Read the Docs build information
Build id: 242833
Project: icb-scanpy
Version: latest
Commit: cd694403c18c15d29c705728f0122c935654e8cf
Date: 2019-09-18T13:30:24.216587Z
State: finished
Success: True
[rtd-command-info] start-time: 2019-09-18T13:30:24.927101Z, end-time: 2019-09-18T13:30:24.944557Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
[rtd-command-info] start-time: 2019-09-18T13:30:25.065224Z, end-time: 2019-09-18T13:30:25.932722Z, duration: 0, exit-code: 0
git fetch origin --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
- [deleted] (none) -> origin/cache-compression
- [deleted] (none) -> origin/recipes
1ec61f4..cd69440 master -> origin/master
[rtd-command-info] start-time: 2019-09-18T13:30:27.330808Z, end-time: 2019-09-18T13:30:27.355616Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 1ec61f4 fix zheng17 and recipe_seurat (#816)
HEAD is now at cd69440 Fix many plotting idiosyncrasies. Fixes #850
[rtd-command-info] start-time: 2019-09-18T13:30:27.446087Z, end-time: 2019-09-18T13:30:27.465861Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-09-18T13:30:28.507509Z, end-time: 2019-09-18T13:30:31.826087Z, duration: 3, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download
Using base prefix '/home/docs/.pyenv/versions/3.6.4'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-09-18T13:30:31.917450Z, end-time: 2019-09-18T13:30:34.800119Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Collecting pip
Using cached https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl
Installing collected packages: pip
Found existing installation: pip 18.1
Uninstalling pip-18.1:
Successfully uninstalled pip-18.1
Successfully installed pip-19.2.3
[rtd-command-info] start-time: 2019-09-18T13:30:34.877466Z, end-time: 2019-09-18T13:30:44.895109Z, duration: 10, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1
Collecting Pygments==2.3.1
Using cached https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl
Collecting setuptools==41.0.1
Using cached https://files.pythonhosted.org/packages/ec/51/f45cea425fd5cb0b0380f5b0f048ebc1da5b417e48d304838c02d6288a1e/setuptools-41.0.1-py2.py3-none-any.whl
Collecting docutils==0.14
Using cached https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl
Collecting mock==1.0.1
Collecting pillow==5.4.1
Using cached https://files.pythonhosted.org/packages/85/5e/e91792f198bbc5a0d7d3055ad552bc4062942d27eaf75c3e2783cf64eae5/Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting alabaster!=0.7.5,<0.8,>=0.7
Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl
Collecting commonmark==0.8.1
Using cached https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl
Collecting recommonmark==0.5.0
Using cached https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl
Collecting sphinx<2
Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl
Collecting sphinx-rtd-theme<0.5
Using cached https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl
Collecting readthedocs-sphinx-ext<1.1
Using cached https://files.pythonhosted.org/packages/51/43/a5a98d9aec325b2824bdf504fa446ae876d0909d03e28667018f9eb01bcd/readthedocs_sphinx_ext-1.0.0-py2.py3-none-any.whl
Collecting future (from commonmark==0.8.1)
Collecting packaging (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/ec/22/630ac83e8f8a9566c4f88038447ed9e16e6f10582767a01f31c769d9a71e/packaging-19.1-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting Jinja2>=2.3 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl
Collecting imagesize (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx<2)
Collecting sphinxcontrib-websupport (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
Collecting attrs (from packaging->sphinx<2)
Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<2)
Using cached https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<2)
Using cached https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting pytz>=2015.7 (from babel!=2.0,>=1.3->sphinx<2)
Using cached https://files.pythonhosted.org/packages/87/76/46d697698a143e05f77bec5a526bf4e56a0be61d63425b68f4ba553b51f2/pytz-2019.2-py2.py3-none-any.whl
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests>=2.0.0->sphinx<2)
Using cached https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<2)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
Using cached https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<2)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, attrs, six, pyparsing, packaging, MarkupSafe, Jinja2, imagesize, pytz, babel, urllib3, idna, certifi, chardet, requests, snowballstemmer, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Found existing installation: setuptools 40.6.3
Uninstalling setuptools-40.6.3:
Successfully uninstalled setuptools-40.6.3
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 attrs-19.1.0 babel-2.7.0 certifi-2019.9.11 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.17.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.1 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.2 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.12.0 snowballstemmer-1.9.1 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.3
[rtd-command-info] start-time: 2019-09-18T13:30:44.984653Z, end-time: 2019-09-18T13:31:17.465030Z, duration: 32, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt
Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3)
