Read the Docs build information Build id: 1649834 Project: icb-scanpy Version: latest Commit: e4510186e3e06cf32ed5b271cc9068526cf95461 Date: 2023-08-09T08:43:17.171908Z State: finished Success: True [rtd-command-info] start-time: 2023-08-09T08:43:20.670623Z, end-time: 2023-08-09T08:43:24.590079Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2023-08-09T08:43:24.849193Z, end-time: 2023-08-09T08:43:25.080667Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at e4510186 fixed `get.rank_genes_groups_df` with logreg (#2601) [rtd-command-info] start-time: 2023-08-09T08:43:25.482540Z, end-time: 2023-08-09T08:43:25.547171Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-09T08:43:25.868455Z, end-time: 2023-08-09T08:43:26.197887Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2023-08-09T08:43:26.534556Z, end-time: 2023-08-09T08:43:40.032876Z, duration: 13, exit-code: 0 git submodule update --init --force docs/tutorials Submodule 'docs/tutorials' (https://github.com/scverse/scanpy-tutorials.git) registered for path 'docs/tutorials' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials'... Submodule path 'docs/tutorials': checked out 'ba8e433ea7c0fc3b1e1e482ecc2e1dd5f59a9d9d' [rtd-command-info] start-time: 2023-08-09T08:43:40.254278Z, end-time: 2023-08-09T08:43:40.355260Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-20.04 tools: python: '3.9' sphinx: configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - leiden submodules: include: - "docs/tutorials" [rtd-command-info] start-time: 2023-08-09T08:43:47.013618Z, end-time: 2023-08-09T08:43:47.107546Z, duration: 0, exit-code: 0 asdf global python 3.9.17 [rtd-command-info] start-time: 2023-08-09T08:43:47.653558Z, end-time: 2023-08-09T08:43:48.608753Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.17.final.0-64 in 602ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder 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setuptools Found existing installation: setuptools 57.4.0 Uninstalling setuptools-57.4.0: Successfully uninstalled setuptools-57.4.0 Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-23.2.1 setuptools-68.0.0 [rtd-command-info] start-time: 2023-08-09T08:44:02.406164Z, end-time: 2023-08-09T08:44:10.945689Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0 Collecting pillow Obtaining dependency information for pillow from https://files.pythonhosted.org/packages/50/e5/0d484d1ac71b934638f91b7156203ba5bf3eb12f596b616a68a85c123808/Pillow-10.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata Downloading Pillow-10.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.5 kB) Collecting mock==1.0.1 Downloading 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Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4 [rtd-command-info] start-time: 2023-08-09T08:44:11.281527Z, end-time: 2023-08-09T08:45:50.317497Z, duration: 99, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,leiden] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting anndata>=0.7.4 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for anndata>=0.7.4 from https://files.pythonhosted.org/packages/a7/ee/767a05c299d95b438ef9c8ab6dbc15896cfb9121cf4327fe1da160a45343/anndata-0.9.2-py3-none-any.whl.metadata Downloading anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB) Collecting numpy>=1.17.0 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for numpy>=1.17.0 from https://files.pythonhosted.org/packages/69/1f/c95b1108a9972a52d7b1b63ed8ca70466b59b8c1811bd121f1e667cc45d8/numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB) Collecting matplotlib>=3.4 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for 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dependency information for tqdm from https://files.pythonhosted.org/packages/c0/ab/bd9ba7f84c509c8b377628bc66696d52623e30c6c0830db3c78748eec4b4/tqdm-4.65.2-py3-none-any.whl.metadata Downloading tqdm-4.65.2-py3-none-any.whl.metadata (56 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.0/57.0 kB 179.4 MB/s eta 0:00:00 Collecting scikit-learn>=0.24 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for scikit-learn>=0.24 from https://files.pythonhosted.org/packages/d4/61/966d3238f6cbcbb13350d31bd0accfc5efdf9e349cd2a42d9761b8b67a18/scikit_learn-1.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading scikit_learn-1.