Read the Docs build information
Build id: 204820
Project: icb-scanpy
Version: latest
Commit: 9e4e5ee02e04cf618872d9b098e24f0542e8b227
Date: 2019-04-30T01:37:53.462901Z
State: finished
Success: True
[rtd-command-info] start-time: 2019-04-30T01:37:53.989963Z, end-time: 2019-04-30T01:37:53.998988Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
[rtd-command-info] start-time: 2019-04-30T01:37:54.059320Z, end-time: 2019-04-30T01:37:54.481999Z, duration: 0, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
0712168..9e4e5ee master -> origin/master
+ bddf170...bdbc3d3 umap_deps -> origin/umap_deps (forced update)
[rtd-command-info] start-time: 2019-04-30T01:37:54.700758Z, end-time: 2019-04-30T01:37:54.714459Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 0712168 Merge pull request #621 from ivirshup/de_quick_fix
HEAD is now at 9e4e5ee Merge pull request #576 from theislab/umap_deps
[rtd-command-info] start-time: 2019-04-30T01:37:54.788214Z, end-time: 2019-04-30T01:37:54.797286Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-04-30T01:37:55.516946Z, end-time: 2019-04-30T01:37:58.773617Z, 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: 2019-04-30T01:37:58.845040Z, end-time: 2019-04-30T01:38:01.564075Z, 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/f9/fb/863012b13912709c13cf5cfdbfb304fa6c727659d6290438e1a88df9d848/pip-19.1-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-19.1
[rtd-command-info] start-time: 2019-04-30T01:38:01.663592Z, end-time: 2019-04-30T01:38:11.526735Z, duration: 9, 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 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<0.6
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
Using cached https://files.pythonhosted.org/packages/44/56/75e64a8fbbe9e0bd30cfdd58ca1856bc0dc15a43e41504a58d8373f34213/setuptools-40.9.0-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<0.6
Using cached https://files.pythonhosted.org/packages/d1/f3/68de6af559ae681921a7b676a86c360454de67f3c8bd5327ae9352897ef4/readthedocs_sphinx_ext-0.5.17-py2.py3-none-any.whl
Collecting future (from commonmark==0.8.1)
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 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 imagesize (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/52/69/3c2fbdc3702358c5b34ee25e387b24838597ef099761fc9a42c166796e8f/sphinxcontrib_websupport-1.1.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl
Collecting packaging (from sphinx<2)
Using cached https://files.pythonhosted.org/packages/91/32/58bc30e646e55eab8b21abf89e353f59c0cc02c417e42929f4a9546e1b1d/packaging-19.0-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 urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<2)
Using cached https://files.pythonhosted.org/packages/df/1c/59cca3abf96f991f2ec3131a4ffe72ae3d9ea1f5894abe8a9c5e3c77cfee/urllib3-1.24.2-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/60/75/f692a584e85b7eaba0e03827b3d51f45f571c2e793dd731e598828d380aa/certifi-2019.3.9-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
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<2)
Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<2)
Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, six, imagesize, snowballstemmer, sphinxcontrib-websupport, urllib3, idna, certifi, chardet, requests, pytz, babel, pyparsing, packaging, 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 babel-2.6.0 certifi-2019.3.9 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-19.0 pillow-5.4.1 pyparsing-2.4.0 pytz-2019.1 readthedocs-sphinx-ext-0.5.17 recommonmark-0.5.0 requests-2.21.0 setuptools-40.9.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.0 urllib3-1.24.2
[rtd-command-info] start-time: 2019-04-30T01:38:11.587225Z, end-time: 2019-04-30T01:38:40.806287Z, duration: 29, 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/9a/b0/a8cf1d35237aebefd63f05543ed49ea24d302239828ca89409b0c1a35b27/Sphinx-2.0.1-py2.py3-none-any.whl
Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 6))
Using cached https://files.pythonhosted.org/packages/de/57/e90dba6e31db7b5c4cc9eaab69a56f2c93a498febd188d35c8216da18b6f/sphinx_autodoc_typehints-1.6.0-py3-none-any.whl
Collecting scanpydoc>=0.3.2 (from -r docs/requirements.txt (line 7))
Using cached https://files.pythonhosted.org/packages/50/65/8472fc898d98291aec6f72bff82e872eb42437cd53ad371c2aae3d87a575/scanpydoc-0.3.3-py3-none-any.whl
Collecting anndata>=0.6.18 (from -r docs/requirements.txt (line 9))
Collecting matplotlib>=2.2 (from -r docs/requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/e9/69/f5e05f578585ed9935247be3788b374f90701296a70c8871bcd6d21edb00/matplotlib-3.0.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting pandas>=0.21 (from -r docs/requirements.txt (line 11))