Collecting sphinx>=2.0.1 (from -r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/8e/4c/95a21788db2e1653e931420f561015a0bbc9bd4660c4520467ab9e733eb2/Sphinx-2.2.0-py3-none-any.whl
Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 6))
Using cached https://files.pythonhosted.org/packages/35/a6/53a5bf7f7645ce5255e17ce10c90882ba4582ced44569999dcca1de21e11/sphinx_autodoc_typehints-1.8.0-py3-none-any.whl
Collecting scanpydoc>=0.4.1 (from -r docs/requirements.txt (line 7))
Using cached https://files.pythonhosted.org/packages/38/96/16d194ec8056a06b5bea16f83d2ee169dee5e2fac5256d8209eecd94ed4d/scanpydoc-0.4.1-py3-none-any.whl
Collecting anndata>=0.6.18 (from -r docs/requirements.txt (line 9))
Using cached https://files.pythonhosted.org/packages/2b/72/87196c15f68d9865c31a43a10cf7c50bcbcedd5607d09f9aada0b3963103/anndata-0.6.22.post1-py3-none-any.whl
Collecting matplotlib>=2.2 (from -r docs/requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/57/4f/dd381ecf6c6ab9bcdaa8ea912e866dedc6e696756156d8ecc087e20817e2/matplotlib-3.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting pandas>=0.21 (from -r docs/requirements.txt (line 11))
Using cached https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy (from -r docs/requirements.txt (line 12))
Using cached https://files.pythonhosted.org/packages/29/50/a552a5aff252ae915f522e44642bb49a7b7b31677f9580cfd11bcc869976/scipy-1.3.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting seaborn (from -r docs/requirements.txt (line 13))
Using cached https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl
Collecting h5py (from -r docs/requirements.txt (line 14))
Using cached https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting tables (from -r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/87/f7/bb0ec32a3f3dd74143a3108fbf737e6dcfd47f0ffd61b52af7106ab7a38a/tables-3.5.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting scikit-learn>=0.19.1 (from -r docs/requirements.txt (line 16))
Using cached https://files.pythonhosted.org/packages/a0/c5/d2238762d780dde84a20b8c761f563fe882b88c5a5fb03c056547c442a19/scikit_learn-0.21.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting networkx (from -r docs/requirements.txt (line 18))
Collecting natsort (from -r docs/requirements.txt (line 19))
Using cached https://files.pythonhosted.org/packages/e7/13/a66bfa0ebf00e17778ca0319d081be686a33384d1f612fc8e0fc542ac5d8/natsort-6.0.0-py2.py3-none-any.whl
Collecting joblib (from -r docs/requirements.txt (line 20))
Using cached https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl
Collecting numba (from -r docs/requirements.txt (line 21))
Using cached https://files.pythonhosted.org/packages/1d/18/75c4c9e75187d80813e0bf5231346e70f40e8f80de6a4554fc8a69e2ffc9/numba-0.45.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting tqdm (from -r docs/requirements.txt (line 22))
Downloading https://files.pythonhosted.org/packages/95/6b/fe4304220f7a9800f820a6379ee9b1b87128ae8a9703cc3e1ec5171e12ac/tqdm-4.36.0-py2.py3-none-any.whl (52kB)
Collecting importlib_metadata (from -r docs/requirements.txt (line 23))
Downloading https://files.pythonhosted.org/packages/f6/d2/40b3fa882147719744e6aa50ac39cf7a22a913cbcba86a0371176c425a3b/importlib_metadata-0.23-py2.py3-none-any.whl
Collecting setuptools_scm (from -r docs/requirements.txt (line 24))
Using cached https://files.pythonhosted.org/packages/1d/70/97966deebaeeda0b81d3cd63ba9f8ec929b838871ed17476de9d8159db3e/setuptools_scm-3.3.3-py2.py3-none-any.whl
Collecting umap-learn (from -r docs/requirements.txt (line 25))
Collecting sphinxcontrib-qthelp (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/ce/5b/4747c3ba98b3a3e21a66faa183d8f79b9ded70e74212a7988d236a6eb78a/sphinxcontrib_qthelp-1.0.2-py2.py3-none-any.whl
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.0)
Collecting sphinxcontrib-htmlhelp (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/e4/35/80a67cc493f4a8a9634ab203a77aaa1b84d79ccb1c02eca72cb084d2c7f7/sphinxcontrib_htmlhelp-1.0.2-py2.py3-none-any.whl
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.3.1)
Collecting sphinxcontrib-applehelp (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/13/9a/4428b3114d654cb1cd34d90d5e6fab938d5436f94a571155187ea1dd78b4/sphinxcontrib_applehelp-1.0.1-py2.py3-none-any.whl
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.9.1)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.14)
Collecting sphinxcontrib-jsmath (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/c2/42/4c8646762ee83602e3fb3fbe774c2fac12f317deb0b5dbeeedd2d3ba4b77/sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (41.0.1)
Collecting sphinxcontrib-devhelp (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/b0/a3/fea98741f0b2f2902fbf6c35c8e91b22cd0dd13387291e81d457f9a93066/sphinxcontrib_devhelp-1.0.1-py2.py3-none-any.whl
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.7.0)
Collecting sphinxcontrib-serializinghtml (from sphinx>=2.0.1->-r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/57/b3/3648e48fa5682e61e9839d62de4e23af1795ceb738d68d73bd974257a95c/sphinxcontrib_serializinghtml-1.1.3-py2.py3-none-any.whl
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.22.0)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.10.1)
Collecting get_version (from scanpydoc>=0.4.1->-r docs/requirements.txt (line 7))
Using cached https://files.pythonhosted.org/packages/23/48/7610e884e62fff2183e7bc8592397c39a020267fb5147905fcd3f9cc820c/get_version-2.1-py3-none-any.whl