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting statsmodels>=0.10.0rc2 (from scanpy==1.10.0.dev98+ge4510186) Downloading statsmodels-0.14.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 146.6 MB/s eta 0:00:00 Collecting 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numba>=0.41.0 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for numba>=0.41.0 from https://files.pythonhosted.org/packages/f2/ef/10dbc0226788cd3704c993b5ab0c32f5ce6b76f176998379a2b5bc386848/numba-0.57.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata Downloading numba-0.57.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB) Collecting umap-learn>=0.3.10 (from scanpy==1.10.0.dev98+ge4510186) Downloading umap-learn-0.5.3.tar.gz (88 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 207.4 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from scanpy==1.10.0.dev98+ge4510186) (23.1) Collecting session-info (from scanpy==1.10.0.dev98+ge4510186) Downloading session_info-1.0.0.tar.gz (24 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sphinx<5,>=4.4 (from scanpy==1.10.0.dev98+ge4510186) Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 221.1 MB/s eta 0:00:00 Collecting scanpydoc>=0.7.11 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for scanpydoc>=0.7.11 from https://files.pythonhosted.org/packages/6e/04/d3668db9d9e6da91896c1bac0e25362cdcae582951f8b7bda14993174d26/scanpydoc-0.9.4-py3-none-any.whl.metadata Downloading scanpydoc-0.9.4-py3-none-any.whl.metadata (2.4 kB) Collecting sphinx-autodoc-typehints (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for sphinx-autodoc-typehints from https://files.pythonhosted.org/packages/a4/a2/71ee28033c218b025348555747cb95993338179875bae75c197138be77ad/sphinx_autodoc_typehints-1.24.0-py3-none-any.whl.metadata Downloading sphinx_autodoc_typehints-1.24.0-py3-none-any.whl.metadata (7.8 kB) 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ipython-8.14.0-py3-none-any.whl.metadata (5.8 kB) Collecting igraph>=0.10 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for igraph>=0.10 from https://files.pythonhosted.org/packages/e4/00/dd03a33a26d684cfdeab9b408daf480fcef1605e3e213c1936728b4e7673/igraph-0.10.6-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading igraph-0.10.6-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB) Collecting leidenalg>=0.9 (from scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for leidenalg>=0.9 from https://files.pythonhosted.org/packages/24/76/0dc45c635cd46a18c77104da0c7ee03076e501b65aa4c8c809b75f9bd0f6/leidenalg-0.10.1-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading leidenalg-0.10.1-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB) Collecting texttable>=1.6.2 (from igraph>=0.10->scanpy==1.10.0.dev98+ge4510186) Downloading texttable-1.6.7-py2.py3-none-any.whl 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dependency information for prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 from https://files.pythonhosted.org/packages/a9/b4/ba77c84edf499877317225d7b7bc047a81f7c2eed9628eeb6bab0ac2e6c9/prompt_toolkit-3.0.39-py3-none-any.whl.metadata Downloading prompt_toolkit-3.0.39-py3-none-any.whl.metadata (6.4 kB) Requirement already satisfied: pygments>=2.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from ipython>=7.20->scanpy==1.10.0.dev98+ge4510186) (2.16.1) Collecting stack-data (from ipython>=7.20->scanpy==1.10.0.dev98+ge4510186) Downloading stack_data-0.6.2-py3-none-any.whl (24 kB) Collecting traitlets>=5 (from ipython>=7.20->scanpy==1.10.0.dev98+ge4510186) Downloading traitlets-5.9.0-py3-none-any.whl (117 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.4/117.4 kB 215.4 MB/s eta 0:00:00 Collecting typing-extensions (from ipython>=7.20->scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for typing-extensions from 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sphinx<5,>=4.4->scanpy==1.10.0.dev98+ge4510186) (2.31.0) Collecting importlib-metadata>=4.4 (from sphinx<5,>=4.4->scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for importlib-metadata>=4.4 from https://files.pythonhosted.org/packages/cc/37/db7ba97e676af155f5fcb1a35466f446eadc9104e25b83366e8088c9c926/importlib_metadata-6.8.0-py3-none-any.whl.metadata Downloading importlib_metadata-6.8.0-py3-none-any.whl.metadata (5.1 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from patsy->scanpy==1.10.0.dev98+ge4510186) (1.16.0) Collecting pynndescent>=0.5 (from umap-learn>=0.3.10->scanpy==1.10.0.dev98+ge4510186) Downloading pynndescent-0.5.10.tar.gz (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 245.4 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting jupyter-cache<0.7,>=0.5 (from 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jupyter-core!