Using cached https://files.pythonhosted.org/packages/19/74/e50234bc82c553fecdbd566d8650801e3fe2d6d8c8d940638e3d8a7c5522/pandas-0.24.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy (from -r docs/requirements.txt (line 12))
Using cached https://files.pythonhosted.org/packages/7f/5f/c48860704092933bf1c4c1574a8de1ffd16bf4fde8bab190d747598844b2/scipy-1.2.1-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/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting tables (from -r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/ab/79/4e1301a87f3b7f27aa6c9cb1aeba4875ff3edb62a6fe3872dc8f04983db4/tables-3.5.1-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/5e/82/c0de5839d613b82bddd088599ac0bbfbbbcbd8ca470680658352d2c435bd/scikit_learn-0.20.3-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/8d/c6/b28f5cada2aca31018a8bb210065f9b6a3174d25a80a9961c7bd3e831c3e/numba-0.43.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting tqdm (from -r docs/requirements.txt (line 22))
Using cached https://files.pythonhosted.org/packages/6c/4b/c38b5144cf167c4f52288517436ccafefe9dc01b8d1c190e18a6b154cd4a/tqdm-4.31.1-py2.py3-none-any.whl
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)) (19.0)
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)) (2.6.0)
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
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: 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)) (2.21.0)
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)) (40.9.0)
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)
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)) (1.2.1)
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-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
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
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: 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)
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 get_version (from scanpydoc>=0.3.2->-r docs/requirements.txt (line 7))
Using cached https://files.pythonhosted.org/packages/2d/27/610ef458455cb1bcc4b454cebab43de3579e43d080af872727b9ac3146c8/get_version-2.0.6-py3-none-any.whl
Collecting future-fstrings (from scanpydoc>=0.3.2->-r docs/requirements.txt (line 7))
Using cached https://files.pythonhosted.org/packages/d5/10/de62670513b7b2e7de32bbabb662cbc05ccee49fadf6f69725388df780e8/future_fstrings-1.0.0-py2.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/c1/e2/4db8df8f6cddc98e7d7c537245ef2f4e41a1ed17bf0c3177ab3cc6beac7f/numpy-1.16.3-cp36-cp36m-manylinux1_x86_64.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
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
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)) (2.4.0)
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
Requirement already satisfied: pytz>=2011k 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)) (2019.1)
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 mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl
Collecting numexpr>=2.6.2 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/0e/13/d38d56c4c49e50b35b6912c80d89f856d50aff605c9e3a4dbba91fc3df44/numexpr-2.6.9-cp36-cp36m-manylinux1_x86_64.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>=0.28.0dev0 (from numba->-r docs/requirements.txt (line 21))
Using cached https://files.pythonhosted.org/packages/b5/f3/6d7f49db45df0276166f99723aa10310862a3783556cd284793da478afed/llvmlite-0.28.0-1-cp36-cp36m-manylinux1_x86_64.whl
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)) (2019.3.9)
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: urllib3<1.25,>=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)) (1.24.2)
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: 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 pbr>=0.11 (from mock>=2.0->tables->-r docs/requirements.txt (line 15))
Downloading https://files.pythonhosted.org/packages/07/3e/22d1d35a4b51706ca3590c54359aeb5fa7ea60df46180143a3ea13d45f29/pbr-5.2.0-py2.py3-none-any.whl (107kB)
Installing collected packages: sphinxcontrib-serializinghtml, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, python-dateutil, pandas, natsort, h5py, scipy, anndata, kiwisolver, cycler, matplotlib, seaborn, pbr, mock, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba, tqdm
