Read the Docs build information Build id: 899766 Project: icb-scanpy Version: latest Commit: 4322e82147eac5a4a6be82cdd22f469e9c5ddf70 Date: 2022-03-29T17:44:26.866953Z State: finished Success: True [rtd-command-info] start-time: 2022-03-29T17:44:28.703427Z, end-time: 2022-03-29T17:44:32.048289Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2022-03-29T17:44:32.271378Z, end-time: 2022-03-29T17:44:32.415465Z, 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 4322e821 Pca loadings n points patch (#2075) [rtd-command-info] start-time: 2022-03-29T17:44:32.657074Z, end-time: 2022-03-29T17:44:32.719356Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-03-29T17:44:37.437515Z, end-time: 2022-03-29T17:44:37.529153Z, duration: 0, exit-code: 0 asdf global python 3.9.7 [rtd-command-info] start-time: 2022-03-29T17:44:37.981635Z, end-time: 2022-03-29T17:44:38.885148Z, duration: 0, exit-code: 0 python -mvirtualenv created virtual environment CPython3.9.7.final.0-64 in 596ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2022-03-29T17:44:39.166828Z, end-time: 2022-03-29T17:44:49.721023Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.0.4-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (57.4.0) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools, pip Attempting uninstall: 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-22.0.4 setuptools-58.2.0 [rtd-command-info] start-time: 2022-03-29T17:44:49.959401Z, end-time: 2022-03-29T17:45:24.521501Z, duration: 34, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 KB 22.6 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 118.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 KB 98.2 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 139.1 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 132.6 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.5-py2.py3-none-any.whl (11 kB) Collecting jinja2<3.1.0 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 KB 127.4 MB/s eta 0:00:00 Collecting future Downloading future-0.18.2.tar.gz (829 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 KB 140.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 KB 144.5 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.8/8.8 MB 133.3 MB/s eta 0:00:00 Collecting requests>=2.0.0 Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.1/63.1 KB 186.3 MB/s eta 0:00:00 Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 KB 26.3 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 KB 162.0 MB/s eta 0:00:00 Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 KB 105.2 MB/s eta 0:00:00 Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Pygments>=2.0 Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 141.7 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<2) (58.2.0) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting pytz>=2015.7 Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 KB 148.8 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.2/149.2 KB 143.6 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 KB 129.9 MB/s eta 0:00:00 Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 KB 122.5 MB/s eta 0:00:00 Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.7-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.0/98.0 KB 116.8 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 KB 126.0 MB/s eta 0:00:00 Building wheels for collected packages: mock, pillow, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=db3408bc0b6f3323f26cfdfa23481329288247bf6e2adcd8dee01ac3f6febae6 Stored in directory: /tmp/pip-ephem-wheel-cache-dx_bmq_i/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp39-cp39-linux_x86_64.whl size=1361231 sha256=cfb67ec1a7d7306d43ab17ebe00e55f6f8df51ecd64124e88452fe8875e636b6 Stored in directory: /tmp/pip-ephem-wheel-cache-dx_bmq_i/wheels/d3/de/21/f0ad1b0453288616d3f4d2ce28431aa7a2adde8f27c9b7a0af Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=149924e33da93a8bf81a278ea085529c4aa95ee8870039850c7feb968fc4f164 Stored in directory: /tmp/pip-ephem-wheel-cache-dx_bmq_i/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 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 urllib3-1.26.9 [rtd-command-info] start-time: 2022-03-29T17:45:24.700137Z, end-time: 2022-03-29T17:46:41.151145Z, duration: 76, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] 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 numpy>=1.17.0 Downloading numpy-1.22.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.8/16.8 MB 196.2 MB/s eta 0:00:00 Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.13.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 202.4 MB/s eta 0:00:00 Collecting pandas>=0.21 Downloading pandas-1.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 185.5 MB/s eta 0:00:00 Collecting numba>=0.41.0 Downloading numba-0.55.1-1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 206.5 MB/s eta 0:00:00 Collecting joblib Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 307.0/307.0 KB 235.2 MB/s eta 0:00:00 Collecting session-info Downloading session_info-1.0.0.tar.gz (24 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting h5py>=3 Downloading h5py-3.6.