Collecting numpy~=1.14 (from anndata>=0.6.18->-r docs/requirements.txt (line 9))
Using cached https://files.pythonhosted.org/packages/e5/e6/c3fdc53aed9fa19d6ff3abf97dfad768ae3afce1b7431f7500000816bda5/numpy-1.17.2-cp36-cp36m-manylinux1_x86_64.whl
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 10)) (2.4.2)
Collecting kiwisolver>=1.0.1 (from matplotlib>=2.2->-r docs/requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib>=2.2->-r docs/requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.1 (from matplotlib>=2.2->-r docs/requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from pandas>=0.21->-r docs/requirements.txt (line 11)) (2019.2)
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from h5py->-r docs/requirements.txt (line 14)) (1.12.0)
Collecting numexpr>=2.6.2 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/06/5e/ee657b36ce1b6baabaafe485e97a31e7200f918c4b8643ebc4fd4fd07ada/numexpr-2.7.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/05/d2/f94e68be6b17f46d2c353564da56e6fb89ef09faeeff3313a046cb810ca9/mock-3.0.5-py2.py3-none-any.whl
Collecting decorator>=4.3.0 (from networkx->-r docs/requirements.txt (line 18))
Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting llvmlite>=0.29.0dev0 (from numba->-r docs/requirements.txt (line 21))
Using cached https://files.pythonhosted.org/packages/1f/bf/c9fc3b6d7d46968186ac37a2453639979edd8fa7199bb9f4b820a813e8c8/llvmlite-0.29.0-1-cp36-cp36m-manylinux1_x86_64.whl
Collecting zipp>=0.5 (from importlib_metadata->-r docs/requirements.txt (line 23))
Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1.0)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.8)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2019.9.11)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.25.3)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.1)
Collecting more-itertools (from zipp>=0.5->importlib_metadata->-r docs/requirements.txt (line 23))
Using cached https://files.pythonhosted.org/packages/45/dc/3241eef99eb45f1def35cf93af35d1cf9ef4c0991792583b8f33ea41b092/more_itertools-7.2.0-py3-none-any.whl
Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinxcontrib-serializinghtml, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, numpy, h5py, scipy, python-dateutil, pandas, natsort, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, mock, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, more-itertools, zipp, importlib-metadata, setuptools-scm, umap-learn
Found existing installation: Sphinx 1.8.5
Uninstalling Sphinx-1.8.5:
Successfully uninstalled Sphinx-1.8.5
Found existing installation: mock 1.0.1
Uninstalling mock-1.0.1:
Successfully uninstalled mock-1.0.1
Successfully installed anndata-0.6.22.post1 cycler-0.10.0 decorator-4.4.0 get-version-2.1 h5py-2.10.0 importlib-metadata-0.23 joblib-0.13.2 kiwisolver-1.1.0 llvmlite-0.29.0 matplotlib-3.1.1 mock-3.0.5 more-itertools-7.2.0 natsort-6.0.0 networkx-2.3 numba-0.45.1 numexpr-2.7.0 numpy-1.17.2 pandas-0.25.1 python-dateutil-2.8.0 scanpydoc-0.4.1 scikit-learn-0.21.3 scipy-1.3.1 seaborn-0.9.0 setuptools-scm-3.3.3 sphinx-2.2.0 sphinx-autodoc-typehints-1.8.0 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 tables-3.5.2 tqdm-4.36.0 umap-learn-0.3.10 zipp-0.6.0
[rtd-command-info] start-time: 2019-09-18T13:31:18.186439Z, end-time: 2019-09-18T13:31:18.504117Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import warnings
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.insert(0, str(HERE.parent))
import scanpy # noqa
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=FutureWarning)
import scanpy.api
on_rtd = os.environ.get('READTHEDOCS') == 'True'
# -- General configuration ------------------------------------------------
nitpicky = True # Warn about broken links
needs_sphinx = '2.0' # Nicer param docs
suppress_warnings = ['ref.citation']
# General information
project = 'Scanpy'
author = scanpy.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = scanpy.__version__.replace('.dirty', '')
release = version
# default settings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.intersphinx',
'sphinx.ext.doctest',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.napoleon',
'sphinx.ext.autosummary',
# 'plot_generator',
# 'plot_directive',
'sphinx_autodoc_typehints', # needs to be after napoleon
# 'ipython_directive',
# 'ipython_console_highlighting',
'scanpydoc',
]
# 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
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=('http://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/', None),
networkx=('https://networkx.github.io/documentation/networkx-1.10/', None),
numpy=('https://docs.scipy.org/doc/numpy/', None),
pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
python=('https://docs.python.org/3', None),
scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
scvelo=('https://scvelo.readthedocs.io/en/stable/', None),
seaborn=('https://seaborn.pydata.org/', None),
sklearn=('https://scikit-learn.org/stable/', None),
scanpy_tutorials=(
'https://scanpy-tutorials.readthedocs.io/en/latest',
None,
),
)
# -- Options for HTML output ----------------------------------------------
html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
navigation_depth=4, logo_only=True # Only show the logo
)
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_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(