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-0.6.19 cycler-0.10.0 decorator-4.4.0 future-fstrings-1.0.0 get-version-2.0.6 h5py-2.9.0 joblib-0.13.2 kiwisolver-1.1.0 llvmlite-0.28.0 matplotlib-3.0.3 mock-2.0.0 natsort-6.0.0 networkx-2.3 numba-0.43.1 numexpr-2.6.9 numpy-1.16.3 pandas-0.24.2 pbr-5.2.0 python-dateutil-2.8.0 scanpydoc-0.3.3 scikit-learn-0.20.3 scipy-1.2.1 seaborn-0.9.0 sphinx-2.0.1 sphinx-autodoc-typehints-1.6.0 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-3.5.1 tqdm-4.31.1
[rtd-command-info] start-time: 2019-04-30T01:38:41.327447Z, end-time: 2019-04-30T01:38:41.390681Z, duration: 0, exit-code: 0
cat docs/conf.py
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.insert(0, str(HERE.parent))
import scanpy # noqa
# -- General configuration ------------------------------------------------
needs_sphinx = '1.7' # autosummary bugfix
# 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/latest/', None),
bbknn=('https://bbknn.readthedocs.io/en/latest/', 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=('http://pandas.pydata.org/pandas-docs/stable/', None),
python=('https://docs.python.org/3', None),
scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
sklearn=('https://scikit-learn.org/stable/', 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_logo = '_static/img/Scanpy_Logo_RGB.png'
def setup(app):
app.add_stylesheet('css/custom.css')
app.connect('autodoc-process-docstring', insert_function_images)
# -- 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', '']
# -- 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
# -- 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
###########################################################################
# 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 mulitple 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/"),
],
'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': '9e4e5ee0',
}
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"]
[rtd-command-info] start-time: 2019-04-30T01:38:41.507785Z, end-time: 2019-04-30T01:39:40.846056Z, duration: 59, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.0.1
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/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 http://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://scikit-learn.org/stable/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, ..., api/scanpy.tl.sim.rst, api/scanpy.tl.tsne.rst, api/scanpy.tl.umap.rst, basic_usage.rst, examples.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 215 source files that are out of date
updating environment: 215 added, 0 changed, 0 removed
reading sources... [ 0%] api/index
reading sources... [ 0%] api/plotting
reading sources... [ 1%] api/scanpy.Neighbors
reading sources... [ 1%] api/scanpy.Neighbors.compute_eigen
reading sources... [ 2%] api/scanpy.Neighbors.compute_neighbors
reading sources... [ 2%] api/scanpy.Neighbors.compute_transitions
reading sources... [ 3%] api/scanpy.Neighbors.connectivities
reading sources... [ 3%] api/scanpy.Neighbors.distances
reading sources... [ 4%] api/scanpy.Neighbors.distances_dpt
reading sources... [ 4%] api/scanpy.Neighbors.eigen_basis
reading sources... [ 5%] api/scanpy.Neighbors.eigen_values
reading sources... [ 5%] api/scanpy.Neighbors.getdoc
reading sources... [ 6%] api/scanpy.Neighbors.laplacian
reading sources... [ 6%] api/scanpy.Neighbors.to_igraph
reading sources... [ 6%] api/scanpy.Neighbors.transitions
reading sources... [ 7%] api/scanpy.Neighbors.transitions_sym
reading sources... [ 7%] api/scanpy._settings.ScanpyConfig
reading sources... [ 8%] api/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 8%] api/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 9%] api/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 9%] api/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 10%] api/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 10%] api/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.getdoc
reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 15%] api/scanpy.api
reading sources... [ 16%] api/scanpy.api.Neighbors
reading sources... [ 16%] api/scanpy.api.Neighbors.compute_eigen
reading sources... [ 17%] api/scanpy.api.Neighbors.compute_neighbors
reading sources... [ 17%] api/scanpy.api.Neighbors.compute_transitions
reading sources... [ 18%] api/scanpy.api.Neighbors.connectivities
reading sources... [ 18%] api/scanpy.api.Neighbors.distances
reading sources... [ 19%] api/scanpy.api.Neighbors.distances_dpt
reading sources... [ 19%] api/scanpy.api.Neighbors.eigen_basis
reading sources... [ 20%] api/scanpy.api.Neighbors.eigen_values
reading sources... [ 20%] api/scanpy.api.Neighbors.getdoc
reading sources... [ 20%] api/scanpy.api.Neighbors.laplacian
reading sources... [ 21%] api/scanpy.api.Neighbors.to_igraph
reading sources... [ 21%] api/scanpy.api.Neighbors.transitions