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 208.9 MB/s eta 0:00:00 Collecting umap-learn>=0.3.10 Downloading umap-learn-0.5.2.tar.gz (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 KB 189.6 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting anndata>=0.7.4 Downloading anndata-0.8.0-py3-none-any.whl (96 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.1/96.1 KB 214.3 MB/s eta 0:00:00 Collecting networkx>=2.3 Downloading networkx-2.7.1-py3-none-any.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 196.7 MB/s eta 0:00:00 Collecting matplotlib>=3.1.2 Downloading matplotlib-3.5.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 186.0 MB/s eta 0:00:00 Collecting scipy>=1.4 Downloading scipy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (42.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.1/42.1 MB 190.3 MB/s eta 0:00:00 Collecting patsy Downloading patsy-0.5.2-py2.py3-none-any.whl (233 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.7/233.7 KB 211.8 MB/s eta 0:00:00 Collecting tqdm Downloading tqdm-4.63.1-py2.py3-none-any.whl (76 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.6/76.6 KB 185.9 MB/s eta 0:00:00 Collecting natsort Downloading natsort-8.1.0-py3-none-any.whl (37 kB) Collecting seaborn Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 292.8/292.8 KB 222.4 MB/s eta 0:00:00 Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from scanpy==1.9.0.dev92+g4322e821) (21.3) Collecting scikit-learn>=0.22 Downloading scikit_learn-1.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (26.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.4/26.4 MB 199.0 MB/s eta 0:00:00 Collecting scanpydoc[typehints]>=0.7.7 Downloading scanpydoc-0.7.7-py3-none-any.whl (29 kB) Collecting myst-parser Downloading myst_parser-0.17.0-py3-none-any.whl (52 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.8/52.8 KB 173.2 MB/s eta 0:00:00 Collecting sphinx>=4.4 Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 206.7 MB/s eta 0:00:00 Collecting sphinx-rtd-theme>=1.0 Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 185.3 MB/s eta 0:00:00 Collecting python-igraph Downloading python_igraph-0.9.9-py3-none-any.whl (9.1 kB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.4.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 240.1 MB/s eta 0:00:00 Collecting python-dateutil>=2.7 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 KB 220.9 MB/s eta 0:00:00 Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from matplotlib>=3.1.2->scanpy==1.9.0.dev92+g4322e821) (3.0.7) Collecting pillow>=6.2.0 Downloading Pillow-9.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 187.6 MB/s eta 0:00:00 Collecting cycler>=0.10 Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting fonttools>=4.22.0 Downloading fonttools-4.31.2-py3-none-any.whl (899 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 899.5/899.5 KB 245.5 MB/s eta 0:00:00 Collecting llvmlite<0.39,>=0.38.0rc1 Downloading llvmlite-0.38.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 190.7 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from numba>=0.41.0->scanpy==1.9.0.dev92+g4322e821) (58.2.0) Collecting setuptools Downloading setuptools-61.2.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 196.7 MB/s eta 0:00:00 Collecting numpy>=1.17.0 Downloading numpy-1.21.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 193.8 MB/s eta 0:00:00 Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from pandas>=0.21->scanpy==1.9.0.dev92+g4322e821) (2022.1) Collecting get_version Downloading get_version-3.5.4-py3-none-any.whl (18 kB) Collecting sphinx-autodoc-typehints>=1.15.2 Downloading sphinx_autodoc_typehints-1.17.0-py3-none-any.whl (12 kB) Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 KB 215.4 MB/s eta 0:00:00 Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (1.3.0) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.9.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (0.7.12) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (1.1.5) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.27.1) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (3.0.3) Collecting Jinja2>=2.3 Downloading Jinja2-3.1.1-py3-none-any.whl (132 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.6/132.6 KB 203.5 MB/s eta 0:00:00 Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 KB 217.4 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.11.2) Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (0.17.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.2.0) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 KB 200.8 MB/s eta 0:00:00 Collecting importlib-metadata>=4.4 Downloading importlib_metadata-4.11.3-py3-none-any.whl (18 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 KB 213.4 MB/s eta 0:00:00 Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from patsy->scanpy==1.9.0.dev92+g4322e821) (1.16.0) Collecting pynndescent>=0.5 Downloading pynndescent-0.5.6.tar.gz (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 217.