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmps31wwt7u/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executed notebook in 8.82 seconds [mystnb]
/tmp/tmps31wwt7u/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Cached executed notebook: ID=8 [mystnb]
reading sources... [ 39%] api/generated/scanpy.pl.dot_area
reading sources... [ 39%] api/generated/scanpy.pl.dotplot
/tmp/tmpiahrsmxr/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpiahrsmxr/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Executed notebook in 4.20 seconds [mystnb]
/tmp/tmpiahrsmxr/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Cached executed notebook: ID=9 [mystnb]
reading sources... [ 39%] api/generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 39%] api/generated/scanpy.pl.dpt_timeseries
reading sources... [ 40%] api/generated/scanpy.pl.draw_graph
/tmp/tmpbxa8l7fb/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpbxa8l7fb/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executed notebook in 33.71 seconds [mystnb]
/tmp/tmpbxa8l7fb/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Cached executed notebook: ID=10 [mystnb]
reading sources... [ 40%] api/generated/scanpy.pl.embedding
/tmp/tmpil6qhul1/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpil6qhul1/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executed notebook in 0.98 seconds [mystnb]
/tmp/tmpil6qhul1/api/generated/scanpy.pl.embedding-exec-1.ipynb: Cached executed notebook: ID=11 [mystnb]
reading sources... [ 40%] api/generated/scanpy.pl.embedding_density
/tmp/tmpgpc3cwi8/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpgpc3cwi8/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Executed notebook in 4.66 seconds [mystnb]
/tmp/tmpgpc3cwi8/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Cached executed notebook: ID=12 [mystnb]
reading sources... [ 41%] api/generated/scanpy.pl.heatmap
/tmp/tmpcryzlmmz/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpcryzlmmz/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Executed notebook in 12.90 seconds [mystnb]
/tmp/tmpcryzlmmz/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Cached executed notebook: ID=13 [mystnb]
reading sources... [ 41%] api/generated/scanpy.pl.highest_expr_genes
/tmp/tmp8pdgtt99/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp8pdgtt99/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Executed notebook in 5.91 seconds [mystnb]
/tmp/tmp8pdgtt99/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Cached executed notebook: ID=14 [mystnb]
reading sources... [ 41%] api/generated/scanpy.pl.highly_variable_genes
/tmp/tmpno381b2r/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpno381b2r/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Executed notebook in 9.37 seconds [mystnb]
/tmp/tmpno381b2r/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Cached executed notebook: ID=15 [mystnb]
reading sources... [ 42%] api/generated/scanpy.pl.matrixplot
/tmp/tmpnv4iomhq/api/generated/scanpy.pl.matrixplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpnv4iomhq/api/generated/scanpy.pl.matrixplot-exec-1.ipynb: Executed notebook in 4.00 seconds [mystnb]
/tmp/tmpnv4iomhq/api/generated/scanpy.pl.matrixplot-exec-1.ipynb: Cached executed notebook: ID=16 [mystnb]
reading sources... [ 42%] api/generated/scanpy.pl.paga
/tmp/tmplay66mpf/api/generated/scanpy.pl.paga-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmplay66mpf/api/generated/scanpy.pl.paga-exec-1.ipynb: Executed notebook in 1.24 seconds [mystnb]
/tmp/tmplay66mpf/api/generated/scanpy.pl.paga-exec-1.ipynb: Cached executed notebook: ID=17 [mystnb]
reading sources... [ 42%] api/generated/scanpy.pl.paga_compare
/tmp/tmpwam5yec7/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpwam5yec7/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Executed notebook in 0.76 seconds [mystnb]
/tmp/tmpwam5yec7/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Cached executed notebook: ID=18 [mystnb]
reading sources... [ 43%] api/generated/scanpy.pl.paga_path
reading sources... [ 43%] api/generated/scanpy.pl.pca
/tmp/tmplgr97iun/api/generated/scanpy.pl.pca-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmplgr97iun/api/generated/scanpy.pl.pca-exec-1.ipynb: Executed notebook in 4.12 seconds [mystnb]
/tmp/tmplgr97iun/api/generated/scanpy.pl.pca-exec-1.ipynb: Cached executed notebook: ID=19 [mystnb]
reading sources... [ 43%] api/generated/scanpy.pl.pca_loadings
/tmp/tmp2scn0ssi/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp2scn0ssi/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Executed notebook in 1.08 seconds [mystnb]
/tmp/tmp2scn0ssi/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Cached executed notebook: ID=20 [mystnb]
reading sources... [ 44%] api/generated/scanpy.pl.pca_overview
/tmp/tmp4c0plf5h/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp4c0plf5h/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Executed notebook in 1.27 seconds [mystnb]
/tmp/tmp4c0plf5h/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Cached executed notebook: ID=21 [mystnb]
reading sources... [ 44%] api/generated/scanpy.pl.pca_variance_ratio
/tmp/tmpn9f1zpdn/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpn9f1zpdn/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Executed notebook in 1.01 seconds [mystnb]
/tmp/tmpn9f1zpdn/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Cached executed notebook: ID=22 [mystnb]
reading sources... [ 44%] api/generated/scanpy.pl.rank_genes_groups
/tmp/tmp4ycwf0ay/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp4ycwf0ay/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Executed notebook in 2.76 seconds [mystnb]
/tmp/tmp4ycwf0ay/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Cached executed notebook: ID=23 [mystnb]
reading sources... [ 45%] api/generated/scanpy.pl.rank_genes_groups_dotplot
/tmp/tmpmb7dq8sn/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpmb7dq8sn/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executed notebook in 6.06 seconds [mystnb]
/tmp/tmpmb7dq8sn/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Cached executed notebook: ID=24 [mystnb]
reading sources... [ 45%] api/generated/scanpy.pl.rank_genes_groups_heatmap
/tmp/tmpajtwkeyu/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpajtwkeyu/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Executed notebook in 3.52 seconds [mystnb]
/tmp/tmpajtwkeyu/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Cached executed notebook: ID=25 [mystnb]
reading sources... [ 45%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
/tmp/tmp6or1tobr/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp6or1tobr/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Executed notebook in 3.27 seconds [mystnb]
/tmp/tmp6or1tobr/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Cached executed notebook: ID=26 [mystnb]
reading sources... [ 46%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
/tmp/tmp989gbiyw/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp989gbiyw/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executed notebook in 5.62 seconds [mystnb]
/tmp/tmp989gbiyw/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Cached executed notebook: ID=27 [mystnb]
reading sources... [ 46%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
/tmp/tmpwdqivlak/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpwdqivlak/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executed notebook in 11.59 seconds [mystnb]
/tmp/tmpwdqivlak/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Cached executed notebook: ID=28 [mystnb]
reading sources... [ 46%] api/generated/scanpy.pl.rank_genes_groups_violin
/tmp/tmpja4hb1x1/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpja4hb1x1/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Executed notebook in 2.16 seconds [mystnb]
/tmp/tmpja4hb1x1/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Cached executed notebook: ID=29 [mystnb]
reading sources... [ 46%] api/generated/scanpy.pl.ranking
/tmp/tmpnc4oar_2/api/generated/scanpy.pl.ranking-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpnc4oar_2/api/generated/scanpy.pl.ranking-exec-1.ipynb: Executed notebook in 4.17 seconds [mystnb]
/tmp/tmpnc4oar_2/api/generated/scanpy.pl.ranking-exec-1.ipynb: Cached executed notebook: ID=30 [mystnb]
reading sources... [ 47%] api/generated/scanpy.pl.scatter