reading sources... [ 22%] api/scanpy.api.Neighbors.transitions_sym
reading sources... [ 22%] api/scanpy.api.datasets.blobs
reading sources... [ 23%] api/scanpy.api.datasets.krumsiek11
reading sources... [ 23%] api/scanpy.api.datasets.moignard15
reading sources... [ 24%] api/scanpy.api.datasets.paul15
reading sources... [ 24%] api/scanpy.api.datasets.pbmc3k
reading sources... [ 25%] api/scanpy.api.datasets.pbmc68k_reduced
reading sources... [ 25%] api/scanpy.api.datasets.toggleswitch
reading sources... [ 26%] api/scanpy.api.export_to.spring_project
reading sources... [ 26%] api/scanpy.api.logging.print_versions
reading sources... [ 26%] api/scanpy.api.pp.bbknn
reading sources... [ 27%] api/scanpy.api.pp.calculate_qc_metrics
reading sources... [ 27%] api/scanpy.api.pp.dca
reading sources... [ 28%] api/scanpy.api.pp.downsample_counts
reading sources... [ 28%] api/scanpy.api.pp.filter_cells
reading sources... [ 29%] api/scanpy.api.pp.filter_genes
reading sources... [ 29%] api/scanpy.api.pp.filter_genes_dispersion
reading sources... [ 30%] api/scanpy.api.pp.highly_variable_genes
reading sources... [ 30%] api/scanpy.api.pp.log1p
reading sources... [ 31%] api/scanpy.api.pp.magic
reading sources... [ 31%] api/scanpy.api.pp.mnn_correct
reading sources... [ 32%] api/scanpy.api.pp.neighbors
reading sources... [ 32%] api/scanpy.api.pp.normalize_per_cell
reading sources... [ 33%] api/scanpy.api.pp.pca
reading sources... [ 33%] api/scanpy.api.pp.recipe_seurat
reading sources... [ 33%] api/scanpy.api.pp.recipe_weinreb17
reading sources... [ 34%] api/scanpy.api.pp.recipe_zheng17
reading sources... [ 34%] api/scanpy.api.pp.regress_out
reading sources... [ 35%] api/scanpy.api.pp.scale
reading sources... [ 35%] api/scanpy.api.pp.subsample
reading sources... [ 36%] api/scanpy.api.queries.mitochondrial_genes
reading sources... [ 36%] api/scanpy.api.read
reading sources... [ 37%] api/scanpy.api.read_10x_h5
reading sources... [ 37%] api/scanpy.api.read_10x_mtx
reading sources... [ 38%] api/scanpy.api.read_csv
reading sources... [ 38%] api/scanpy.api.read_excel
reading sources... [ 39%] api/scanpy.api.read_h5ad
reading sources... [ 39%] api/scanpy.api.read_hdf
reading sources... [ 40%] api/scanpy.api.read_loom
reading sources... [ 40%] api/scanpy.api.read_mtx
reading sources... [ 40%] api/scanpy.api.read_text
reading sources... [ 41%] api/scanpy.api.read_umi_tools
reading sources... [ 41%] api/scanpy.api.set_figure_params
reading sources... [ 42%] api/scanpy.api.tl.cyclone
reading sources... [ 42%] api/scanpy.api.tl.diffmap
reading sources... [ 43%] api/scanpy.api.tl.dpt
reading sources... [ 43%] api/scanpy.api.tl.draw_graph
reading sources... [ 44%] api/scanpy.api.tl.leiden
reading sources... [ 44%] api/scanpy.api.tl.louvain
reading sources... [ 45%] api/scanpy.api.tl.paga
reading sources... [ 45%] api/scanpy.api.tl.pca
reading sources... [ 46%] api/scanpy.api.tl.phate
reading sources... [ 46%] api/scanpy.api.tl.rank_genes_groups
reading sources... [ 46%] api/scanpy.api.tl.sandbag
reading sources... [ 47%] api/scanpy.api.tl.score_genes
reading sources... [ 47%] api/scanpy.api.tl.score_genes_cell_cycle
reading sources... [ 48%] api/scanpy.api.tl.sim
reading sources... [ 48%] api/scanpy.api.tl.tsne
reading sources... [ 49%] api/scanpy.api.tl.umap
reading sources... [ 49%] api/scanpy.datasets.blobs
reading sources... [ 50%] api/scanpy.datasets.ebi_expression_atlas
reading sources... [ 50%] api/scanpy.datasets.krumsiek11
reading sources... [ 51%] api/scanpy.datasets.moignard15
reading sources... [ 51%] api/scanpy.datasets.paul15
reading sources... [ 52%] api/scanpy.datasets.pbmc3k
reading sources... [ 52%] api/scanpy.datasets.pbmc68k_reduced
reading sources... [ 53%] api/scanpy.datasets.toggleswitch
reading sources... [ 53%] api/scanpy.external
reading sources... [ 53%] api/scanpy.external.exporting.cellbrowser
reading sources... [ 54%] api/scanpy.external.exporting.spring_project
reading sources... [ 54%] api/scanpy.external.pl.phate
reading sources... [ 55%] api/scanpy.external.pp.bbknn
reading sources... [ 55%] api/scanpy.external.pp.dca
reading sources... [ 56%] api/scanpy.external.pp.magic
reading sources... [ 56%] api/scanpy.external.pp.mnn_correct
reading sources... [ 57%] api/scanpy.external.tl.cyclone
reading sources... [ 57%] api/scanpy.external.tl.palantir
reading sources... [ 58%] api/scanpy.external.tl.phate
reading sources... [ 58%] api/scanpy.external.tl.phenograph
reading sources... [ 59%] api/scanpy.external.tl.sandbag
reading sources... [ 59%] api/scanpy.logging.print_versions
reading sources... [ 60%] api/scanpy.pl.clustermap
reading sources... [ 60%] api/scanpy.pl.diffmap
reading sources... [ 60%] api/scanpy.pl.dotplot