html_context
)
def setup(app):
app.warningiserror = on_rtd
app.add_stylesheet('css/custom.css')
app.connect('autodoc-process-docstring', insert_function_images)
app.connect('build-finished', show_param_warnings)
app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))
# -- 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',
)
]
# -- Images for plot functions -------------------------------------------------
def insert_function_images(app, what, name, obj, options, lines):
path = Path(__file__).parent / 'api' / f'{name}.png'
if what != 'function' or not path.is_file():
return
lines[0:0] = [
f'.. image:: {path.name}',
' :width: 200',
' :align: right',
'',
]
# -- GitHub links --------------------------------------------------------------
def autolink(url_template, title_template='{}'):
from docutils import nodes
def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
url = url_template.format(text)
title = title_template.format(text)
node = nodes.reference(rawtext, title, refuri=url, **options)
return [node], []
return role
# -- Test for new scanpydoc functionality --------------------------------------
import re
from sphinx.ext.napoleon import NumpyDocstring
def process_return(lines):
for line in lines:
m = re.fullmatch(r'(?P\w+)\s+:\s+(?P[\w.]+)', line)
if m:
# Once this is in scanpydoc, we can use the fancy hover stuff
yield f'**{m["param"]}** : :class:`~{m["type"]}`'
else:
yield line
def scanpy_parse_returns_section(self, section):
lines_raw = list(
process_return(self._dedent(self._consume_to_next_section()))
)
lines = self._format_block(':returns: ', lines_raw)
if lines and lines[-1]:
lines.append('')
return lines
NumpyDocstring._parse_returns_section = scanpy_parse_returns_section
# -- Warn for non-annotated params ---------------------------------------------
_format_docutils_params_orig = NumpyDocstring._format_docutils_params
param_warnings = {}
def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
for _name, _type, _desc in fields:
if not _type:
continue
set_item = r"`'[a-z0-9_.-]+'`"
if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type):
continue
param_warnings.setdefault((self._name, self._obj), []).append(
(_name, _type)
)
return _format_docutils_params_orig(self, fields, field_role, type_role)
def show_param_warnings(app, exception):
import inspect
for (fname, fun), params in param_warnings.items():
_, line = inspect.getsourcelines(fun)
file_name = inspect.getsourcefile(fun)
params_str = '\n'.join(f'\t{n}: {t}' for n, t in params)
warnings.warn_explicit(
f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n'
'Convert to this format or replace with type annotations:\n'
+ params_str,
UserWarning,
file_name,
line,
)
NumpyDocstring._format_docutils_params = scanpy_log_param_types
# -- Debug code ----------------------------------------------------------------
# Just do the following to see the rst of a function:
# rm -f _build/doctrees/api/scanpy..doctree; DEBUG=1 make html
import os
if os.environ.get('DEBUG') is not None:
import sphinx.ext.napoleon
pd = sphinx.ext.napoleon._process_docstring
def pd_new(app, what, name, obj, options, lines):
pd(app, what, name, obj, options, lines)
print(*lines, sep='\n')
sphinx.ext.napoleon._process_docstring = pd_new
# -- Suppress link warnings ----------------------------------------------------
qualname_overrides = {
"sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric"
}
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.readwrite.Empty'),
]
for mod_name in [
'pp',
'tl',
'pl',
'queries',
'logging',
'datasets',
'export_to',
None,
]:
if mod_name is None:
mod = scanpy.api
mod_name = 'scanpy.api'
else:
mod = getattr(scanpy.api, mod_name)
mod_name = f'scanpy.api.{mod_name}'
for name, item in vars(mod).items():
if not callable(item):
continue
for kind in ['func', 'obj']:
nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}'))
###########################################################################
# 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
#
import importlib
import sys
import os.path
from six import string_types
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://media.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://media.readthedocs.com/",
'PRODUCTION_DOMAIN': "readthedocs.com",
'versions': [
("latest", "/en/latest/"),
("stable", "/en/stable/"),
("contributors", "/en/contributors/"),
],
'downloads': [
("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"),
],
'subprojects': [
],
'slug': 'icb-scanpy',
'name': u'scanpy',
'rtd_language': u'en',
'programming_language': u'py',
'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/',
'analytics_code': 'None',
'single_version': False,
'conf_py_path': '/docs/',
'api_host': 'https://readthedocs.com',
'github_user': 'theislab',
'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,
'user_analytics_code': '',
'global_analytics_code': 'UA-17997319-2',
'commit': 'cd694403',
}
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")
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'
[rtd-command-info] start-time: 2019-09-18T13:31:18.597357Z, end-time: 2019-09-18T13:33:06.852839Z, duration: 108, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.0
loading translations [en]... done
making output directory... done
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 http://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/objects.inv...
loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/en/stable/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: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 153 source files that are out of date
updating environment: [new config] 153 added, 0 changed, 0 removed
reading sources... [ 0%] api/index
reading sources... [ 1%] api/plotting
reading sources... [ 1%] api/scanpy.Neighbors
reading sources... [ 2%] api/scanpy.Neighbors.compute_eigen
reading sources... [ 3%] api/scanpy.Neighbors.compute_neighbors
reading sources... [ 3%] api/scanpy.Neighbors.compute_transitions
reading sources... [ 4%] api/scanpy.Neighbors.connectivities
reading sources... [ 5%] api/scanpy.Neighbors.distances
reading sources... [ 5%] api/scanpy.Neighbors.distances_dpt
reading sources... [ 6%] api/scanpy.Neighbors.eigen_basis
reading sources... [ 7%] api/scanpy.Neighbors.eigen_values
reading sources... [ 7%] api/scanpy.Neighbors.getdoc
reading sources... [ 8%] api/scanpy.Neighbors.rp_forest
reading sources... [ 9%] api/scanpy.Neighbors.to_igraph
reading sources... [ 9%] api/scanpy.Neighbors.transitions
reading sources... [ 10%] api/scanpy.Neighbors.transitions_sym
reading sources... [ 11%] api/scanpy._settings.ScanpyConfig
reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 17%] api/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 18%] api/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 18%] api/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 19%] api/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 21%] api/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 22%] api/scanpy.api
reading sources... [ 22%] api/scanpy.datasets.blobs
reading sources... [ 23%] api/scanpy.datasets.ebi_expression_atlas
reading sources... [ 24%] api/scanpy.datasets.krumsiek11
reading sources... [ 24%] api/scanpy.datasets.moignard15
reading sources... [ 25%] api/scanpy.datasets.paul15
reading sources... [ 26%] api/scanpy.datasets.pbmc3k
reading sources... [ 26%] api/scanpy.datasets.pbmc68k_reduced
reading sources... [ 27%] api/scanpy.datasets.toggleswitch
reading sources... [ 28%] api/scanpy.external
reading sources... [ 28%] api/scanpy.get.obs_df
reading sources... [ 29%] api/scanpy.get.rank_genes_groups_df
reading sources... [ 30%] api/scanpy.get.var_df
reading sources... [ 30%] api/scanpy.logging.print_versions
reading sources... [ 31%] api/scanpy.pl.clustermap
reading sources... [ 32%] api/scanpy.pl.diffmap
reading sources... [ 32%] api/scanpy.pl.dotplot
reading sources... [ 33%] api/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 33%] api/scanpy.pl.dpt_timeseries
reading sources... [ 34%] api/scanpy.pl.draw_graph
reading sources... [ 35%] api/scanpy.pl.embedding
reading sources... [ 35%] api/scanpy.pl.embedding_density
reading sources... [ 36%] api/scanpy.pl.filter_genes_dispersion
reading sources... [ 37%] api/scanpy.pl.heatmap
reading sources... [ 37%] api/scanpy.pl.highest_expr_genes
reading sources... [ 38%] api/scanpy.pl.highly_variable_genes
reading sources... [ 39%] api/scanpy.pl.matrixplot
reading sources... [ 39%] api/scanpy.pl.paga
reading sources... [ 40%] api/scanpy.pl.paga_compare
reading sources... [ 41%] api/scanpy.pl.paga_path
reading sources... [ 41%] api/scanpy.pl.pca
reading sources... [ 42%] api/scanpy.pl.pca_loadings
reading sources... [ 43%] api/scanpy.pl.pca_overview
reading sources... [ 43%] api/scanpy.pl.pca_variance_ratio
reading sources... [ 44%] api/scanpy.pl.rank_genes_groups
reading sources... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot
reading sources... [ 45%] api/scanpy.pl.rank_genes_groups_heatmap
reading sources... [ 46%] api/scanpy.pl.rank_genes_groups_matrixplot
reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot
reading sources... [ 48%] api/scanpy.pl.rank_genes_groups_violin
reading sources... [ 49%] api/scanpy.pl.ranking
reading sources... [ 49%] api/scanpy.pl.scatter
reading sources... [ 50%] api/scanpy.pl.sim
reading sources... [ 50%] api/scanpy.pl.stacked_violin
reading sources... [ 51%] api/scanpy.pl.tracksplot
reading sources... [ 52%] api/scanpy.pl.tsne
reading sources... [ 52%] api/scanpy.pl.umap
reading sources... [ 53%] api/scanpy.pl.violin
reading sources... [ 54%] api/scanpy.plotting
reading sources... [ 54%] api/scanpy.pp.calculate_qc_metrics