/tmp/tmphs7l4dt4/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmphs7l4dt4/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executed notebook in 3.80 seconds [mystnb]
/tmp/tmphs7l4dt4/api/generated/scanpy.pl.scatter-exec-1.ipynb: Cached executed notebook: ID=31 [mystnb]
reading sources... [ 47%] api/generated/scanpy.pl.scrublet_score_distribution
/tmp/tmpvl6i1dj4/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpvl6i1dj4/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executed notebook in 4.95 seconds [mystnb]
/tmp/tmpvl6i1dj4/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Cached executed notebook: ID=32 [mystnb]
reading sources... [ 47%] api/generated/scanpy.pl.sim
reading sources... [ 48%] api/generated/scanpy.pl.spatial
reading sources... [ 48%] api/generated/scanpy.pl.stacked_violin
/tmp/tmpqhmwhug7/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpqhmwhug7/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executed notebook in 19.82 seconds [mystnb]
/tmp/tmpqhmwhug7/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Cached executed notebook: ID=33 [mystnb]
reading sources... [ 48%] api/generated/scanpy.pl.tracksplot
/tmp/tmpy5z_evmb/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpy5z_evmb/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executed notebook in 14.36 seconds [mystnb]
/tmp/tmpy5z_evmb/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Cached executed notebook: ID=34 [mystnb]
reading sources... [ 49%] api/generated/scanpy.pl.tsne
/tmp/tmplmuevwdf/api/generated/scanpy.pl.tsne-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmplmuevwdf/api/generated/scanpy.pl.tsne-exec-1.ipynb: Executed notebook in 11.03 seconds [mystnb]
/tmp/tmplmuevwdf/api/generated/scanpy.pl.tsne-exec-1.ipynb: Cached executed notebook: ID=35 [mystnb]
reading sources... [ 49%] api/generated/scanpy.pl.umap
/tmp/tmpza82u1t0/api/generated/scanpy.pl.umap-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpza82u1t0/api/generated/scanpy.pl.umap-exec-1.ipynb: Executed notebook in 6.15 seconds [mystnb]
/tmp/tmpza82u1t0/api/generated/scanpy.pl.umap-exec-1.ipynb: Cached executed notebook: ID=36 [mystnb]
reading sources... [ 49%] api/generated/scanpy.pl.violin
/tmp/tmp077w32mj/api/generated/scanpy.pl.violin-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp077w32mj/api/generated/scanpy.pl.violin-exec-1.ipynb: Executed notebook in 9.82 seconds [mystnb]
/tmp/tmp077w32mj/api/generated/scanpy.pl.violin-exec-1.ipynb: Cached executed notebook: ID=37 [mystnb]
reading sources... [ 50%] api/generated/scanpy.pp.HashsoloOut
reading sources... [ 50%] api/generated/scanpy.pp.HashsoloResult
reading sources... [ 50%] api/generated/scanpy.pp.HashsoloResult.classification
reading sources... [ 51%] api/generated/scanpy.pp.HashsoloResult.probabilities
reading sources... [ 51%] api/generated/scanpy.pp.NeighborsOut
reading sources... [ 51%] api/generated/scanpy.pp.NeighborsResult
reading sources... [ 52%] api/generated/scanpy.pp.NeighborsResult.connectivities
reading sources... [ 52%] api/generated/scanpy.pp.NeighborsResult.distances
reading sources... [ 52%] api/generated/scanpy.pp.NormalizeTotalOut
reading sources... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult
reading sources... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult.norm_factor
reading sources... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult.normalized
reading sources... [ 54%] api/generated/scanpy.pp.PcaOut
reading sources... [ 54%] api/generated/scanpy.pp.PcaResult
reading sources... [ 54%] api/generated/scanpy.pp.PcaResult.embedding
reading sources... [ 54%] api/generated/scanpy.pp.PcaResult.loadings
reading sources... [ 55%] api/generated/scanpy.pp.QcMetricsOut
reading sources... [ 55%] api/generated/scanpy.pp.QcMetricsResult
reading sources... [ 55%] api/generated/scanpy.pp.QcMetricsResult.obs
reading sources... [ 56%] api/generated/scanpy.pp.QcMetricsResult.var
reading sources... [ 56%] api/generated/scanpy.pp.ScaleOut
reading sources... [ 56%] api/generated/scanpy.pp.ScaleResult
reading sources... [ 57%] api/generated/scanpy.pp.ScaleResult.mean
reading sources... [ 57%] api/generated/scanpy.pp.ScaleResult.scaled
reading sources... [ 57%] api/generated/scanpy.pp.ScaleResult.std
reading sources... [ 58%] api/generated/scanpy.pp.ScrubletOut
reading sources... [ 58%] api/generated/scanpy.pp.ScrubletResult
reading sources... [ 58%] api/generated/scanpy.pp.ScrubletResult.doublet_score
reading sources... [ 59%] api/generated/scanpy.pp.ScrubletResult.predicted_doublet
reading sources... [ 59%] api/generated/scanpy.pp.bbknn
reading sources... [ 59%] api/generated/scanpy.pp.calculate_qc_metrics
/tmp/tmpz751ktor/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmpz751ktor/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Executed notebook in 15.48 seconds [mystnb]
/tmp/tmpz751ktor/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Cached executed notebook: ID=38 [mystnb]
reading sources... [ 60%] api/generated/scanpy.pp.combat
reading sources... [ 60%] api/generated/scanpy.pp.downsample_counts
reading sources... [ 60%] api/generated/scanpy.pp.filter_cells
reading sources... [ 61%] api/generated/scanpy.pp.filter_genes
reading sources... [ 61%] api/generated/scanpy.pp.harmony_integrate
reading sources... [ 61%] api/generated/scanpy.pp.hashsolo
reading sources... [ 61%] api/generated/scanpy.pp.highly_variable_genes
reading sources... [ 62%] api/generated/scanpy.pp.log1p
reading sources... [ 62%] api/generated/scanpy.pp.neighbors
reading sources... [ 62%] api/generated/scanpy.pp.normalize_shifted_clr
reading sources... [ 63%] api/generated/scanpy.pp.normalize_total
reading sources... [ 63%] api/generated/scanpy.pp.pca
reading sources... [ 63%] api/generated/scanpy.pp.recipe_seurat
reading sources... [ 64%] api/generated/scanpy.pp.recipe_weinreb17
reading sources... [ 64%] api/generated/scanpy.pp.recipe_zheng17
reading sources... [ 64%] api/generated/scanpy.pp.regress_out
reading sources... [ 65%] api/generated/scanpy.pp.sample
reading sources... [ 65%] api/generated/scanpy.pp.scale
reading sources... [ 65%] api/generated/scanpy.pp.scrublet
reading sources... [ 66%] api/generated/scanpy.pp.scrublet_simulate_doublets
reading sources... [ 66%] api/generated/scanpy.pp.subsample
reading sources... [ 66%] api/generated/scanpy.queries.biomart_annotations
reading sources... [ 67%] api/generated/scanpy.queries.enrich
reading sources... [ 67%] api/generated/scanpy.queries.gene_coordinates
reading sources... [ 67%] api/generated/scanpy.queries.mitochondrial_genes
reading sources... [ 68%] api/generated/scanpy.read_loom
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/sphinx/util/inspect.py:459: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  return getattr(obj, name, *defargs)
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/sphinx_autodoc_typehints/_objects.py:135: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  found = getattr(found, part, None)
/home/docs/.local/share/hatch/env/virtual/scanpy/2-1k4rz3/docs/lib/python3.14/site-packages/scverse_doc/source.py:203: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead
  obj = getattr(obj, part)
reading sources... [ 68%] api/generated/scanpy.read_visium
reading sources... [ 68%] api/generated/scanpy.set_figure_params
reading sources... [ 68%] api/generated/scanpy.settings
reading sources... [ 69%] api/generated/scanpy.settings.override
reading sources... [ 69%] api/generated/scanpy.tl.CellCycleOut
reading sources... [ 69%] api/generated/scanpy.tl.CellCycleResult
reading sources... [ 70%] api/generated/scanpy.tl.CellCycleResult.g2m_score
reading sources... [ 70%] api/generated/scanpy.tl.CellCycleResult.phase
reading sources... [ 70%] api/generated/scanpy.tl.CellCycleResult.s_score
reading sources... [ 71%] api/generated/scanpy.tl.DptOut
reading sources... [ 71%] api/generated/scanpy.tl.DptResult
reading sources... [ 71%] api/generated/scanpy.tl.DptResult.groups
reading sources... [ 72%] api/generated/scanpy.tl.DptResult.order
reading sources... [ 72%] api/generated/scanpy.tl.DptResult.order_indices
reading sources... [ 72%] api/generated/scanpy.tl.DptResult.pseudotime
reading sources... [ 73%] api/generated/scanpy.tl.dendrogram
reading sources... [ 73%] api/generated/scanpy.tl.diffmap
reading sources... [ 73%] api/generated/scanpy.tl.dpt
reading sources... [ 74%] api/generated/scanpy.tl.draw_graph
reading sources... [ 74%] api/generated/scanpy.tl.embedding_density