reading sources... [ 61%] api/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 61%] api/scanpy.pl.dpt_timeseries
reading sources... [ 62%] api/scanpy.pl.draw_graph
reading sources... [ 62%] api/scanpy.pl.embedding_density
reading sources... [ 63%] api/scanpy.pl.filter_genes_dispersion
reading sources... [ 63%] api/scanpy.pl.heatmap
reading sources... [ 64%] api/scanpy.pl.highest_expr_genes
reading sources... [ 64%] api/scanpy.pl.highly_variable_genes
reading sources... [ 65%] api/scanpy.pl.matrixplot
reading sources... [ 65%] api/scanpy.pl.paga
reading sources... [ 66%] api/scanpy.pl.paga_compare
reading sources... [ 66%] api/scanpy.pl.paga_path
reading sources... [ 66%] api/scanpy.pl.pca
reading sources... [ 67%] api/scanpy.pl.pca_loadings
reading sources... [ 67%] api/scanpy.pl.pca_overview
reading sources... [ 68%] api/scanpy.pl.pca_variance_ratio
reading sources... [ 68%] api/scanpy.pl.rank_genes_groups
reading sources... [ 69%] api/scanpy.pl.rank_genes_groups_dotplot
reading sources... [ 69%] api/scanpy.pl.rank_genes_groups_heatmap
reading sources... [ 70%] api/scanpy.pl.rank_genes_groups_matrixplot
reading sources... [ 70%] api/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 71%] api/scanpy.pl.rank_genes_groups_violin
reading sources... [ 71%] api/scanpy.pl.ranking
reading sources... [ 72%] api/scanpy.pl.scatter
reading sources... [ 72%] api/scanpy.pl.sim
reading sources... [ 73%] api/scanpy.pl.stacked_violin
reading sources... [ 73%] api/scanpy.pl.tsne
reading sources... [ 73%] api/scanpy.pl.umap
reading sources... [ 74%] api/scanpy.pl.violin
reading sources... [ 74%] api/scanpy.plotting
reading sources... [ 75%] api/scanpy.pp.calculate_qc_metrics
reading sources... [ 75%] api/scanpy.pp.combat
reading sources... [ 76%] api/scanpy.pp.downsample_counts
reading sources... [ 76%] api/scanpy.pp.filter_cells
reading sources... [ 77%] api/scanpy.pp.filter_genes
reading sources... [ 77%] api/scanpy.pp.filter_genes_dispersion
reading sources... [ 78%] api/scanpy.pp.highly_variable_genes
reading sources... [ 78%] api/scanpy.pp.log1p
reading sources... [ 79%] api/scanpy.pp.neighbors
reading sources... [ 79%] api/scanpy.pp.normalize_per_cell
reading sources... [ 80%] api/scanpy.pp.normalize_total
reading sources... [ 80%] api/scanpy.pp.pca
reading sources... [ 80%] api/scanpy.pp.recipe_seurat
reading sources... [ 81%] api/scanpy.pp.recipe_weinreb17
reading sources... [ 81%] api/scanpy.pp.recipe_zheng17
reading sources... [ 82%] api/scanpy.pp.regress_out
reading sources... [ 82%] api/scanpy.pp.scale
reading sources... [ 83%] api/scanpy.pp.subsample
reading sources... [ 83%] api/scanpy.queries.mitochondrial_genes
reading sources... [ 84%] api/scanpy.read
reading sources... [ 84%] api/scanpy.read_10x_h5
reading sources... [ 85%] api/scanpy.read_10x_mtx
reading sources... [ 85%] api/scanpy.read_csv
reading sources... [ 86%] api/scanpy.read_excel
reading sources... [ 86%] api/scanpy.read_h5ad
reading sources... [ 86%] api/scanpy.read_hdf
reading sources... [ 87%] api/scanpy.read_loom
reading sources... [ 87%] api/scanpy.read_mtx
reading sources... [ 88%] api/scanpy.read_text
reading sources... [ 88%] api/scanpy.read_umi_tools
reading sources... [ 89%] api/scanpy.set_figure_params
reading sources... [ 89%] api/scanpy.tl.dendrogram
reading sources... [ 90%] api/scanpy.tl.diffmap
reading sources... [ 90%] api/scanpy.tl.dpt
reading sources... [ 91%] api/scanpy.tl.draw_graph
reading sources... [ 91%] api/scanpy.tl.filter_rank_genes_groups
reading sources... [ 92%] api/scanpy.tl.leiden
reading sources... [ 92%] api/scanpy.tl.louvain
reading sources... [ 93%] api/scanpy.tl.marker_gene_overlap
reading sources... [ 93%] api/scanpy.tl.paga
reading sources... [ 93%] api/scanpy.tl.pca
reading sources... [ 94%] api/scanpy.tl.rank_genes_groups
reading sources... [ 94%] api/scanpy.tl.score_genes
reading sources... [ 95%] api/scanpy.tl.score_genes_cell_cycle
reading sources... [ 95%] api/scanpy.tl.sim
reading sources... [ 96%] api/scanpy.tl.tsne
reading sources... [ 96%] api/scanpy.tl.umap
reading sources... [ 97%] basic_usage
reading sources... [ 97%] examples
reading sources... [ 98%] index
reading sources... [ 98%] installation
reading sources... [ 99%] references
reading sources... [ 99%] release_notes
reading sources... [100%] tutorials
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:210: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:114: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:10: WARNING: Unexpected section title.
Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:33: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:40: WARNING: Unexpected section title.