reading sources... [ 55%] api/scanpy.pp.combat
reading sources... [ 56%] api/scanpy.pp.downsample_counts
reading sources... [ 56%] api/scanpy.pp.filter_cells
reading sources... [ 57%] api/scanpy.pp.filter_genes
reading sources... [ 58%] api/scanpy.pp.filter_genes_dispersion
reading sources... [ 58%] api/scanpy.pp.highly_variable_genes
reading sources... [ 59%] api/scanpy.pp.log1p
reading sources... [ 60%] api/scanpy.pp.neighbors
reading sources... [ 60%] api/scanpy.pp.normalize_per_cell
reading sources... [ 61%] api/scanpy.pp.normalize_total
reading sources... [ 62%] api/scanpy.pp.pca
reading sources... [ 62%] api/scanpy.pp.recipe_seurat
reading sources... [ 63%] api/scanpy.pp.recipe_weinreb17
reading sources... [ 64%] api/scanpy.pp.recipe_zheng17
reading sources... [ 64%] api/scanpy.pp.regress_out
reading sources... [ 65%] api/scanpy.pp.scale
reading sources... [ 66%] api/scanpy.pp.subsample
reading sources... [ 66%] api/scanpy.queries.biomart_annotations
reading sources... [ 67%] api/scanpy.queries.enrich
reading sources... [ 67%] api/scanpy.queries.gene_coordinates
reading sources... [ 68%] api/scanpy.queries.mitochondrial_genes
reading sources... [ 69%] api/scanpy.read
reading sources... [ 69%] api/scanpy.read_10x_h5
reading sources... [ 70%] api/scanpy.read_10x_mtx
reading sources... [ 71%] api/scanpy.read_csv
reading sources... [ 71%] api/scanpy.read_excel
reading sources... [ 72%] api/scanpy.read_h5ad
reading sources... [ 73%] api/scanpy.read_hdf
reading sources... [ 73%] api/scanpy.read_loom
reading sources... [ 74%] api/scanpy.read_mtx
reading sources... [ 75%] api/scanpy.read_text
reading sources... [ 75%] api/scanpy.read_umi_tools
reading sources... [ 76%] api/scanpy.set_figure_params
reading sources... [ 77%] api/scanpy.tl.dendrogram
reading sources... [ 77%] api/scanpy.tl.diffmap
reading sources... [ 78%] api/scanpy.tl.dpt
reading sources... [ 79%] api/scanpy.tl.draw_graph
reading sources... [ 79%] api/scanpy.tl.filter_rank_genes_groups
reading sources... [ 80%] api/scanpy.tl.leiden
reading sources... [ 81%] api/scanpy.tl.louvain
reading sources... [ 81%] api/scanpy.tl.marker_gene_overlap
reading sources... [ 82%] api/scanpy.tl.paga
reading sources... [ 83%] api/scanpy.tl.pca
reading sources... [ 83%] api/scanpy.tl.rank_genes_groups
reading sources... [ 84%] api/scanpy.tl.score_genes
reading sources... [ 84%] api/scanpy.tl.score_genes_cell_cycle
reading sources... [ 85%] api/scanpy.tl.sim
reading sources... [ 86%] api/scanpy.tl.tsne
reading sources... [ 86%] api/scanpy.tl.umap
reading sources... [ 87%] basic_usage
reading sources... [ 88%] examples
reading sources... [ 88%] external/index
reading sources... [ 89%] external/scanpy.external.exporting.cellbrowser
reading sources... [ 90%] external/scanpy.external.exporting.spring_project
reading sources... [ 90%] external/scanpy.external.pl.phate
reading sources... [ 91%] external/scanpy.external.pp.bbknn
reading sources... [ 92%] external/scanpy.external.pp.dca
reading sources... [ 92%] external/scanpy.external.pp.magic
reading sources... [ 93%] external/scanpy.external.pp.mnn_correct
reading sources... [ 94%] external/scanpy.external.tl.cyclone
reading sources... [ 94%] external/scanpy.external.tl.palantir
reading sources... [ 95%] external/scanpy.external.tl.phate
reading sources... [ 96%] external/scanpy.external.tl.phenograph
reading sources... [ 96%] external/scanpy.external.tl.sandbag
reading sources... [ 97%] index
reading sources... [ 98%] installation
reading sources... [ 98%] references
reading sources... [ 99%] release_notes
reading sources... [100%] tutorials
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 0%] api/index
writing output... [ 1%] api/plotting
writing output... [ 1%] api/scanpy.Neighbors
writing output... [ 2%] api/scanpy.Neighbors.compute_eigen
writing output... [ 3%] api/scanpy.Neighbors.compute_neighbors
writing output... [ 3%] api/scanpy.Neighbors.compute_transitions
writing output... [ 4%] api/scanpy.Neighbors.connectivities
writing output... [ 5%] api/scanpy.Neighbors.distances
writing output... [ 5%] api/scanpy.Neighbors.distances_dpt
writing output... [ 6%] api/scanpy.Neighbors.eigen_basis
writing output... [ 7%] api/scanpy.Neighbors.eigen_values