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pyyaml Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 661.8/661.8 KB 204.1 MB/s eta 0:00:00 Collecting mdit-py-plugins~=0.3.0 Downloading mdit_py_plugins-0.3.0-py3-none-any.whl (43 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.7/43.7 KB 181.9 MB/s eta 0:00:00 Collecting typing-extensions Downloading typing_extensions-4.1.1-py3-none-any.whl (26 kB) Collecting markdown-it-py<3.0.0,>=1.0.0 Downloading markdown_it_py-2.0.1-py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.1/84.1 KB 210.9 MB/s eta 0:00:00 Collecting igraph==0.9.9 Downloading igraph-0.9.9-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 204.3 MB/s eta 0:00:00 Collecting texttable>=1.6.2 Downloading texttable-1.6.4-py2.py3-none-any.whl (10 kB) Collecting stdlib_list Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.5/63.5 KB 192.8 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.7.0-py3-none-any.whl (5.3 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from Jinja2>=2.3->sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.1.1) Collecting mdurl~=0.1 Downloading mdurl-0.1.0-py3-none-any.whl (11 kB) Collecting attrs<22,>=19 Downloading attrs-21.4.0-py2.py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 KB 202.8 MB/s eta 0:00:00 Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2021.10.8) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (2.0.12) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (3.3) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx>=4.4->scanpy==1.9.0.dev92+g4322e821) (1.26.9) Collecting dunamai Downloading dunamai-1.11.0-py3-none-any.whl (19 kB) 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-0.5.2-py3-none-any.whl size=82709 sha256=3f42aff37f26188af707bdd33e06019a61a8aa5497aa5e8f44c20f8edffe8d4d Stored in directory: /tmp/pip-ephem-wheel-cache-tbz_nald/wheels/4a/66/81/205d77bd58539a1d07fb8b795fcea0b17f4d59912c0f4202b7 Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.9.0.dev92+g4322e821-py3-none-any.whl size=11458404 sha256=332e282ffb6dd2529d17d0861d777ea5f92de506da13a8e18e6a4ab014fb70d0 Stored in directory: /tmp/pip-ephem-wheel-cache-tbz_nald/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=8045 sha256=ce2481e19e0218e19ba7a8fefae214842f112063f91dc841c791131c296bf833 Stored in directory: /tmp/pip-ephem-wheel-cache-tbz_nald/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-0.5.6-py3-none-any.whl size=53945 sha256=9198ed7fca662ba48196709b40c3d9200fae84b04a85a24ce58690b1b552aef4 Stored in directory: /tmp/pip-ephem-wheel-cache-tbz_nald/wheels/c0/f0/1d/20aa0dcee54ef40c179a4a4f57fad413437864a67757013a99 Successfully built umap-learn scanpy session-info pynndescent Installing collected packages: texttable, stdlib_list, zipp, typing-extensions, tqdm, threadpoolctl, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, session-info, pyyaml, python-dateutil, pillow, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, Jinja2, igraph, fonttools, cycler, attrs, scipy, python-igraph, patsy, pandas, numba, matplotlib, markdown-it-py, importlib-metadata, h5py, dunamai, statsmodels, sphinx, seaborn, scikit-learn, mdit-py-plugins, get_version, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpydoc, pynndescent, myst-parser, umap-learn, scanpy Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed Jinja2-3.1.1 anndata-0.8.0 attrs-21.4.0 cycler-0.11.0 dunamai-1.11.0 fonttools-4.31.2 get_version-3.5.4 h5py-3.6.0 igraph-0.9.9 importlib-metadata-4.11.3 joblib-1.1.0 kiwisolver-1.4.2 llvmlite-0.38.0 markdown-it-py-2.0.1 matplotlib-3.5.1 mdit-py-plugins-0.3.0 mdurl-0.1.0 myst-parser-0.17.0 natsort-8.1.0 networkx-2.7.1 numba-0.55.1 numpy-1.21.5 pandas-1.4.1 patsy-0.5.2 pillow-9.0.1 pynndescent-0.5.6 python-dateutil-2.8.2 python-igraph-0.9.9 pyyaml-6.0 scanpy-1.9.0.dev92+g4322e821 scanpydoc-0.7.7 scikit-learn-1.0.2 scipy-1.8.0 seaborn-0.11.2 session-info-1.0.0 setuptools-61.2.0 sphinx-4.5.0 sphinx-autodoc-typehints-1.17.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.13.2 stdlib_list-0.8.0 texttable-1.6.4 threadpoolctl-3.1.0 tqdm-4.63.1 typing-extensions-4.1.1 umap-learn-0.5.2 zipp-3.7.0 [rtd-command-info] start-time: 2022-03-29T17:46:42.503494Z, end-time: 2022-03-29T17:46:42.566751Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa # 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 = '2.0' # 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' copyright = f'{datetime.now():%Y}, the Scanpy development team.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'myst_parser', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', *[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 scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' 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 = 'scanpydoc' html_theme_options = dict( navigation_depth=4, logo_only=True, docsearch_index='scanpy', docsearch_key='fa4304eb95d2134997e3729553a674b2', ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.warningiserror = on_rtd # -- 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 ########################################################################### # 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/master/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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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", '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': 'https://scanpy.readthedocs.io/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', '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': '4322e821', } # 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(): html_context.update(context) 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/899766/' 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: 2022-03-29T17:46:42.744688Z, end-time: 2022-03-29T17:50:51.081918Z, duration: 248, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/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 v0.17.