Examples
--------
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:45: WARNING: Citation [Fruchterman91] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:49: WARNING: Citation [Hagberg08] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:53: WARNING: Citation [Hastie09] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:70: WARNING: Citation [Huber15] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:90: WARNING: Citation [Krumsiek10] is not referenced.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:138: WARNING: Citation [Murphy12] is not referenced.
done
preparing documents... done
writing output... [ 0%] api/index
writing output... [ 0%] api/plotting
writing output... [ 1%] api/scanpy.Neighbors
writing output... [ 1%] api/scanpy.Neighbors.compute_eigen
writing output... [ 2%] api/scanpy.Neighbors.compute_neighbors
writing output... [ 2%] api/scanpy.Neighbors.compute_transitions
writing output... [ 3%] api/scanpy.Neighbors.connectivities
writing output... [ 3%] api/scanpy.Neighbors.distances
writing output... [ 4%] api/scanpy.Neighbors.distances_dpt
writing output... [ 4%] api/scanpy.Neighbors.eigen_basis
writing output... [ 5%] api/scanpy.Neighbors.eigen_values
writing output... [ 5%] api/scanpy.Neighbors.getdoc
writing output... [ 6%] api/scanpy.Neighbors.laplacian
writing output... [ 6%] api/scanpy.Neighbors.to_igraph
writing output... [ 6%] api/scanpy.Neighbors.transitions
writing output... [ 7%] api/scanpy.Neighbors.transitions_sym
writing output... [ 7%] api/scanpy._settings.ScanpyConfig
writing output... [ 8%] api/scanpy._settings.ScanpyConfig.autosave
writing output... [ 8%] api/scanpy._settings.ScanpyConfig.autoshow
writing output... [ 9%] api/scanpy._settings.ScanpyConfig.cachedir
writing output... [ 9%] api/scanpy._settings.ScanpyConfig.categories_to_ignore
writing output... [ 10%] api/scanpy._settings.ScanpyConfig.datasetdir
writing output... [ 10%] api/scanpy._settings.ScanpyConfig.figdir
writing output... [ 11%] api/scanpy._settings.ScanpyConfig.file_format_data
writing output... [ 11%] api/scanpy._settings.ScanpyConfig.file_format_figs
writing output... [ 12%] api/scanpy._settings.ScanpyConfig.getdoc
writing output... [ 12%] api/scanpy._settings.ScanpyConfig.logfile
writing output... [ 13%] api/scanpy._settings.ScanpyConfig.max_memory
writing output... [ 13%] api/scanpy._settings.ScanpyConfig.n_jobs
writing output... [ 13%] api/scanpy._settings.ScanpyConfig.plot_suffix
writing output... [ 14%] api/scanpy._settings.ScanpyConfig.set_figure_params
writing output... [ 14%] api/scanpy._settings.ScanpyConfig.verbosity
writing output... [ 15%] api/scanpy._settings.ScanpyConfig.writedir
writing output... [ 15%] api/scanpy.api
writing output... [ 16%] api/scanpy.api.Neighbors
writing output... [ 16%] api/scanpy.api.Neighbors.compute_eigen
writing output... [ 17%] api/scanpy.api.Neighbors.compute_neighbors
writing output... [ 17%] api/scanpy.api.Neighbors.compute_transitions
writing output... [ 18%] api/scanpy.api.Neighbors.connectivities
writing output... [ 18%] api/scanpy.api.Neighbors.distances
writing output... [ 19%] api/scanpy.api.Neighbors.distances_dpt
writing output... [ 19%] api/scanpy.api.Neighbors.eigen_basis
writing output... [ 20%] api/scanpy.api.Neighbors.eigen_values
writing output... [ 20%] api/scanpy.api.Neighbors.getdoc
writing output... [ 20%] api/scanpy.api.Neighbors.laplacian
writing output... [ 21%] api/scanpy.api.Neighbors.to_igraph
writing output... [ 21%] api/scanpy.api.Neighbors.transitions
writing output... [ 22%] api/scanpy.api.Neighbors.transitions_sym
writing output... [ 22%] api/scanpy.api.datasets.blobs
writing output... [ 23%] api/scanpy.api.datasets.krumsiek11
writing output... [ 23%] api/scanpy.api.datasets.moignard15
writing output... [ 24%] api/scanpy.api.datasets.paul15
writing output... [ 24%] api/scanpy.api.datasets.pbmc3k
writing output... [ 25%] api/scanpy.api.datasets.pbmc68k_reduced
writing output... [ 25%] api/scanpy.api.datasets.toggleswitch
writing output... [ 26%] api/scanpy.api.export_to.spring_project
writing output... [ 26%] api/scanpy.api.logging.print_versions
writing output... [ 26%] api/scanpy.api.pp.bbknn
writing output... [ 27%] api/scanpy.api.pp.calculate_qc_metrics
writing output... [ 27%] api/scanpy.api.pp.dca
writing output... [ 28%] api/scanpy.api.pp.downsample_counts