/tmp/tmp4xu6di3_/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Executing notebook using local CWD [mystnb]
/tmp/tmp4xu6di3_/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Executed notebook in 2.07 seconds [mystnb]
/tmp/tmp4xu6di3_/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Cached executed notebook: ID=39 [mystnb]
reading sources... [ 74%] api/generated/scanpy.tl.filter_rank_genes_groups
reading sources... [ 75%] api/generated/scanpy.tl.ingest
reading sources... [ 75%] api/generated/scanpy.tl.leiden
reading sources... [ 75%] api/generated/scanpy.tl.louvain
reading sources... [ 75%] api/generated/scanpy.tl.marker_gene_overlap
reading sources... [ 76%] api/generated/scanpy.tl.paga
reading sources... [ 76%] api/generated/scanpy.tl.rank_genes_groups
reading sources... [ 76%] api/generated/scanpy.tl.score_genes
reading sources... [ 77%] api/generated/scanpy.tl.score_genes_cell_cycle
reading sources... [ 77%] api/generated/scanpy.tl.sim
reading sources... [ 77%] api/generated/scanpy.tl.tsne
reading sources... [ 78%] api/generated/scanpy.tl.umap
reading sources... [ 78%] api/get
reading sources... [ 78%] api/index
reading sources... [ 79%] api/io
reading sources... [ 79%] api/metrics
reading sources... [ 79%] api/plotting
reading sources... [ 80%] api/preprocessing
reading sources... [ 80%] api/queries
reading sources... [ 80%] api/settings
reading sources... [ 81%] api/tools
reading sources... [ 81%] basic_usage
reading sources... [ 81%] citation
reading sources... [ 82%] community
reading sources... [ 82%] contributors
reading sources... [ 82%] dev/ci
reading sources... [ 82%] dev/code
reading sources... [ 83%] dev/documentation
reading sources... [ 83%] dev/getting-set-up
reading sources... [ 83%] dev/index
reading sources... [ 84%] dev/release
reading sources... [ 84%] dev/testing
reading sources... [ 84%] dev/versioning
reading sources... [ 85%] external/exporting
reading sources... [ 85%] external/generated/scanpy.external.exporting.cellbrowser
reading sources... [ 85%] external/generated/scanpy.external.exporting.spring_project
reading sources... [ 86%] external/generated/scanpy.external.pl.phate
reading sources... [ 86%] external/generated/scanpy.external.pl.sam
reading sources... [ 86%] external/generated/scanpy.external.pl.trimap
reading sources... [ 87%] external/generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 87%] external/generated/scanpy.external.pp.bbknn
reading sources... [ 87%] external/generated/scanpy.external.pp.hashsolo
reading sources... [ 88%] external/generated/scanpy.external.pp.magic
reading sources... [ 88%] external/generated/scanpy.external.pp.mnn_correct
reading sources... [ 88%] external/generated/scanpy.external.pp.scanorama_integrate
reading sources... [ 89%] external/generated/scanpy.external.tl.cyclone
reading sources... [ 89%] external/generated/scanpy.external.tl.harmony_timeseries
reading sources... [ 89%] external/generated/scanpy.external.tl.palantir
reading sources... [ 89%] external/generated/scanpy.external.tl.palantir_results
reading sources... [ 90%] external/generated/scanpy.external.tl.phate
reading sources... [ 90%] external/generated/scanpy.external.tl.phenograph
reading sources... [ 90%] external/generated/scanpy.external.tl.sam
reading sources... [ 91%] external/generated/scanpy.external.tl.sandbag
reading sources... [ 91%] external/generated/scanpy.external.tl.trimap
reading sources... [ 91%] external/generated/scanpy.external.tl.wishbone
reading sources... [ 92%] external/index
reading sources... [ 92%] external/plotting
reading sources... [ 92%] external/preprocessing
reading sources... [ 93%] external/tools
reading sources... [ 93%] how-to/cell-cycle
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/how-to/cell-cycle.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb]
reading sources... [ 93%] how-to/index
reading sources... [ 94%] how-to/knn-transformers
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/how-to/knn-transformers.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb]
reading sources... [ 94%] how-to/plotting-with-marsilea
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/how-to/plotting-with-marsilea.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb]
reading sources... [ 94%] index
reading sources... [ 95%] installation
reading sources... [ 95%] quickstart
reading sources... [ 95%] references
reading sources... [ 96%] release-notes/index
reading sources... [ 96%] tutorials/basics/clustering
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/basics/clustering.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 96%] tutorials/basics/clustering-2017
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/basics/clustering-2017.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 96%] tutorials/basics/index
reading sources... [ 97%] tutorials/basics/integrating-data-using-ingest
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/basics/integrating-data-using-ingest.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 97%] tutorials/experimental/dask
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/experimental/dask.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 97%] tutorials/experimental/index
reading sources... [ 98%] tutorials/experimental/pearson_residuals
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/experimental/pearson_residuals.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 98%] tutorials/index
reading sources... [ 98%] tutorials/plotting/advanced
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/plotting/advanced.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 99%] tutorials/plotting/core
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/plotting/core.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [ 99%] tutorials/plotting/index
reading sources... [ 99%] tutorials/trajectories/index
reading sources... [100%] tutorials/trajectories/paga-paul15
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/tutorials/trajectories/paga-paul15.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb]
reading sources... [100%] usage-principles

looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.pl.ranking.rst: document is referenced in multiple toctrees: ['api/plotting', 'api/plotting'], selecting: api/plotting <- api/generated/scanpy.pl.ranking
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/api/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- api/generated/scanpy.pp.pca
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/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
done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/_build/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/_build/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/_build/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4487/docs/_build/html/_static/copybutton.js
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  0%] api/classes
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_COLORMAP
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.legend
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.style
writing output... [  7%] api/generated/classes/scanpy.pl.MatrixPlot
writing output... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
writing output... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  8%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
writing output... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
writing output... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
writing output... [  9%] api/generated/classes/scanpy.pl.MatrixPlot.style
writing output... [ 10%] api/generated/classes/scanpy.pl.StackedViolin
writing output... [ 10%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
writing output... [ 10%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
writing output... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
writing output... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
writing output... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
writing output... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
writing output... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
writing output... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
writing output... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.style
writing output... [ 15%] api/generated/scanpy.Neighbors
writing output... [ 15%] api/generated/scanpy.Neighbors.compute_eigen