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], 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', disable_syntax=[], all_links_external=False, url_schemes=['http', 'https', 'mailto', 'ftp'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200) 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: _key_contributors.rst, api.md, basic_usage.md, community.md, contributors.md, dev/ci.md, dev/code.md, dev/documentation.md, dev/external-tools.md, dev/getting-set-up.md, ..., release-notes/1.7.2.md, release-notes/1.8.0.md, release-notes/1.8.1.md, release-notes/1.8.2.md, release-notes/1.8.3.md, release-notes/1.9.0.md, release-notes/index.md, release-notes/release-latest.md, tutorials.md, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.paul15.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/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/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 61 source files that are out of date updating environment: [new config] 316 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 0%] api reading sources... [ 0%] basic_usage reading sources... [ 1%] community reading sources... [ 1%] contributors reading sources... [ 1%] dev/ci reading sources... [ 2%] dev/code reading sources... [ 2%] dev/documentation reading sources... [ 2%] dev/external-tools reading sources... [ 3%] dev/getting-set-up reading sources... [ 3%] dev/index reading sources... [ 3%] dev/release reading sources... [ 4%] dev/testing reading sources... [ 4%] dev/versioning reading sources... [ 4%] ecosystem reading sources... [ 5%] external reading sources... [ 5%] generated/classes/scanpy.pl.DotPlot reading sources... [ 5%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.add_dendrogram reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.add_totals reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.get_axes reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.getdoc reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.legend reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.make_figure reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.savefig reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.show reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.style reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.swap_axes reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.add_dendrogram reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_totals reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.get_axes reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.getdoc reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.legend reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.make_figure reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.savefig reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.show reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.swap_axes reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_dendrogram reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_totals reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.get_axes reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.getdoc reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.legend reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.make_figure reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.savefig reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.show reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.swap_axes reading sources... [ 32%] generated/scanpy.Neighbors reading sources... [ 32%] generated/scanpy.Neighbors.compute_eigen reading sources... [ 32%] generated/scanpy.Neighbors.compute_neighbors reading sources... [ 33%] generated/scanpy.Neighbors.compute_transitions reading sources... [ 33%] generated/scanpy.Neighbors.connectivities reading sources... [ 33%] generated/scanpy.Neighbors.distances reading sources... [ 34%] generated/scanpy.Neighbors.distances_dpt reading sources... [ 34%] generated/scanpy.Neighbors.eigen_basis reading sources... [ 34%] generated/scanpy.Neighbors.eigen_values reading sources... [ 35%] generated/scanpy.Neighbors.getdoc reading sources... [ 35%] generated/scanpy.Neighbors.rp_forest reading sources... [ 35%] generated/scanpy.Neighbors.to_igraph reading sources... [ 36%] generated/scanpy.Neighbors.transitions reading sources... [ 36%] generated/scanpy.Neighbors.transitions_sym