writing output... [ 28%] api/scanpy.api.pp.filter_cells
writing output... [ 29%] api/scanpy.api.pp.filter_genes
writing output... [ 29%] api/scanpy.api.pp.filter_genes_dispersion
writing output... [ 30%] api/scanpy.api.pp.highly_variable_genes
writing output... [ 30%] api/scanpy.api.pp.log1p
writing output... [ 31%] api/scanpy.api.pp.magic
writing output... [ 31%] api/scanpy.api.pp.mnn_correct
writing output... [ 32%] api/scanpy.api.pp.neighbors
writing output... [ 32%] api/scanpy.api.pp.normalize_per_cell
writing output... [ 33%] api/scanpy.api.pp.pca
writing output... [ 33%] api/scanpy.api.pp.recipe_seurat
writing output... [ 33%] api/scanpy.api.pp.recipe_weinreb17
writing output... [ 34%] api/scanpy.api.pp.recipe_zheng17
writing output... [ 34%] api/scanpy.api.pp.regress_out
writing output... [ 35%] api/scanpy.api.pp.scale
writing output... [ 35%] api/scanpy.api.pp.subsample
writing output... [ 36%] api/scanpy.api.queries.mitochondrial_genes
writing output... [ 36%] api/scanpy.api.read
writing output... [ 37%] api/scanpy.api.read_10x_h5
writing output... [ 37%] api/scanpy.api.read_10x_mtx
writing output... [ 38%] api/scanpy.api.read_csv
writing output... [ 38%] api/scanpy.api.read_excel
writing output... [ 39%] api/scanpy.api.read_h5ad
writing output... [ 39%] api/scanpy.api.read_hdf
writing output... [ 40%] api/scanpy.api.read_loom
writing output... [ 40%] api/scanpy.api.read_mtx
writing output... [ 40%] api/scanpy.api.read_text
writing output... [ 41%] api/scanpy.api.read_umi_tools
writing output... [ 41%] api/scanpy.api.set_figure_params
writing output... [ 42%] api/scanpy.api.tl.cyclone
writing output... [ 42%] api/scanpy.api.tl.diffmap
writing output... [ 43%] api/scanpy.api.tl.dpt
writing output... [ 43%] api/scanpy.api.tl.draw_graph
writing output... [ 44%] api/scanpy.api.tl.leiden
writing output... [ 44%] api/scanpy.api.tl.louvain
writing output... [ 45%] api/scanpy.api.tl.paga
writing output... [ 45%] api/scanpy.api.tl.pca
writing output... [ 46%] api/scanpy.api.tl.phate
writing output... [ 46%] api/scanpy.api.tl.rank_genes_groups
writing output... [ 46%] api/scanpy.api.tl.sandbag
writing output... [ 47%] api/scanpy.api.tl.score_genes
writing output... [ 47%] api/scanpy.api.tl.score_genes_cell_cycle
writing output... [ 48%] api/scanpy.api.tl.sim
writing output... [ 48%] api/scanpy.api.tl.tsne
writing output... [ 49%] api/scanpy.api.tl.umap
writing output... [ 49%] api/scanpy.datasets.blobs
writing output... [ 50%] api/scanpy.datasets.ebi_expression_atlas
writing output... [ 50%] api/scanpy.datasets.krumsiek11
writing output... [ 51%] api/scanpy.datasets.moignard15
writing output... [ 51%] api/scanpy.datasets.paul15
writing output... [ 52%] api/scanpy.datasets.pbmc3k
writing output... [ 52%] api/scanpy.datasets.pbmc68k_reduced
writing output... [ 53%] api/scanpy.datasets.toggleswitch
writing output... [ 53%] api/scanpy.external
writing output... [ 53%] api/scanpy.external.exporting.cellbrowser
writing output... [ 54%] api/scanpy.external.exporting.spring_project
writing output... [ 54%] api/scanpy.external.pl.phate
writing output... [ 55%] api/scanpy.external.pp.bbknn
writing output... [ 55%] api/scanpy.external.pp.dca
writing output... [ 56%] api/scanpy.external.pp.magic
writing output... [ 56%] api/scanpy.external.pp.mnn_correct
writing output... [ 57%] api/scanpy.external.tl.cyclone
writing output... [ 57%] api/scanpy.external.tl.palantir
writing output... [ 58%] api/scanpy.external.tl.phate
writing output... [ 58%] api/scanpy.external.tl.phenograph
writing output... [ 59%] api/scanpy.external.tl.sandbag
writing output... [ 59%] api/scanpy.logging.print_versions
writing output... [ 60%] api/scanpy.pl.clustermap
writing output... [ 60%] api/scanpy.pl.diffmap
writing output... [ 60%] api/scanpy.pl.dotplot
writing output... [ 61%] api/scanpy.pl.dpt_groups_pseudotime
writing output... [ 61%] api/scanpy.pl.dpt_timeseries
writing output... [ 62%] api/scanpy.pl.draw_graph
writing output... [ 62%] api/scanpy.pl.embedding_density
writing output... [ 63%] api/scanpy.pl.filter_genes_dispersion
writing output... [ 63%] api/scanpy.pl.heatmap
writing output... [ 64%] api/scanpy.pl.highest_expr_genes
writing output... [ 64%] api/scanpy.pl.highly_variable_genes
writing output... [ 65%] api/scanpy.pl.matrixplot
writing output... [ 65%] api/scanpy.pl.paga
writing output... [ 66%] api/scanpy.pl.paga_compare