writing output... [ 16%] api/generated/scanpy.Neighbors.compute_neighbors
writing output... [ 16%] api/generated/scanpy.Neighbors.compute_transitions
writing output... [ 16%] api/generated/scanpy.Neighbors.connectivities
writing output... [ 17%] api/generated/scanpy.Neighbors.distances
writing output... [ 17%] api/generated/scanpy.Neighbors.distances_dpt
writing output... [ 17%] api/generated/scanpy.Neighbors.eigen_basis
writing output... [ 18%] api/generated/scanpy.Neighbors.eigen_values
writing output... [ 18%] api/generated/scanpy.Neighbors.rp_forest
writing output... [ 18%] api/generated/scanpy.Neighbors.to_igraph
writing output... [ 18%] api/generated/scanpy.Neighbors.transitions
writing output... [ 19%] api/generated/scanpy.Neighbors.transitions_sym
writing output... [ 19%] api/generated/scanpy.Preset
writing output... [ 19%] api/generated/scanpy.Preset.calculate_qc_metrics
writing output... [ 20%] api/generated/scanpy.Preset.check
writing output... [ 20%] api/generated/scanpy.Preset.diffmap
writing output... [ 20%] api/generated/scanpy.Preset.draw_graph
writing output... [ 21%] api/generated/scanpy.Preset.highly_variable_genes
writing output... [ 21%] api/generated/scanpy.Preset.leiden
writing output... [ 21%] api/generated/scanpy.Preset.override
writing output... [ 22%] api/generated/scanpy.Preset.pca
writing output... [ 22%] api/generated/scanpy.Preset.rank_genes_groups
writing output... [ 22%] api/generated/scanpy.Preset.scale
writing output... [ 23%] api/generated/scanpy.Preset.score_genes
writing output... [ 23%] api/generated/scanpy.Preset.tsne
writing output... [ 23%] api/generated/scanpy.Preset.umap
writing output... [ 24%] api/generated/scanpy.Verbosity
writing output... [ 24%] api/generated/scanpy.Verbosity.debug
writing output... [ 24%] api/generated/scanpy.Verbosity.error
writing output... [ 25%] api/generated/scanpy.Verbosity.hint
writing output... [ 25%] api/generated/scanpy.Verbosity.info
writing output... [ 25%] api/generated/scanpy.Verbosity.level
writing output... [ 25%] api/generated/scanpy.Verbosity.warning
writing output... [ 26%] api/generated/scanpy.datasets.blobs
writing output... [ 26%] api/generated/scanpy.datasets.ebi_expression_atlas
writing output... [ 26%] api/generated/scanpy.datasets.krumsiek11
writing output... [ 27%] api/generated/scanpy.datasets.moignard15
writing output... [ 27%] api/generated/scanpy.datasets.paul15
writing output... [ 27%] api/generated/scanpy.datasets.pbmc3k
writing output... [ 28%] api/generated/scanpy.datasets.pbmc3k_processed
writing output... [ 28%] api/generated/scanpy.datasets.pbmc68k_reduced
writing output... [ 28%] api/generated/scanpy.datasets.toggleswitch
writing output... [ 29%] api/generated/scanpy.datasets.visium_sge
writing output... [ 29%] api/generated/scanpy.experimental.pp.highly_variable_genes
writing output... [ 29%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals
writing output... [ 30%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
writing output... [ 30%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals
writing output... [ 30%] api/generated/scanpy.get.aggregate
writing output... [ 31%] api/generated/scanpy.get.obs_df
writing output... [ 31%] api/generated/scanpy.get.pca
writing output... [ 31%] api/generated/scanpy.get.rank_genes_groups_df
writing output... [ 32%] api/generated/scanpy.get.var_df
writing output... [ 32%] api/generated/scanpy.io.read
writing output... [ 32%] api/generated/scanpy.io.read_10x_h5
writing output... [ 32%] api/generated/scanpy.io.read_10x_mtx
writing output... [ 33%] api/generated/scanpy.io.read_csv
writing output... [ 33%] api/generated/scanpy.io.read_excel
writing output... [ 33%] api/generated/scanpy.io.read_h5ad
writing output... [ 34%] api/generated/scanpy.io.read_hdf
writing output... [ 34%] api/generated/scanpy.io.read_mtx
writing output... [ 34%] api/generated/scanpy.io.read_text
writing output... [ 35%] api/generated/scanpy.io.read_umi_tools
writing output... [ 35%] api/generated/scanpy.io.write
writing output... [ 35%] api/generated/scanpy.logging.print_header
writing output... [ 36%] api/generated/scanpy.logging.print_versions
writing output... [ 36%] api/generated/scanpy.metrics.confusion_matrix
writing output... [ 36%] api/generated/scanpy.metrics.gearys_c
writing output... [ 37%] api/generated/scanpy.metrics.modularity
writing output... [ 37%] api/generated/scanpy.metrics.morans_i
writing output... [ 37%] api/generated/scanpy.pl.clustermap
writing output... [ 38%] api/generated/scanpy.pl.correlation_matrix
writing output... [ 38%] api/generated/scanpy.pl.dendrogram
writing output... [ 38%] api/generated/scanpy.pl.diffmap
writing output... [ 39%] api/generated/scanpy.pl.dot_area
writing output... [ 39%] api/generated/scanpy.pl.dotplot
writing output... [ 39%] api/generated/scanpy.pl.dpt_groups_pseudotime
writing output... [ 39%] api/generated/scanpy.pl.dpt_timeseries
writing output... [ 40%] api/generated/scanpy.pl.draw_graph
writing output... [ 40%] api/generated/scanpy.pl.embedding
writing output... [ 40%] api/generated/scanpy.pl.embedding_density
writing output... [ 41%] api/generated/scanpy.pl.heatmap
writing output... [ 41%] api/generated/scanpy.pl.highest_expr_genes
writing output... [ 41%] api/generated/scanpy.pl.highly_variable_genes
writing output... [ 42%] api/generated/scanpy.pl.matrixplot
writing output... [ 42%] api/generated/scanpy.pl.paga
writing output... [ 42%] api/generated/scanpy.pl.paga_compare
writing output... [ 43%] api/generated/scanpy.pl.paga_path
writing output... [ 43%] api/generated/scanpy.pl.pca
writing output... [ 43%] api/generated/scanpy.pl.pca_loadings
writing output... [ 44%] api/generated/scanpy.pl.pca_overview
writing output... [ 44%] api/generated/scanpy.pl.pca_variance_ratio
writing output... [ 44%] api/generated/scanpy.pl.rank_genes_groups
writing output... [ 45%] api/generated/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 45%] api/generated/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 45%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 46%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 46%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
writing output... [ 46%] api/generated/scanpy.pl.rank_genes_groups_violin
writing output... [ 46%] api/generated/scanpy.pl.ranking
writing output... [ 47%] api/generated/scanpy.pl.scatter
writing output... [ 47%] api/generated/scanpy.pl.scrublet_score_distribution
writing output... [ 47%] api/generated/scanpy.pl.sim
writing output... [ 48%] api/generated/scanpy.pl.spatial
writing output... [ 48%] api/generated/scanpy.pl.stacked_violin
writing output... [ 48%] api/generated/scanpy.pl.tracksplot
writing output... [ 49%] api/generated/scanpy.pl.tsne
writing output... [ 49%] api/generated/scanpy.pl.umap
writing output... [ 49%] api/generated/scanpy.pl.violin
writing output... [ 50%] api/generated/scanpy.pp.HashsoloOut
writing output... [ 50%] api/generated/scanpy.pp.HashsoloResult
writing output... [ 50%] api/generated/scanpy.pp.HashsoloResult.classification
writing output... [ 51%] api/generated/scanpy.pp.HashsoloResult.probabilities
writing output... [ 51%] api/generated/scanpy.pp.NeighborsOut
writing output... [ 51%] api/generated/scanpy.pp.NeighborsResult
writing output... [ 52%] api/generated/scanpy.pp.NeighborsResult.connectivities
writing output... [ 52%] api/generated/scanpy.pp.NeighborsResult.distances
writing output... [ 52%] api/generated/scanpy.pp.NormalizeTotalOut
writing output... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult
writing output... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult.norm_factor
writing output... [ 53%] api/generated/scanpy.pp.NormalizeTotalResult.normalized
writing output... [ 54%] api/generated/scanpy.pp.PcaOut
writing output... [ 54%] api/generated/scanpy.pp.PcaResult
writing output... [ 54%] api/generated/scanpy.pp.PcaResult.embedding
writing output... [ 54%] api/generated/scanpy.pp.PcaResult.loadings
writing output... [ 55%] api/generated/scanpy.pp.QcMetricsOut
writing output... [ 55%] api/generated/scanpy.pp.QcMetricsResult
writing output... [ 55%] api/generated/scanpy.pp.QcMetricsResult.obs
writing output... [ 56%] api/generated/scanpy.pp.QcMetricsResult.var
writing output... [ 56%] api/generated/scanpy.pp.ScaleOut
writing output... [ 56%] api/generated/scanpy.pp.ScaleResult
writing output... [ 57%] api/generated/scanpy.pp.ScaleResult.mean
writing output... [ 57%] api/generated/scanpy.pp.ScaleResult.scaled