writing output... [ 7%] api/scanpy.Neighbors.getdoc
writing output... [ 8%] api/scanpy.Neighbors.rp_forest
writing output... [ 9%] api/scanpy.Neighbors.to_igraph
writing output... [ 9%] api/scanpy.Neighbors.transitions
writing output... [ 10%] api/scanpy.Neighbors.transitions_sym
writing output... [ 11%] api/scanpy._settings.ScanpyConfig
writing output... [ 11%] api/scanpy._settings.ScanpyConfig.autosave
writing output... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow
writing output... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir
writing output... [ 13%] api/scanpy._settings.ScanpyConfig.categories_to_ignore
writing output... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir
writing output... [ 15%] api/scanpy._settings.ScanpyConfig.figdir
writing output... [ 15%] api/scanpy._settings.ScanpyConfig.file_format_data
writing output... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_figs
writing output... [ 16%] api/scanpy._settings.ScanpyConfig.logfile
writing output... [ 17%] api/scanpy._settings.ScanpyConfig.logpath
writing output... [ 18%] api/scanpy._settings.ScanpyConfig.max_memory
writing output... [ 18%] api/scanpy._settings.ScanpyConfig.n_jobs
writing output... [ 19%] api/scanpy._settings.ScanpyConfig.plot_suffix
writing output... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params
writing output... [ 20%] api/scanpy._settings.ScanpyConfig.verbosity
writing output... [ 21%] api/scanpy._settings.ScanpyConfig.writedir
writing output... [ 22%] api/scanpy.api
writing output... [ 22%] api/scanpy.datasets.blobs
writing output... [ 23%] api/scanpy.datasets.ebi_expression_atlas
writing output... [ 24%] api/scanpy.datasets.krumsiek11
writing output... [ 24%] api/scanpy.datasets.moignard15
writing output... [ 25%] api/scanpy.datasets.paul15
writing output... [ 26%] api/scanpy.datasets.pbmc3k
writing output... [ 26%] api/scanpy.datasets.pbmc68k_reduced
writing output... [ 27%] api/scanpy.datasets.toggleswitch
writing output... [ 28%] api/scanpy.external
writing output... [ 28%] api/scanpy.get.obs_df
writing output... [ 29%] api/scanpy.get.rank_genes_groups_df
writing output... [ 30%] api/scanpy.get.var_df
writing output... [ 30%] api/scanpy.logging.print_versions
writing output... [ 31%] api/scanpy.pl.clustermap
writing output... [ 32%] api/scanpy.pl.diffmap
writing output... [ 32%] api/scanpy.pl.dotplot
writing output... [ 33%] api/scanpy.pl.dpt_groups_pseudotime
writing output... [ 33%] api/scanpy.pl.dpt_timeseries
writing output... [ 34%] api/scanpy.pl.draw_graph
writing output... [ 35%] api/scanpy.pl.embedding
writing output... [ 35%] api/scanpy.pl.embedding_density
writing output... [ 36%] api/scanpy.pl.filter_genes_dispersion
writing output... [ 37%] api/scanpy.pl.heatmap
writing output... [ 37%] api/scanpy.pl.highest_expr_genes
writing output... [ 38%] api/scanpy.pl.highly_variable_genes
writing output... [ 39%] api/scanpy.pl.matrixplot
writing output... [ 39%] api/scanpy.pl.paga
writing output... [ 40%] api/scanpy.pl.paga_compare
writing output... [ 41%] api/scanpy.pl.paga_path
writing output... [ 41%] api/scanpy.pl.pca
writing output... [ 42%] api/scanpy.pl.pca_loadings
writing output... [ 43%] api/scanpy.pl.pca_overview
writing output... [ 43%] api/scanpy.pl.pca_variance_ratio
writing output... [ 44%] api/scanpy.pl.rank_genes_groups
writing output... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 45%] api/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 46%] api/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot
writing output... [ 48%] api/scanpy.pl.rank_genes_groups_violin
writing output... [ 49%] api/scanpy.pl.ranking
writing output... [ 49%] api/scanpy.pl.scatter
writing output... [ 50%] api/scanpy.pl.sim
writing output... [ 50%] api/scanpy.pl.stacked_violin
writing output... [ 51%] api/scanpy.pl.tracksplot
writing output... [ 52%] api/scanpy.pl.tsne
writing output... [ 52%] api/scanpy.pl.umap
writing output... [ 53%] api/scanpy.pl.violin
writing output... [ 54%] api/scanpy.plotting
writing output... [ 54%] api/scanpy.pp.calculate_qc_metrics
writing output... [ 55%] api/scanpy.pp.combat
writing output... [ 56%] api/scanpy.pp.downsample_counts
writing output... [ 56%] api/scanpy.pp.filter_cells
writing output... [ 57%] api/scanpy.pp.filter_genes