writing output... [ 66%] api/scanpy.pl.paga_path
writing output... [ 66%] api/scanpy.pl.pca
writing output... [ 67%] api/scanpy.pl.pca_loadings
writing output... [ 67%] api/scanpy.pl.pca_overview
writing output... [ 68%] api/scanpy.pl.pca_variance_ratio
writing output... [ 68%] api/scanpy.pl.rank_genes_groups
writing output... [ 69%] api/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 69%] api/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 70%] api/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 70%] api/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 71%] api/scanpy.pl.rank_genes_groups_violin
writing output... [ 71%] api/scanpy.pl.ranking
writing output... [ 72%] api/scanpy.pl.scatter
writing output... [ 72%] api/scanpy.pl.sim
writing output... [ 73%] api/scanpy.pl.stacked_violin
writing output... [ 73%] api/scanpy.pl.tsne
writing output... [ 73%] api/scanpy.pl.umap
writing output... [ 74%] api/scanpy.pl.violin
writing output... [ 74%] api/scanpy.plotting
writing output... [ 75%] api/scanpy.pp.calculate_qc_metrics
writing output... [ 75%] api/scanpy.pp.combat
writing output... [ 76%] api/scanpy.pp.downsample_counts
writing output... [ 76%] api/scanpy.pp.filter_cells
writing output... [ 77%] api/scanpy.pp.filter_genes
writing output... [ 77%] api/scanpy.pp.filter_genes_dispersion
writing output... [ 78%] api/scanpy.pp.highly_variable_genes
writing output... [ 78%] api/scanpy.pp.log1p
writing output... [ 79%] api/scanpy.pp.neighbors
writing output... [ 79%] api/scanpy.pp.normalize_per_cell
writing output... [ 80%] api/scanpy.pp.normalize_total
writing output... [ 80%] api/scanpy.pp.pca
writing output... [ 80%] api/scanpy.pp.recipe_seurat
writing output... [ 81%] api/scanpy.pp.recipe_weinreb17
writing output... [ 81%] api/scanpy.pp.recipe_zheng17
writing output... [ 82%] api/scanpy.pp.regress_out
writing output... [ 82%] api/scanpy.pp.scale
writing output... [ 83%] api/scanpy.pp.subsample
writing output... [ 83%] api/scanpy.queries.mitochondrial_genes
writing output... [ 84%] api/scanpy.read
writing output... [ 84%] api/scanpy.read_10x_h5
writing output... [ 85%] api/scanpy.read_10x_mtx
writing output... [ 85%] api/scanpy.read_csv
writing output... [ 86%] api/scanpy.read_excel
writing output... [ 86%] api/scanpy.read_h5ad
writing output... [ 86%] api/scanpy.read_hdf
writing output... [ 87%] api/scanpy.read_loom
writing output... [ 87%] api/scanpy.read_mtx
writing output... [ 88%] api/scanpy.read_text
writing output... [ 88%] api/scanpy.read_umi_tools
writing output... [ 89%] api/scanpy.set_figure_params
writing output... [ 89%] api/scanpy.tl.dendrogram
writing output... [ 90%] api/scanpy.tl.diffmap
writing output... [ 90%] api/scanpy.tl.dpt
writing output... [ 91%] api/scanpy.tl.draw_graph
writing output... [ 91%] api/scanpy.tl.filter_rank_genes_groups
writing output... [ 92%] api/scanpy.tl.leiden
writing output... [ 92%] api/scanpy.tl.louvain
writing output... [ 93%] api/scanpy.tl.marker_gene_overlap
writing output... [ 93%] api/scanpy.tl.paga
writing output... [ 93%] api/scanpy.tl.pca
writing output... [ 94%] api/scanpy.tl.rank_genes_groups
writing output... [ 94%] api/scanpy.tl.score_genes
writing output... [ 95%] api/scanpy.tl.score_genes_cell_cycle
writing output... [ 95%] api/scanpy.tl.sim
writing output... [ 96%] api/scanpy.tl.tsne
writing output... [ 96%] api/scanpy.tl.umap
writing output... [ 97%] basic_usage
writing output... [ 97%] examples
writing output... [ 98%] index
writing output... [ 98%] installation
writing output... [ 99%] references
writing output... [ 99%] release_notes
writing output... [100%] tutorials
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:148: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:150: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:36: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:30: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:29: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tl.filter_rank_genes_groups:22: WARNING: undefined label: scanpy.tl.rank_genes_groups (if the link has no caption the label must precede a section header)
generating indices... genindex py-modindex
writing additional pages... search
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, 19 warnings.
The HTML pages are in _build/html.
/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