writing output... [ 57%] api/generated/scanpy.pp.ScaleResult.std
writing output... [ 58%] api/generated/scanpy.pp.ScrubletOut
writing output... [ 58%] api/generated/scanpy.pp.ScrubletResult
writing output... [ 58%] api/generated/scanpy.pp.ScrubletResult.doublet_score
writing output... [ 59%] api/generated/scanpy.pp.ScrubletResult.predicted_doublet
writing output... [ 59%] api/generated/scanpy.pp.bbknn
writing output... [ 59%] api/generated/scanpy.pp.calculate_qc_metrics
writing output... [ 60%] api/generated/scanpy.pp.combat
writing output... [ 60%] api/generated/scanpy.pp.downsample_counts
writing output... [ 60%] api/generated/scanpy.pp.filter_cells
writing output... [ 61%] api/generated/scanpy.pp.filter_genes
writing output... [ 61%] api/generated/scanpy.pp.harmony_integrate
writing output... [ 61%] api/generated/scanpy.pp.hashsolo
writing output... [ 61%] api/generated/scanpy.pp.highly_variable_genes
writing output... [ 62%] api/generated/scanpy.pp.log1p
writing output... [ 62%] api/generated/scanpy.pp.neighbors
writing output... [ 62%] api/generated/scanpy.pp.normalize_shifted_clr
writing output... [ 63%] api/generated/scanpy.pp.normalize_total
writing output... [ 63%] api/generated/scanpy.pp.pca
writing output... [ 63%] api/generated/scanpy.pp.recipe_seurat
writing output... [ 64%] api/generated/scanpy.pp.recipe_weinreb17
writing output... [ 64%] api/generated/scanpy.pp.recipe_zheng17
writing output... [ 64%] api/generated/scanpy.pp.regress_out
writing output... [ 65%] api/generated/scanpy.pp.sample
writing output... [ 65%] api/generated/scanpy.pp.scale
writing output... [ 65%] api/generated/scanpy.pp.scrublet
writing output... [ 66%] api/generated/scanpy.pp.scrublet_simulate_doublets
writing output... [ 66%] api/generated/scanpy.pp.subsample
writing output... [ 66%] api/generated/scanpy.queries.biomart_annotations
writing output... [ 67%] api/generated/scanpy.queries.enrich
writing output... [ 67%] api/generated/scanpy.queries.gene_coordinates
writing output... [ 67%] api/generated/scanpy.queries.mitochondrial_genes
writing output... [ 68%] api/generated/scanpy.read_loom
writing output... [ 68%] api/generated/scanpy.read_visium
writing output... [ 68%] api/generated/scanpy.set_figure_params
writing output... [ 68%] api/generated/scanpy.settings
writing output... [ 69%] api/generated/scanpy.settings.override
writing output... [ 69%] api/generated/scanpy.tl.CellCycleOut
writing output... [ 69%] api/generated/scanpy.tl.CellCycleResult
writing output... [ 70%] api/generated/scanpy.tl.CellCycleResult.g2m_score
writing output... [ 70%] api/generated/scanpy.tl.CellCycleResult.phase
writing output... [ 70%] api/generated/scanpy.tl.CellCycleResult.s_score
writing output... [ 71%] api/generated/scanpy.tl.DptOut
writing output... [ 71%] api/generated/scanpy.tl.DptResult
writing output... [ 71%] api/generated/scanpy.tl.DptResult.groups
writing output... [ 72%] api/generated/scanpy.tl.DptResult.order
writing output... [ 72%] api/generated/scanpy.tl.DptResult.order_indices
writing output... [ 72%] api/generated/scanpy.tl.DptResult.pseudotime
writing output... [ 73%] api/generated/scanpy.tl.dendrogram
writing output... [ 73%] api/generated/scanpy.tl.diffmap
writing output... [ 73%] api/generated/scanpy.tl.dpt
writing output... [ 74%] api/generated/scanpy.tl.draw_graph
writing output... [ 74%] api/generated/scanpy.tl.embedding_density
writing output... [ 74%] api/generated/scanpy.tl.filter_rank_genes_groups
writing output... [ 75%] api/generated/scanpy.tl.ingest
writing output... [ 75%] api/generated/scanpy.tl.leiden
writing output... [ 75%] api/generated/scanpy.tl.louvain
writing output... [ 75%] api/generated/scanpy.tl.marker_gene_overlap
writing output... [ 76%] api/generated/scanpy.tl.paga
writing output... [ 76%] api/generated/scanpy.tl.rank_genes_groups
writing output... [ 76%] api/generated/scanpy.tl.score_genes
writing output... [ 77%] api/generated/scanpy.tl.score_genes_cell_cycle
writing output... [ 77%] api/generated/scanpy.tl.sim
writing output... [ 77%] api/generated/scanpy.tl.tsne
writing output... [ 78%] api/generated/scanpy.tl.umap
writing output... [ 78%] api/get
writing output... [ 78%] api/index
writing output... [ 79%] api/io
writing output... [ 79%] api/metrics
writing output... [ 79%] api/plotting
writing output... [ 80%] api/preprocessing
writing output... [ 80%] api/queries
writing output... [ 80%] api/settings
writing output... [ 81%] api/tools
writing output... [ 81%] basic_usage
writing output... [ 81%] citation
writing output... [ 82%] community
writing output... [ 82%] contributors
writing output... [ 82%] dev/ci
writing output... [ 82%] dev/code
writing output... [ 83%] dev/documentation
writing output... [ 83%] dev/getting-set-up
writing output... [ 83%] dev/index
writing output... [ 84%] dev/release
writing output... [ 84%] dev/testing
writing output... [ 84%] dev/versioning
writing output... [ 85%] external/exporting
writing output... [ 85%] external/generated/scanpy.external.exporting.cellbrowser
writing output... [ 85%] external/generated/scanpy.external.exporting.spring_project
writing output... [ 86%] external/generated/scanpy.external.pl.phate
writing output... [ 86%] external/generated/scanpy.external.pl.sam
writing output... [ 86%] external/generated/scanpy.external.pl.trimap
writing output... [ 87%] external/generated/scanpy.external.pl.wishbone_marker_trajectory
writing output... [ 87%] external/generated/scanpy.external.pp.bbknn
writing output... [ 87%] external/generated/scanpy.external.pp.hashsolo
writing output... [ 88%] external/generated/scanpy.external.pp.magic
writing output... [ 88%] external/generated/scanpy.external.pp.mnn_correct
writing output... [ 88%] external/generated/scanpy.external.pp.scanorama_integrate
writing output... [ 89%] external/generated/scanpy.external.tl.cyclone
writing output... [ 89%] external/generated/scanpy.external.tl.harmony_timeseries
writing output... [ 89%] external/generated/scanpy.external.tl.palantir
writing output... [ 89%] external/generated/scanpy.external.tl.palantir_results
writing output... [ 90%] external/generated/scanpy.external.tl.phate
writing output... [ 90%] external/generated/scanpy.external.tl.phenograph
writing output... [ 90%] external/generated/scanpy.external.tl.sam
writing output... [ 91%] external/generated/scanpy.external.tl.sandbag
writing output... [ 91%] external/generated/scanpy.external.tl.trimap
writing output... [ 91%] external/generated/scanpy.external.tl.wishbone
writing output... [ 92%] external/index
writing output... [ 92%] external/plotting
writing output... [ 92%] external/preprocessing
writing output... [ 93%] external/tools
writing output... [ 93%] how-to/cell-cycle
writing output... [ 93%] how-to/index
writing output... [ 94%] how-to/knn-transformers
writing output... [ 94%] how-to/plotting-with-marsilea
writing output... [ 94%] index
writing output... [ 95%] installation
writing output... [ 95%] quickstart
writing output... [ 95%] references
writing output... [ 96%] release-notes/index
writing output... [ 96%] tutorials/basics/clustering
writing output... [ 96%] tutorials/basics/clustering-2017
writing output... [ 96%] tutorials/basics/index
writing output... [ 97%] tutorials/basics/integrating-data-using-ingest
writing output... [ 97%] tutorials/experimental/dask
writing output... [ 97%] tutorials/experimental/index
writing output... [ 98%] tutorials/experimental/pearson_residuals
writing output... [ 98%] tutorials/index
writing output... [ 98%] tutorials/plotting/advanced
writing output... [ 99%] tutorials/plotting/core
writing output... [ 99%] tutorials/plotting/index
writing output... [ 99%] tutorials/trajectories/index
writing output... [100%] tutorials/trajectories/paga-paul15
writing output... [100%] usage-principles

generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [  0%] _build/jupyter_execute/059f0475959504e77c2ebf3ef2bde9d29f795d541931587f30036fb487265a98.png
copying images... [  1%] _build/jupyter_execute/0079f316078279b60542ce537c8147ac24e9d3f9d71a224939d3b4088cb166df.png
copying images... [  1%] _build/jupyter_execute/ed3890cb3ace4f82646f046a911073d3e8ef54d60cc8c722467ab55c3dcdd720.png
copying images... [  2%] _build/jupyter_execute/8d1262b71eb7ff49ed3f3b775b3a6b14c89dbad8375c982b6c68780dac86b0e7.png
copying images... [  2%] _build/jupyter_execute/f9f25d5c7056d5429f8c7c93842837fb470e39b84ed087ba8378b2b3850aa3dc.png
copying images... [  3%] _build/jupyter_execute/078a48ff8d71b4e3b4a552fc9d3e2d33dbe4413634fc05caa2dcc88017cde970.png