=5.0.*,>=4.12 (from nbclient->myst-nb->scanpy==1.10.0.dev98+ge4510186) Obtaining dependency information for jupyter-core!=5.0.*,>=4.12 from https://files.pythonhosted.org/packages/8c/e0/3f9061c5e99a03612510f892647b15a91f910c5275b7b77c6c72edae1494/jupyter_core-5.3.1-py3-none-any.whl.metadata Downloading jupyter_core-5.3.1-py3-none-any.whl.metadata (3.4 kB) Collecting beautifulsoup4 (from nbconvert!=5.4->nbsphinx->scanpy==1.10.0.dev98+ge4510186) Downloading beautifulsoup4-4.12.2-py3-none-any.whl (142 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.0/143.0 kB 217.2 MB/s eta 0:00:00 Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx->scanpy==1.10.0.dev98+ge4510186) Downloading bleach-6.0.0-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 231.7 MB/s eta 0:00:00 Collecting defusedxml (from nbconvert!=5.4->nbsphinx->scanpy==1.10.0.dev98+ge4510186) Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments (from 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rpds_py-0.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 246.2 MB/s eta 0:00:00 Building wheels for collected packages: umap-learn, scanpy, session-info, pynndescent Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82813 sha256=56a59d51753e9701f0ce86427425c034f0e08e9477af92d3023b184b025e8d1e Stored in directory: /tmp/pip-ephem-wheel-cache-f5_8_tff/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9 Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.10.0.dev98+ge4510186-py3-none-any.whl size=11838626 sha256=58b7425e9dafef30bb18f177b95ee2cdc42eed3691334e0fca9719c869061794 Stored in directory: /tmp/pip-ephem-wheel-cache-f5_8_tff/wheels/2c/ca/a8/b038e303156487f1950e65fb14990e1642cd81a73929959d71 Building wheel for session-info (setup.py): started Building wheel for session-info (setup.py): finished with status 'done' Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8026 sha256=a9ec4973bb91d41a649b8897863ef993876889052c1269e2e4356084e2c50ecc Stored in directory: /tmp/pip-ephem-wheel-cache-f5_8_tff/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6 Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.10-py3-none-any.whl size=55624 sha256=d5505061d649846d13ce084aecbeb64e986ddd23599f49cec1651571da56a6b1 Stored in directory: /tmp/pip-ephem-wheel-cache-f5_8_tff/wheels/12/f9/4d/ec5ad1c823c710fcc4473669fdcffc8891f4bc398c841af22e Successfully built umap-learn scanpy session-info pynndescent Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, threadpoolctl, tabulate, stdlib_list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, rpds-py, pyzmq, pyyaml, python-dateutil, pyparsing, psutil, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, llvmlite, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fonttools, defusedxml, decorator, debugpy, cycler, click, bleach, attrs, asttokens, accessible-pygments, stack-data, sqlalchemy, session-info, scipy, referencing, patsy, pandas, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib-resources, importlib-metadata, h5py, contourpy, comm, beautifulsoup4, statsmodels, sphinx, scikit-learn, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, anndata, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, pydata-sphinx-theme, myst-parser, jsonschema, ipykernel, umap-learn, sphinx-book-theme, nbformat, scanpy, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Successfully installed accessible-pygments-0.0.4 anndata-0.9.2 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 click-8.1.6 comm-0.1.4 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7.post1 decorator-5.1.1 defusedxml-0.7.1 executing-1.2.0 fastjsonschema-2.18.0 fonttools-4.42.0 greenlet-2.0.2 h5py-3.9.0 igraph-0.10.6 importlib-metadata-6.8.0 importlib-resources-6.0.1 ipykernel-6.25.1 ipython-8.14.0 jedi-0.19.0 joblib-1.3.1 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 jupyter-cache-0.6.1 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 leidenalg-0.10.1 llvmlite-0.40.1 markdown-it-py-2.2.0 matplotlib-3.7.