reading sources... [ 36%] generated/scanpy._settings.ScanpyConfig reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.autosave reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.autoshow reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.cache_compression reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.cachedir reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.figdir reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.file_format_figs reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.logfile reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.logpath reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.max_memory reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.n_jobs reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.plot_suffix reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.set_figure_params reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.verbosity reading sources... [ 42%] generated/scanpy._settings.ScanpyConfig.writedir reading sources... [ 42%] generated/scanpy.datasets.blobs reading sources... [ 42%] generated/scanpy.datasets.ebi_expression_atlas reading sources... [ 43%] generated/scanpy.datasets.krumsiek11 reading sources... [ 43%] generated/scanpy.datasets.moignard15 reading sources... [ 43%] generated/scanpy.datasets.paul15 reading sources... [ 43%] generated/scanpy.datasets.pbmc3k reading sources... [ 44%] generated/scanpy.datasets.pbmc3k_processed reading sources... [ 44%] generated/scanpy.datasets.pbmc68k_reduced reading sources... [ 44%] generated/scanpy.datasets.toggleswitch reading sources... [ 45%] generated/scanpy.datasets.visium_sge reading sources... [ 45%] generated/scanpy.experimental.pp.highly_variable_genes reading sources... [ 45%] generated/scanpy.experimental.pp.normalize_pearson_residuals reading sources... [ 46%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca reading sources... [ 46%] generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 46%] generated/scanpy.external.exporting.cellbrowser reading sources... [ 47%] generated/scanpy.external.exporting.spring_project reading sources... [ 47%] generated/scanpy.external.pl.phate reading sources... [ 47%] generated/scanpy.external.pl.sam reading sources... [ 48%] generated/scanpy.external.pl.scrublet_score_distribution reading sources... [ 48%] generated/scanpy.external.pl.trimap reading sources... [ 48%] generated/scanpy.external.pl.wishbone_marker_trajectory reading sources... [ 49%] generated/scanpy.external.pp.bbknn reading sources... [ 49%] generated/scanpy.external.pp.dca reading sources... [ 49%] generated/scanpy.external.pp.harmony_integrate reading sources... [ 50%] generated/scanpy.external.pp.hashsolo reading sources... [ 50%] generated/scanpy.external.pp.magic reading sources... [ 50%] generated/scanpy.external.pp.mnn_correct reading sources... [ 50%] generated/scanpy.external.pp.scanorama_integrate reading sources... [ 51%] generated/scanpy.external.pp.scrublet reading sources... [ 51%] generated/scanpy.external.pp.scrublet_simulate_doublets reading sources... [ 51%] generated/scanpy.external.tl.cyclone reading sources... [ 52%] generated/scanpy.external.tl.harmony_timeseries reading sources... [ 52%] generated/scanpy.external.tl.palantir reading sources... [ 52%] generated/scanpy.external.tl.palantir_results reading sources... [ 53%] generated/scanpy.external.tl.phate reading sources... [ 53%] generated/scanpy.external.tl.phenograph reading sources... [ 53%] generated/scanpy.external.tl.sam reading sources... [ 54%] generated/scanpy.external.tl.sandbag reading sources... [ 54%] generated/scanpy.external.tl.trimap reading sources... [ 54%] generated/scanpy.external.tl.wishbone reading sources... [ 55%] generated/scanpy.get.obs_df reading sources... [ 55%] generated/scanpy.get.rank_genes_groups_df reading sources... [ 55%] generated/scanpy.get.var_df reading sources... [ 56%] generated/scanpy.logging.print_header reading sources... [ 56%] generated/scanpy.logging.print_versions reading sources... [ 56%] generated/scanpy.metrics.confusion_matrix reading sources... [ 56%] generated/scanpy.metrics.gearys_c reading sources... [ 57%] generated/scanpy.metrics.morans_i reading sources... [ 57%] generated/scanpy.pl.clustermap reading sources... [ 57%] generated/scanpy.pl.dendrogram reading sources... [ 58%] generated/scanpy.pl.diffmap reading sources... [ 58%] generated/scanpy.pl.dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 59%] generated/scanpy.pl.dpt_timeseries reading sources... [ 59%] 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`). reading sources... [ 59%] generated/scanpy.pl.embedding reading sources... [ 60%] generated/scanpy.pl.embedding_density reading sources... [ 60%] generated/scanpy.pl.filter_genes_dispersion reading sources... [ 60%] generated/scanpy.pl.heatmap reading sources... [ 61%] generated/scanpy.pl.highest_expr_genes reading sources... [ 61%] generated/scanpy.pl.highly_variable_genes reading sources... [ 61%] generated/scanpy.pl.matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 62%] generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00