copying images... [  3%] _build/jupyter_execute/251e02259e2e57c34c5329ea7d7c1a2554c802ed4645eab8d35793af2d6f94a1.png
copying images... [  4%] _build/jupyter_execute/d5a285731c203c8bbdbfbe3c46a0c524d681fae5485ec6830c0b99ff7c696556.png
copying images... [  4%] _build/jupyter_execute/0f6681613c7b24e050fd7692c8223dac76f37c04b72a280817bcfb1ff05583fb.png
copying images... [  5%] _build/jupyter_execute/5c949e19cdebe561536f79bf5a3f0355059b073bc39e0abf205626cf139781e2.png
copying images... [  5%] _build/jupyter_execute/d98a6a9999b9af78bd28ca557d358a118914c8766fff30b9883fd2596b48edda.png
copying images... [  5%] _build/jupyter_execute/926a2dac78703a8cc0f07795d18626a1dc161cda2f4bfbff80fdadf456037e47.png
copying images... [  6%] _build/jupyter_execute/2cb95dbd7c716fea54ce324cdca22fd235a2d3e5387df166f64745db7cf48f88.png
copying images... [  6%] _build/jupyter_execute/f0cec1085c747bbfb05c5b0999b84f24a65f2c77f84cc9b2283c6306fdb48129.png
copying images... [  7%] _build/jupyter_execute/804f12cecd000e3118433d56007c8d725153ec7eafdee6ce05f03f1daa15d8b3.png
copying images... [  7%] _build/jupyter_execute/53c8937d56a42294348919bf4290f6ea526ff0ac28f6e5112d97cde0c7cb8b5a.png
copying images... [  8%] _build/jupyter_execute/f8a847d511933af266f1d8f63241fdaf26626bd5e17bb3b3ec57a1f7b200d9d6.png
copying images... [  8%] _build/jupyter_execute/4524066492893113f1b5cbb010c57fce5727feb6cb66b90b44f3de083b75c95f.png
copying images... [  9%] _build/jupyter_execute/f2835b50f6c8ea6e3b399d6ed1f9c33cb1dc16006ea4512352c804a8e64541af.png
copying images... [  9%] _build/jupyter_execute/c3a959002823071f5d2290c316843d4135b56a16cc13464e90ca28c30e9a5bb9.png
copying images... [  9%] _build/jupyter_execute/74c41daddeddf9e004347deaaea8b0a7b180a30eaed33ed7cd94735ceddb3e3b.png
copying images... [ 10%] _build/jupyter_execute/d9353fe4b78b7f72245d6389bada18153f81c62fb0d766bd10b86b541169579c.png
copying images... [ 10%] _build/jupyter_execute/fa4d76cdd35ff63e3cbfe4600e4a06cb1dec7241c6671d7eb9f9498078833b80.png
copying images... [ 11%] _build/jupyter_execute/27d12698d1c6e8de3f78d60c3bbd264739c11434c9229c787529b1cab037e0f0.png
copying images... [ 11%] _build/jupyter_execute/f1863a58ee397d6579dfe642a652343d3dafca7a9fe1c18b6d0f5934fc758fbe.png
copying images... [ 12%] _build/jupyter_execute/96933aa992712e9a66710f8f88970f68b347fa3d6ffd530990a8b95d2546a153.png
copying images... [ 12%] _build/jupyter_execute/b8c41ce869c2bbf78f4d777736110775c853797c74c43ea3b2720af94238da15.png
copying images... [ 13%] _build/jupyter_execute/3ce0597fedbe03de4f7b3154c7c90a0253bc6b3b4ba45e8b8e569b3f22146035.png
copying images... [ 13%] _build/jupyter_execute/9ea89c95d8968083cc75c8cd66abf2621805aaedc0a252dc1c91f8bb59b1245c.png
copying images... [ 14%] _build/jupyter_execute/a0a0417aca8c09ef873e900195f6d3ad1d1f77a6a56e08fab3a9c51db036f158.png
copying images... [ 14%] _build/jupyter_execute/9fedbb398027948b19c8abf96ed79d539ac05b975fcfc4140eaf22e41cd3be9e.png
copying images... [ 14%] _build/jupyter_execute/3f6c30a6c4ce8ed39c1f1fc0dbfe43004c37f4fb7ae4cd203df68ac17f0f03c0.png
copying images... [ 15%] _build/jupyter_execute/7a8a5032f0e337c69c3cfc8abc9d127accc4417e28581fea33c72481b38d7624.png
copying images... [ 15%] _build/jupyter_execute/d5522c49313267df11f9dbad5e4fca97ab27aeb47d4bc6c00b305c43a6c2e9dd.png
copying images... [ 16%] _build/jupyter_execute/16a73dd822025acc6891a5e6fbfd6f1e7bbb5e8bdcbf2a195584845c769a17e9.png
copying images... [ 16%] _build/jupyter_execute/290c75c701b8da1cf703a47937493760be178d11cb9da9e2e0818e4182b4f17c.png
copying images... [ 17%] _build/jupyter_execute/dcd5606269a9b41896da97b5fd2c9c4301762436cc90ca3c2a05632c724cca5a.png
copying images... [ 17%] _build/jupyter_execute/f1ed964000d0e529116fca2e816c52ffb781f2aa2d101bed96c3bd611a52d2d5.png
copying images... [ 18%] _build/jupyter_execute/eda5a8c0ae15de5dce19fea93690fed01cd706d2b7be386f057468d4c9f12362.png
copying images... [ 18%] _build/jupyter_execute/a843e544945e4b9a173fd1c43893ea21ed6190dfbcacdbfcc2f25bee9a2ede9d.png
copying images... [ 18%] _build/jupyter_execute/b6737f46786b05fdf9d43da64d93fa6d1d5f4160bc9c82b29b5b52fddcd8da13.png
copying images... [ 19%] _build/jupyter_execute/71e1af348f803fb47cfb50413c3b7cc96ab471a213735339820896b524e3a61a.png
copying images... [ 19%] _build/jupyter_execute/a9718532fb5c072090d2a94585e2f8d1f08b65ff078b2cfe1c5ea6e97544b0dd.png
copying images... [ 20%] _build/jupyter_execute/57121daba55d52c25937cf832bdcd9fdb1336a45a0b053ecbaa36c1dd1d6a4cf.png
copying images... [ 20%] _build/jupyter_execute/3b3b5b43f4dd3f78cd87b5a7d0fbf379ad919cf2dfb01f387e22802bed043562.png
copying images... [ 21%] _build/jupyter_execute/c9fe36703f9542b425dcb39f989bde57559922ef93180d226fd568eeb430a944.png
copying images... [ 21%] _build/jupyter_execute/2a666ed927f86bf08736fc2967a630494c8aa550f103c2e1599d9ba94dfb7d00.png
copying images... [ 22%] _build/jupyter_execute/8aed7a9618dab94e3fc511d86ec0bc34412e4d13c469528622d3a9cd09bd02fb.png
copying images... [ 22%] _build/jupyter_execute/da6c491370e9a621d718afd3490abfe05f36a7192c0440b662b59a82b0d8106e.png
copying images... [ 23%] _build/jupyter_execute/59a604be9f04d08813845e3bd632df3815db2c67f00a4fbe03496bdf0402d2e9.png
copying images... [ 23%] _build/jupyter_execute/b3b807da3ca1c4443eb0900815543dfca3eba94122dbf31dd9b8aba3857c37aa.png
copying images... [ 23%] _build/jupyter_execute/25a65ff111f045bf46f2ebc8ca0230d7850bfb48e320a901b698fdcf62430a92.png
copying images... [ 24%] _build/jupyter_execute/cd23fad2e4f4ba83220691c75f6567663e0ae64d6b13b350114db8d795056a07.png
copying images... [ 24%] _build/jupyter_execute/aa6354aaa1e566cb9b5828618412a03bb937595662514877c6f95b33d9ec33f5.png
copying images... [ 25%] _build/jupyter_execute/fae7ad13d00d0a4370e8adb88ea313038db669568bb9d64aff909a746e1d5809.png
copying images... [ 25%] _build/jupyter_execute/7995d44bd7308d0c0e5c8313db09a54524762c9ab2a433088f036f6bde138eec.png
copying images... [ 26%] _build/jupyter_execute/c69fc4ef6ba69bb6ce0d72a7c293e17aaeb9696ae7320523026e7289bf48861e.png
copying images... [ 26%] _build/jupyter_execute/aea834267d7674fa12e809f7bd98125eb30cccdabd1150345c8bfbe196f33878.png
copying images... [ 27%] _build/jupyter_execute/703ce63afc13eda8afe022419c32ca901b0c08b4be95f757efaf2f900212c13f.png
copying images... [ 27%] _build/jupyter_execute/4882baf1e8a6f1d82a782d5edc29c2867b02494b9c5ca7a3de345697dd4d794a.png
copying images... [ 27%] _build/jupyter_execute/e685dd100a9efc06741c2d8a95b6f9542fec8899338fb87cc77fc791c5dbe597.png
copying images... [ 28%] _build/jupyter_execute/f0f4572e7e9b4acece351820a122b9ec191f7f448cb79e92446583368c8f5ed7.png
copying images... [ 28%] _build/jupyter_execute/1cc45ebbe1b0aaed7f28af7da8f37b2897d46021743654d4b96b0540b3f8e65d.png
copying images... [ 29%] _build/jupyter_execute/3a4f941f58b6056e86ca1a8b132c8398eacf48d8bc11c032743d2997755c92d2.png
copying images... [ 29%] _build/jupyter_execute/c102aee01f0ebaabe8bc281421f73d2b74dd61b0ecc5ebbca144aec7db687f54.png
copying images... [ 30%] _build/jupyter_execute/d5eaef1e59b3ddb89145acd9734ee6790982fa280488959ca35b7aeb43e0658d.png
copying images... [ 30%] _build/jupyter_execute/4ce06bc19d88a1260671524fabea1743e8f4e6df4ad0bb4f9793d4e0b65a6f24.png
copying images... [ 31%] _build/jupyter_execute/a5720b7352fdbe3abbb1dc74ce8b50f91ea41abc6b03151aa5944a55e5b25acc.png
copying images... [ 31%] _build/jupyter_execute/1bd9c92f707e63eab7de90f0262f4326a779e37bf936c5965c0bbaf69243a70f.png
copying images... [ 32%] _build/jupyter_execute/169ba9df560614b13f1950057ddf35d29a964fd0f303ed32edd5cdeb338c2f01.png
copying images... [ 32%] _build/jupyter_execute/b6f118af174ba7572ad5a8e2e933f56985073aeabd8756aa327e94bf1aa382eb.png
copying images... [ 32%] _build/jupyter_execute/b93b59f25fe96f477bae8192f805d5438bbb8fc4e0e52c5204cd0eeffb774c5e.png
copying images... [ 33%] _build/jupyter_execute/93c6721acfc1800b726e3b39a6205b0d11f83a2e92dbe0f9fb15265d3f074bec.png
copying images... [ 33%] _build/jupyter_execute/b65562164c7f976f8dc969ca82d26e4a402b575c97b60a9f23817b3ec2f9ca9e.png
copying images... [ 34%] _build/jupyter_execute/f4d011e2f42590432d4fa47ede0272dd8d2add5020f67fb0444d8079312da112.png
copying images... [ 34%] _static/img/ci-workflow.png
copying images... [ 35%] _static/img/ci-artifacts.png
copying images... [ 35%] _build/jupyter_execute/1d57a6a6f897c88b6acfc435bbfeb70798036d973008ed199b9b93305844c407.png
copying images... [ 36%] _build/jupyter_execute/9201238033dc3d71525ffa4c3fd342931493cbc4154f10dad379a148746ccc9b.png