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-3.0.1 myst-nb-0.17.2 myst-parser-0.18.1 natsort-8.4.0 nbclient-0.7.4 nbconvert-7.7.3 nbformat-5.9.2 nbsphinx-0.9.2 nest-asyncio-1.5.7 networkx-3.1 numba-0.57.1 numpy-1.24.4 pandas-2.0.3 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.10.0 prompt-toolkit-3.0.39 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.13.3 pynndescent-0.5.10 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2023.3 pyyaml-6.0.1 pyzmq-25.1.0 referencing-0.30.2 rpds-py-0.9.2 scanpy-1.10.0.dev98+ge4510186 scanpydoc-0.9.4 scikit-learn-1.3.0 scipy-1.11.1 seaborn-0.12.2 session-info-1.0.0 soupsieve-2.4.1 sphinx-4.5.0 sphinx-autodoc-typehints-1.19.1 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-design-0.4.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext-opengraph-0.8.2 sqlalchemy-2.0.19 stack-data-0.6.2 statsmodels-0.14.0 stdlib_list-0.9.0 tabulate-0.9.0 texttable-1.6.7 threadpoolctl-3.2.0 tinycss2-1.2.1 tornado-6.3.2 tqdm-4.65.2 traitlets-5.9.0 typing-extensions-4.7.1 tzdata-2023.3 umap-learn-0.5.3 wcwidth-0.2.6 webencodings-0.5.1 zipp-3.16.2 [rtd-command-info] start-time: 2023-08-09T08:45:53.267731Z, end-time: 2023-08-09T08:45:53.327990Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys import importlib.util import inspect import re import subprocess from pathlib import Path from datetime import datetime from typing import Any import matplotlib # noqa from packaging.version import parse as parse_version # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '4.0' # Nicer param docs suppress_warnings = [ 'ref.citation', 'myst.header', # https://github.com/executablebooks/MyST-Parser/issues/262 ] # General information project = 'Scanpy' author = 'Scanpy development team' repository_url = "https://github.com/scverse/scanpy" copyright = f'{datetime.now():%Y}, the Scanpy development team.' version = scanpy.__version__.replace('.dirty', '') # Bumping the version updates all docs, so don't do that if parse_version(version).is_devrelease: parsed = parse_version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # default settings templates_path = ['_templates'] master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] extensions = [ 'myst_nb', 'sphinx_copybutton', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', 'sphinx.ext.linkcode', 'sphinx.ext.extlinks', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon 'scanpydoc.autosummary_generate_imported', 'scanpydoc.definition_list_typed_field', 'sphinx_design', 'sphinxext.opengraph', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images myst_enable_extensions = [ "amsmath", "colon_fence", "deflist", "dollarmath", "html_image", "html_admonition", ] myst_url_schemes = ("http", "https", "mailto") nb_output_stderr = "remove" nb_execution_mode = "off" nb_merge_streams = True ogp_site_url = "https://scanpy.readthedocs.io/en/stable/" ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg" typehints_defaults = 'braces' scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' pygments_style = "default" pygments_dark_style = "native" intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('https://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/stable/', None), networkx=('https://networkx.org/documentation/stable/', None), numpy=('https://numpy.org/doc/stable/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), pytest=('https://docs.pytest.org/en/latest/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = "sphinx_book_theme" html_theme_options = { "repository_url": repository_url, "use_repository_button": True, "logo_only": True, "show_toc_level": 4, # show all levels in the sidebar } html_static_path = ['_static'] html_css_files = ["css/override.css"] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' html_title = "scanpy" def setup(app): """App setup hook.""" # TODO: fix all warnings in a future PR # Many come from the tutorials, like the workshop directory # which is not included in the docs # app.warningiserror = on_rtd app.add_config_value( "recommonmark_config", { "auto_toc_tree_section": "Contents", "enable_auto_toc_tree": True, "enable_math": True, "enable_inline_math": False, "enable_eval_rst": True, }, True, ) # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", # If the docs are built with an old version of numpy, this will make it work: "numpy.random.RandomState": "numpy.random.mtrand.RandomState", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", "pandas.core.series.Series": "pandas.Series", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.plotting._utils._AxesSubplot'), ('py:class', 