writing output... [ 58%] api/scanpy.pp.filter_genes_dispersion
writing output... [ 58%] api/scanpy.pp.highly_variable_genes
writing output... [ 59%] api/scanpy.pp.log1p
writing output... [ 60%] api/scanpy.pp.neighbors
writing output... [ 60%] api/scanpy.pp.normalize_per_cell
writing output... [ 61%] api/scanpy.pp.normalize_total
writing output... [ 62%] api/scanpy.pp.pca
writing output... [ 62%] api/scanpy.pp.recipe_seurat
writing output... [ 63%] api/scanpy.pp.recipe_weinreb17
writing output... [ 64%] api/scanpy.pp.recipe_zheng17
writing output... [ 64%] api/scanpy.pp.regress_out
writing output... [ 65%] api/scanpy.pp.scale
writing output... [ 66%] api/scanpy.pp.subsample
writing output... [ 66%] api/scanpy.queries.biomart_annotations
writing output... [ 67%] api/scanpy.queries.enrich
writing output... [ 67%] api/scanpy.queries.gene_coordinates
writing output... [ 68%] api/scanpy.queries.mitochondrial_genes
writing output... [ 69%] api/scanpy.read
writing output... [ 69%] api/scanpy.read_10x_h5
writing output... [ 70%] api/scanpy.read_10x_mtx
writing output... [ 71%] api/scanpy.read_csv
writing output... [ 71%] api/scanpy.read_excel
writing output... [ 72%] api/scanpy.read_h5ad
writing output... [ 73%] api/scanpy.read_hdf
writing output... [ 73%] api/scanpy.read_loom
writing output... [ 74%] api/scanpy.read_mtx
writing output... [ 75%] api/scanpy.read_text
writing output... [ 75%] api/scanpy.read_umi_tools
writing output... [ 76%] api/scanpy.set_figure_params
writing output... [ 77%] api/scanpy.tl.dendrogram
writing output... [ 77%] api/scanpy.tl.diffmap
writing output... [ 78%] api/scanpy.tl.dpt
writing output... [ 79%] api/scanpy.tl.draw_graph
writing output... [ 79%] api/scanpy.tl.filter_rank_genes_groups
writing output... [ 80%] api/scanpy.tl.leiden
writing output... [ 81%] api/scanpy.tl.louvain
writing output... [ 81%] api/scanpy.tl.marker_gene_overlap
writing output... [ 82%] api/scanpy.tl.paga
writing output... [ 83%] api/scanpy.tl.pca
writing output... [ 83%] api/scanpy.tl.rank_genes_groups
writing output... [ 84%] api/scanpy.tl.score_genes
writing output... [ 84%] api/scanpy.tl.score_genes_cell_cycle
writing output... [ 85%] api/scanpy.tl.sim
writing output... [ 86%] api/scanpy.tl.tsne
writing output... [ 86%] api/scanpy.tl.umap
writing output... [ 87%] basic_usage
writing output... [ 88%] examples
writing output... [ 88%] external/index
writing output... [ 89%] external/scanpy.external.exporting.cellbrowser
writing output... [ 90%] external/scanpy.external.exporting.spring_project
writing output... [ 90%] external/scanpy.external.pl.phate
writing output... [ 91%] external/scanpy.external.pp.bbknn
writing output... [ 92%] external/scanpy.external.pp.dca
writing output... [ 92%] external/scanpy.external.pp.magic
writing output... [ 93%] external/scanpy.external.pp.mnn_correct
writing output... [ 94%] external/scanpy.external.tl.cyclone
writing output... [ 94%] external/scanpy.external.tl.palantir
writing output... [ 95%] external/scanpy.external.tl.phate
writing output... [ 96%] external/scanpy.external.tl.phenograph
writing output... [ 96%] external/scanpy.external.tl.sandbag
writing output... [ 97%] index
writing output... [ 98%] installation
writing output... [ 98%] references
writing output... [ 99%] release_notes
writing output... [100%] tutorials
generating indices... genindex py-modindexdone
writing additional pages... searchdone
copying images... [ 11%] api/scanpy.pl.dotplot.png
copying images... [ 22%] api/scanpy.pl.heatmap.png
copying images... [ 33%] api/scanpy.pl.matrixplot.png
copying images... [ 44%] api/scanpy.pl.rank_genes_groups_dotplot.png
copying images... [ 55%] api/scanpy.pl.rank_genes_groups_heatmap.png
copying images... [ 66%] api/scanpy.pl.rank_genes_groups_matrixplot.png
copying images... [ 77%] api/scanpy.pl.rank_genes_groups_stacked_violin.png
copying images... [ 88%] api/scanpy.pl.stacked_violin.png
copying images... [100%] api/scanpy.pl.violin.png
copying static files... ... done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.
The HTML pages are in _build/html.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors
warnings.warn('"%s" is shallow and may cause errors' % (wd.path,))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a