copying images... [ 36%] _build/jupyter_execute/ad8d8a4b869e02ab2b2ca1c0cddab9f8150214bfc27e6036a49ab5d854f5983c.png
copying images... [ 36%] _build/jupyter_execute/1efc332ed14787b27fca1c17ceae1c19d1743283d84b53209c05deba50873a4c.png
copying images... [ 37%] _build/jupyter_execute/49b318b9b4f436f6ac7b2217fa525dad31f1ad438096e9caa100f9890338b9ab.png
copying images... [ 37%] _build/jupyter_execute/6dd0481f67ef212ccfd203a21d50eadf7cc9b716398bb26c0b8ceb27da239bec.png
copying images... [ 38%] _build/jupyter_execute/51876e50d475e1a98f1280ba2aa03c484ce0d2de2f6e3cbd089eefd2fd68b701.png
copying images... [ 38%] _build/jupyter_execute/dc7a2f8c05fabff2c114db7de12526a364d8d59e32f382907910c4310d1e6243.png
copying images... [ 39%] _build/jupyter_execute/9e95ff87c2e323c538a3078dd430e6b81bf3b51037b380869fe1cc97b2f986fb.png
copying images... [ 39%] _build/jupyter_execute/932c385493bf32d7129db4defddad5b07b9af493bc920242eac2c67316c21117.png
copying images... [ 40%] _build/jupyter_execute/c9b56775caddde7bb4f089cd8d3621372a98b1f457f1ba8376cadfb1b4069979.png
copying images... [ 40%] _build/jupyter_execute/b9c8eb50a997aa92d7012c11dfab25ca69bb35086a57f7e0d857d6f3bfce8774.png
copying images... [ 41%] _build/jupyter_execute/a3fe83fff8559fa5c0cb4ebd6574f97faa4479ecf76184b84f79b1f89db00895.png
copying images... [ 41%] _build/jupyter_execute/cd4722d0940da9e47d9184142442941052d2b38304b00ebca45d14cf9c38b60a.png
copying images... [ 41%] _build/jupyter_execute/afb22dbb78cd2a44fbe55c8a5ce53abd98c771194846bf830ea35f44d11abffc.png
copying images... [ 42%] _build/jupyter_execute/2369cb7f97a8853b39251e0ca2ccae217e8613cbea0bf8c599d13adfed54622b.png
copying images... [ 42%] _build/jupyter_execute/3385e74bc3cd67483b2cc40687bbe1089c590fd399799f887c24323ea25ea637.png
copying images... [ 43%] _build/jupyter_execute/83a982f840b154da4420735c806689e16b150ad10ab64372e4ad9c0404390dd3.png
copying images... [ 43%] _build/jupyter_execute/9a168f2d7a68905521ea3fb1ef5a0ac2a22d65e6a5e7c3796a55da1c24c28cb1.png
copying images... [ 44%] _build/jupyter_execute/bd436a0a79afac682ff8132b32d4c90d3f74738d57e07f5743a03a55d9f82f68.png
copying images... [ 44%] _build/jupyter_execute/12e4e27cf02e408effd640d9a5846b20c0b4ea4856511e9af58f5743897aaf38.png
copying images... [ 45%] _build/jupyter_execute/e77d6bf9cd6e938808b2d57ffd8840f0d1aa27233c819a4f8f7b9fdd1d6a44cb.png
copying images... [ 45%] _build/jupyter_execute/610d17bf258b0cc0d840713ebac7867cf292c626df2e807ebd78b459a03ebd28.png
copying images... [ 45%] _build/jupyter_execute/08cb70daba840353bbf8529bf9f27d6121451a8200114c5b77f581df4bbf1a7b.png
copying images... [ 46%] _build/jupyter_execute/2b92963adeb5c28502e023b24967f509deb537d668944e8bec22585c1e66e341.png
copying images... [ 46%] _build/jupyter_execute/7c615842aa3a955f46581c1333bbb91b74a2fb9d38b7f18966a67a39cb1ce0f2.png
copying images... [ 47%] _build/jupyter_execute/17e024239d09ec7c14e90bdb43ea70d7959aab70f7e5d3d2f1620a8f96b77809.png
copying images... [ 47%] _build/jupyter_execute/e103233bd60eaaf71b1bee1293d49a4732a3e96a1e206df311d8166de065a188.png
copying images... [ 48%] _build/jupyter_execute/d016caf498b3b59f81afddca30abfa1354fc0d904eaa8c69776bf7c4e305996e.png
copying images... [ 48%] _build/jupyter_execute/7ab7710568efacc3fcbcc8db7885b30e22db6ad7378ff0066a5bba5f361e065b.png
copying images... [ 49%] _build/jupyter_execute/8107930e37d0eafac40456afc53660e627a7e8aff939fdad1739e6c92b339ca1.png
copying images... [ 49%] _build/jupyter_execute/fe4652b5bd85c01a706bcc93db6c339dd350de04d627e4ef5fca03de302e6645.png
copying images... [ 50%] _build/jupyter_execute/2790ff5a1d746af5c3cddd2b9f6a01dffc82af62fa724a41dba40310b072dadb.png
copying images... [ 50%] _build/jupyter_execute/1c3c62cdb30781ddde75b5168f150794c33e30a2eac387a07c59109d806a8af1.png
copying images... [ 50%] _build/jupyter_execute/ce00e90fb7bec4e416b07a495c303c0bb48c5e3322abe38320b4f98e4c7bf8c7.png
copying images... [ 51%] _build/jupyter_execute/b33128be615a2b323623ecc32c332bab41abbe66c9e4d92e29b14f7e2a65c25f.png
copying images... [ 51%] _build/jupyter_execute/a785da9a2a7b016091062159786f39353ea020780d58f478c874cd068037a82f.png
copying images... [ 52%] _build/jupyter_execute/6922a7ae96be672bcf25f5ae2b5461a6edce80dc0ae0c8b2545ab7a2b6cdf33b.png
copying images... [ 52%] _build/jupyter_execute/7a7d1bfab01e7b0068e7ee926964efeb8d89ffd1cd1b845768be6a7d08e230d2.png
copying images... [ 53%] _build/jupyter_execute/e1f3cb4f01fdc24afcbd9ed1b8e820fc53a57b919830e78473855a6706b6ca8d.png
copying images... [ 53%] _build/jupyter_execute/4632938fb4db7519939461a858c1030d618b13b23a2d3c2ed4da00637d2764d9.png
copying images... [ 54%] _build/jupyter_execute/e2b6fba2faaec41ee9da18283a730844ba9e2eab5a876d3e7c8bb2811df11c01.png
copying images... [ 54%] _build/jupyter_execute/88aa4fcc109c878a374a7361bbf99b87b1c3ee5ad41957c3c695ade45960c104.png
copying images... [ 55%] _build/jupyter_execute/70675aebfc80dcc9fc70fb92aa56f1262c94fc1f42438391d3f5b29d971e2106.png
copying images... [ 55%] _build/jupyter_execute/3a9d72ea573f04a7eb5ee2f1ef2ba2927e434ab65fad265b993a0350053f34db.png
copying images... [ 55%] _build/jupyter_execute/d2237124534fa2abfee97367a26620a9ff3898e6f0091608f6e5c06b9562c509.png
copying images... [ 56%] _build/jupyter_execute/b70775c7fa5fbbb119b9ce5cd9c829177e17a29336ff12221903431ddbdb1d89.png
copying images... [ 56%] _build/jupyter_execute/9309793bba6f25f718659e6ad9c686807b635ecf2fad7aae7c45cbef5ebe8170.png
copying images... [ 57%] _build/jupyter_execute/019de1cdde7388e76e22ab5f4c813b4a2513c977f75ff179e148db6c183dbe61.png
copying images... [ 57%] _build/jupyter_execute/b3514cbca07c9d355f66075ace5d4a16aacb62f6147dcd62a736f1e937938bbd.png
copying images... [ 58%] _build/jupyter_execute/d4527a4e03bbd6fe4dd09c91d02efc2faf580783935ae9bb5a222db257521af8.png
copying images... [ 58%] _build/jupyter_execute/6c8974cc011958acd47098c3a1a932191a7876764f737b820d16390a5ec783ac.png
copying images... [ 59%] _build/jupyter_execute/30aa821349148a81487ab563d4a6a75e3c0e020dca4fb21b0139509cfceea398.png
copying images... [ 59%] _build/jupyter_execute/3f2faaf30df23cf5c7dc5a27dc4d9e4de270fa4e9c4e5e26fbec40d1c0c387ce.png
copying images... [ 59%] _build/jupyter_execute/e99df2c4982238793f5b4ac08047e40a7678573d6271fca7f7745ec296d115d9.png
copying images... [ 60%] _build/jupyter_execute/d98c6dde98a2b75c80d393a309920062f038c5c38183705b573c8e3b538a38b9.png
copying images... [ 60%] _build/jupyter_execute/61fa512d676d7e19397cd18d4333e7429601886e60f2d54178db1bcdb8e89880.png
copying images... [ 61%] _build/jupyter_execute/7a6bd5a47fad48feef0b93724055e620e7500410149d6bca969c6b72f9857b6c.png
copying images... [ 61%] _build/jupyter_execute/b9b0f6d973000a37268783e706bfbb973a9817010756dfd5fb4652496a2a8fb9.png
copying images... [ 62%] _build/jupyter_execute/628660e3a52a692ea4efaddc5db8b60a1a10880a63a27602a8e82350aaff529a.png
copying images... [ 62%] _build/jupyter_execute/fa0c98ce178a6f4397cff03e594908df66ade84306568b7660e14258413e837c.png
copying images... [ 63%] _build/jupyter_execute/7280e7628c2d51572ba50bdeb1600d6b8579ff7c9fab4536e4a730b1904a789a.png
copying images... [ 63%] _build/jupyter_execute/7892b8f497b868bf4353f873b5762e96e73c1fa06356dbf9e971f51c5e41aa37.png
copying images... [ 64%] _build/jupyter_execute/13cc6c1d53e9a3aba72799cd93759ce396bc0cf762f3b46d5a762e2e276cd168.png
copying images... [ 64%] _build/jupyter_execute/5f159fa54af4fc9b8f206c572e1b24b1f1eb24f3711032a9892df784cc5bdd7c.png
copying images... [ 64%] _build/jupyter_execute/2eba1ec7ea236ae4f0ec8644785ccb3e4c08e44a3615eb1f0fcecbf277c408ae.png
copying images... [ 65%] _build/jupyter_execute/67a8f588f5e935db5d190240996d7ef24c757b99131454c54c9a4463823244a5.png
copying images... [ 65%] _build/jupyter_execute/915d74a745633da1ae5a4b91ea8bde5ace438f0cb3c103f3908c86e8166b46b1.png
copying images... [ 66%] _build/jupyter_execute/2e949f6382ce68273faebe569154569a3ee12f69ebcd948c449e0354db3c3858.png
copying images... [ 66%] _build/jupyter_execute/c4c7363df186dd1e25bb52b3ab60a88f27e65c5fd273d15d0e8e90d084b61a10.png
copying images... [ 67%] _build/jupyter_execute/58a1e8c7549f5784c7d394c45d782825e39f1bdf074e3fdded8f85138303dbb8.png
copying images... [ 67%] _build/jupyter_execute/f70cfa87abeee08705f1c0f68850c7f473f43cd828bd61d505236881b3929ea3.png
copying images... [ 68%] _build/jupyter_execute/18bc84a5f8b79b26336676391d299a04a557a748cf1d07ed08e6e8cac7da4c96.png
copying images... [ 68%] _build/jupyter_execute/db7abd6c2ccafd0838aad46c2bc2b048630dbb12171d5517102e5c05ff61195e.png