'scanpy._utils.Empty'), ('py:class', 'numpy.random.mtrand.RandomState'), # Will work once scipy 1.8 is released ('py:class', 'scipy.sparse.base.spmatrix'), ('py:class', 'scipy.sparse.csr.csr_matrix'), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root # Linkcode config def git(*args): return subprocess.check_output(["git", *args]).strip().decode() # https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192 # Current git reference. Uses branch/tag name if found, otherwise uses commit hash git_ref = None try: git_ref = git("name-rev", "--name-only", "--no-undefined", "HEAD") git_ref = re.sub(r"^(remotes/[^/]+|tags)/", "", git_ref) except Exception: pass # (if no name found or relative ref, use commit hash instead) if not git_ref or re.search(r"[\^~]", git_ref): try: git_ref = git("rev-parse", "HEAD") except Exception: git_ref = "master" # https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192 _module_path = os.path.dirname(importlib.util.find_spec("scanpy").origin) # type: ignore def linkcode_resolve(domain, info): if domain != "py": return None try: obj: Any = sys.modules[info["module"]] for part in info["fullname"].split("."): obj = getattr(obj, part) obj = inspect.unwrap(obj) if isinstance(obj, property): obj = inspect.unwrap(obj.fget) # type: ignore path = os.path.relpath(inspect.getsourcefile(obj), start=_module_path) # type: ignore src, lineno = inspect.getsourcelines(obj) except Exception: return None path = f"{path}#L{lineno}-L{lineno + len(src) - 1}" return f"{repository_url}/blob/{git_ref}/scanpy/{path}" # extlinks config extlinks = { "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"), "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"), "tutorial": ( "https://github.com/scverse/scanpy-tutorials/%s.ipynb", "tutorial: %s", ), } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'e4510186', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1649834/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-08-09T08:45:53.565796Z, end-time: 2023-08-09T08:51:11.222298Z, duration: 317, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v4.5.0 Matplotlib is building the font cache; this may take a moment. loading translations [en]... done making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_image', 'html_admonition'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), 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') myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/_readthedocs/.jupyter_cache loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv... loading intersphinx inventory from https://docs.h5py.org/en/stable/objects.inv... loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/scanpy_workshop/day2_01_DE_Colabs.ipynb, tutorials/scanpy_workshop/day2_01_DifferentialExpression.ipynb, tutorials/scanpy_workshop/day2_02_GSEA_Colabs.ipynb, tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis.ipynb, tutorials/scanpy_workshop/day2_03_RNAvelocity.ipynb, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/integration-scanorama.ipynb, tutorials/tutorial_pearson_residuals.ipynb, tutorials/visualizing-marker-genes.rst, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 99 source files that are out of date updating environment: [new config] 354 added, 0 changed, 0 removed reading sources... 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[ 26%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 26%] api/generated/scanpy.pl.draw_graph WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`). /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( reading sources... [ 26%] api/generated/scanpy.pl.embedding reading sources... [ 27%] api/generated/scanpy.pl.embedding_density /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. @numba.jit() /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. @numba.jit() /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. @numba.jit() /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. @numba.jit() reading sources... [ 27%] api/generated/scanpy.pl.filter_genes_dispersion reading sources... [ 27%] api/generated/scanpy.pl.highest_expr_genes reading sources... [ 27%] api/generated/scanpy.pl.highly_variable_genes reading sources... [ 28%] api/generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00