copying images... [ 68%] _build/jupyter_execute/dfecea44c594db8a640293ba3b83b768f0f8fffb11feb06bb02a9db87ac88f07.png
copying images... [ 69%] _build/jupyter_execute/dd9bd20407057e3f381a408e020551eab4a8158f49ffb9a4a5df3182d2245762.png
copying images... [ 69%] _build/jupyter_execute/5894ed27c5482d0a22c852ad7ec122674a5403866dfc7b981dc53aaa358cd43c.png
copying images... [ 70%] _build/jupyter_execute/9dde4846823e894d0bd646d737d64babb11955d44121dd294a676ecda2030ff7.png
copying images... [ 70%] _build/jupyter_execute/56b1242b1fc93eb876458f16b792cfc8f378a7ecc1fd970d8a885833f3d7a134.png
copying images... [ 71%] _build/jupyter_execute/75e95ac30061d0a6c4b5bbf3d3e5a9680b19ff08269fe2d8ea59ab10a023914e.png
copying images... [ 71%] _build/jupyter_execute/71c776827198f5562510afe4c17873f7d10a2a35357ffe4aeaa128a78e788e1b.png
copying images... [ 72%] _build/jupyter_execute/2d65107bba327ff05ed6987cc4c2777b641bed01c1ba09b6cc252a8e67c11998.png
copying images... [ 72%] _build/jupyter_execute/656a59ad999749dafe447f6f02f9dc776d629197c94870a322466e09d20cb963.png
copying images... [ 73%] _build/jupyter_execute/1e16be2728eeb5c9ab9542cc63fb3644e3b7c76f944de373115f046e2bddaa41.png
copying images... [ 73%] _build/jupyter_execute/00e09d35a6edfcfa22e4469241715ce73a888cecd411514d94cd40d382f41e22.png
copying images... [ 73%] _build/jupyter_execute/fec4e153d5cfd92a83fcba1cc62c2cdec87e8e91e1cb6f6b083ba8bf0f20f406.png
copying images... [ 74%] _build/jupyter_execute/5a26fa44dcc471d706f3f7ecf801d3cf31743edbb836a393073e937ab85c7237.png
copying images... [ 74%] _build/jupyter_execute/a7ed97e5192d909da6c3aef055bd93d31530c357a5110bf8219524f59aea1f47.png
copying images... [ 75%] _build/jupyter_execute/114213c032705aeaf87f170cedba7f54024e21f20b59eff12c40067b3eff9d64.png
copying images... [ 75%] _build/jupyter_execute/4b80a8ebb2fe694a361810d5829ad423339dec1272a186549a7f918f37259dd9.png
copying images... [ 76%] _build/jupyter_execute/0f9a0935c010d0ca3f3e91c8fa02275b0be7c9ee8e544f273cbb72a6a0ce3350.png
copying images... [ 76%] _build/jupyter_execute/03cce8ccfd5513f7ddc46190831f275b68395b19629c77570c13b7bb2ef5c0fd.png
copying images... [ 77%] _build/jupyter_execute/95d4d301cb8d8f1010e6cd414b366f4226bcaa19ee061e88e0366e862ceca920.png
copying images... [ 77%] _build/jupyter_execute/d5a3a68c99b881daa67c137c3d7bc76e191396f0a10909e3c86a00a4a5c3075c.png
copying images... [ 77%] _build/jupyter_execute/fc25f73c02ceb1211cb72c585ad3dc7b21852f9c79f8a4477e41a704f851dbaf.png
copying images... [ 78%] _build/jupyter_execute/f8a3a5f206cfdbc8fb57787377fb9f7ed9aee4755e69529878a36325eb9d9d3e.png
copying images... [ 78%] _build/jupyter_execute/014721e47639c9d7f9c1d1a707959e3c7d87bee55dab814b24034ef26bee0cd8.png
copying images... [ 79%] _build/jupyter_execute/82bf8185351514bbacde2d71cdbed19bd39ad9914092251bd40b07b1cc9ec0dc.png
copying images... [ 79%] _build/jupyter_execute/47e219415022be69ebab4ddc0dc565d07df0d0e7ec71e622d328381286b0cdb3.png
copying images... [ 80%] _build/jupyter_execute/bc2843555a0c778a2bc285fea5f772e8357d4f62eff7531e77a08e1c58094456.png
copying images... [ 80%] _build/jupyter_execute/3a82d437cedadd52481ef022d5d5ac673e0870db60f66a000e7c06be9804b29d.png
copying images... [ 81%] _build/jupyter_execute/a04173d282b7225af891853648454277c62aa658e3ed12b0e5a82cbdb2bc1bbf.png
copying images... [ 81%] _build/jupyter_execute/c1e530b06deed8e1a2861304d545d88ceaa563443748219fc5782a11bfed8bab.png
copying images... [ 82%] _build/jupyter_execute/2c9701ef266c8b3b9490dcb11623e4e2a3d69eaadb9f187953a8c0613a65ad00.png
copying images... [ 82%] _build/jupyter_execute/d4f91a929016b982fdee738f747f0a8d1809c43e7e3d33245259adb7b1338791.png
copying images... [ 82%] _build/jupyter_execute/b083f58cdecea3e188f5448696676033caad5295288a66e6200fe35079cd4cec.png
copying images... [ 83%] _build/jupyter_execute/ab8ceac0ade73d69c35dae952929be9a16a21b7e5a9612e76511dcf341274cad.png
copying images... [ 83%] _build/jupyter_execute/d9dcabc0cdd72d9908378b6689153e8b23c803c4078439c92b6aeb3e47787a58.png
copying images... [ 84%] _build/jupyter_execute/08940b0dd5b929575cafae1e9d952d7177831ff7796a50edc2331e78b7ec073d.png
copying images... [ 84%] _build/jupyter_execute/352f3ecd06ce5d90c523472f90e001df88d69becc556dba6dfd4aaaceea7e1f4.png
copying images... [ 85%] _build/jupyter_execute/4d4980d62f791299b4db8748e42969abcf258c24a8e16b6dbc4c4f0b6f3c0954.png
copying images... [ 85%] _build/jupyter_execute/6fc7410a8fe298e3f12b23877016321dc26fc5084064a189722cb82abb675c57.png
copying images... [ 86%] _build/jupyter_execute/fc2449724f50fc3a4891f902f64112fc8d709eb0c11b3ea02648dfba0b8b49cb.png
copying images... [ 86%] _build/jupyter_execute/2991fe558766f086411c6f1949c4c664c819a0ed608a34f7d3f878fb2a8bd46d.png
copying images... [ 86%] _build/jupyter_execute/dd2fab22e25749d072c93ec385a1f448cf3fb7665eb2f992c9515ebdea1d4e70.png
copying images... [ 87%] _build/jupyter_execute/2fdf057d113584ecc12239fb66397e9636b946d24fd9f6250b8e189a3c2dd238.png
copying images... [ 87%] _build/jupyter_execute/bcf01e7a13a626a9d44a9f87b1a2c719f829981b46ec34b7f6ec6942e411ec64.png
copying images... [ 88%] _build/jupyter_execute/4e39081732f70423300980f2b389aa5ae21497dc3f9446681e22f5a8a1525a6f.png
copying images... [ 88%] _build/jupyter_execute/50b2b99a1a055abb06df268721d9be07613f992127cda844f616625219955568.png
copying images... [ 89%] _build/jupyter_execute/92c8c115b1c591c74b8cb6e9d0835a859d6707b376d57f5b4f946258c9fdd8a4.png
copying images... [ 89%] _build/jupyter_execute/c8a97f882cf8e155013d4ce88b30b12db459333f31fee35eb80d12633c02cddd.png
copying images... [ 90%] _build/jupyter_execute/1653ef8b3d91e89e509984dd8cc5d19145350beaedaaab86a3a6c07672a28ef6.png
copying images... [ 90%] _build/jupyter_execute/052f07fe780438b12d496b3ddaed3f958cc22f5a321991ae7ae593c773a35b76.png
copying images... [ 91%] _build/jupyter_execute/e679f7ec42621cd951b12ed129b4f6474d24b5043fcb2fecdc96479a77531681.png
copying images... [ 91%] _build/jupyter_execute/93488e44a5f2084884177480f5d1f8f1dbe87f53b44d9f1cc7058b983ff35938.png
copying images... [ 91%] _build/jupyter_execute/f7e0871712a60e23b35c9f3379edb644d0dfeb0fd817a7e126b69d519253307f.png
copying images... [ 92%] _build/jupyter_execute/72ca059296ecfe466026a5012c4c135420684573ae6e42aabc2968efb1290002.png
copying images... [ 92%] _build/jupyter_execute/2a280bd3e22958f78430cfd4c41d5d37b44469e45a82ac05f5ccbca717b17457.png
copying images... [ 93%] _build/jupyter_execute/daa55f3a8d5cc51906bb0897a81840e0c18cc86a174bf3eb891139934c50140d.png
copying images... [ 93%] _build/jupyter_execute/f9429a2e1aaf6d889692fb40258efd524f12209e521b2b03f95b222f00c9e6df.png
copying images... [ 94%] _build/jupyter_execute/5cfbe9eb92b9a937a933a0a604a872e7914012b0a7d2008e62bf8363a6cd5b42.png
copying images... [ 94%] _build/jupyter_execute/600e370a6717ab2f4fea7b390eb08c45b8a20a5e3d0ad61a09a06adaed6e81d4.png
copying images... [ 95%] _build/jupyter_execute/4b1be5ff87b37ad710d192a2dd9b53793c01f155b84f1d13932229b4583f7a37.png
copying images... [ 95%] _build/jupyter_execute/c018c4b6b1363e6601efbaa0dc27c3f9e12cdddfeb15d75739291ddf554fa91e.png
copying images... [ 95%] _static/img/tutorials/paga_planaria.png
copying images... [ 96%] _build/jupyter_execute/b29e2eca5649a24042512f543f420cc021b77b8b9412c5bf77e1529588f06125.png
copying images... [ 96%] _build/jupyter_execute/effe244049eb70377b606638583e2122c66538497cc7b1509820624883ea8580.png
copying images... [ 97%] _build/jupyter_execute/199cd4d8abf199025931fd9fd2a043006cf2499cdd39ec71938a70db7ca91073.png
copying images... [ 97%] _build/jupyter_execute/8f933a8f5774c68d14c62f9eaba449929338793be23ab1fc2b74fd6d3abff70b.png
copying images... [ 98%] _build/jupyter_execute/2592ae333c0e7528751820f8406144b1f4aaf8eadee0dd37578ddbfb4b80ec08.png
copying images... [ 98%] _build/jupyter_execute/44ce029c56c32532a6decdf808dd4e4f6b4e41dfad3597791df4a2763b9188cb.png
copying images... [ 99%] _build/jupyter_execute/43f8eabe0205c95dc1674637d23c1a4912c9de0f0b874fb8fda2d9e61377a492.png
copying images... [ 99%] _build/jupyter_execute/8d249fd99ddebeb2f583b36f78d8b745ef118be493cdc158ab0b18ee904fb8aa.png
copying images... [100%] _build/jupyter_execute/6c3b6c2fef8ccfbbaa0b16b5baa60d3ce29c14b5d1703c87f6cea468813577a5.png
copying images... [100%] _build/jupyter_execute/86278d709cf8712744109ad897a4c314d2ce612cf45f807bd702a3786a0d9d68.png

dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in docs/_build/html.

[rtd-command-info] start-time: 2026-11-05T13:33:12.497890Z, end-time: 2026-11-05T13:33:12.563799Z, duration: 0, exit-code: 0
mv docs/_build $READTHEDOCS_OUTPUT