Read the Docs build information Build id: 278155 Project: icb-scanpy Version: latest Commit: 9dd2e94846aad8dde75763a97a775a8e4616440e Date: 2020-01-20T18:34:33.333820Z State: finished Success: True [rtd-command-info] start-time: 2020-01-20T18:35:05.850934Z, end-time: 2020-01-20T18:35:07.976011Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2020-01-20T18:35:08.365034Z, end-time: 2020-01-20T18:35:08.465049Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 9dd2e94 Use include_package_data=True again (#997) [rtd-command-info] start-time: 2020-01-20T18:35:08.545323Z, end-time: 2020-01-20T18:35:08.556402Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-01-20T18:35:09.494353Z, end-time: 2020-01-20T18:35:14.141017Z, duration: 4, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.8' 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: 2020-01-20T18:35:14.222707Z, end-time: 2020-01-20T18:35:16.692882Z, 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 Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2020-01-20T18:35:16.784816Z, end-time: 2020-01-20T18:35:28.316767Z, duration: 11, 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 Downloading https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl (849kB) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (41.0.1) Collecting docutils==0.14 Downloading https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl (543kB) Collecting mock==1.0.1 Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB) Collecting pillow==5.4.1 Downloading https://files.pythonhosted.org/packages/85/5e/e91792f198bbc5a0d7d3055ad552bc4062942d27eaf75c3e2783cf64eae5/Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl Collecting commonmark==0.8.1 Downloading https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl (47kB) Collecting recommonmark==0.5.0 Downloading https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl Collecting sphinx<2 Downloading https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl (3.1MB) Collecting sphinx-rtd-theme<0.5 Downloading https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4MB) Collecting readthedocs-sphinx-ext<1.1 Downloading https://files.pythonhosted.org/packages/8a/b5/73b740dc7182b4f458de18ab54adaf5698ace3a723569c5e2a748130a314/readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl Collecting future Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829kB) Collecting imagesize Downloading https://files.pythonhosted.org/packages/31/b2/b5522a0c8d11e4aff83f8342f3f0dea68c2fb25aa44403e420587f0ce204/imagesize-1.2.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 Downloading https://files.pythonhosted.org/packages/15/a1/522dccd23e5d2e47aed4b6a16795b8213e3272c7506e625f2425ad025a19/Babel-2.8.0-py2.py3-none-any.whl (8.6MB) Collecting snowballstemmer>=1.1 Downloading https://files.pythonhosted.org/packages/7d/4b/cdf1113a0e88b641893b814e9c36f69a6fda28cd88b62c7f0d858cde3166/snowballstemmer-2.0.0-py2.py3-none-any.whl (97kB) Collecting Jinja2>=2.3 Downloading https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl (125kB) Collecting requests>=2.0.0 Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB) Collecting sphinxcontrib-websupport Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl Collecting six>=1.5 Downloading https://files.pythonhosted.org/packages/65/eb/1f97cb97bfc2390a276969c6fae16075da282f5058082d4cb10c6c5c1dba/six-1.14.0-py2.py3-none-any.whl Collecting packaging Downloading https://files.pythonhosted.org/packages/d8/5b/3098db49a61ccc8583ffead6aedc226f08ff56dc03106b6ec54451e27a30/packaging-20.0-py2.py3-none-any.whl Collecting pytz>=2015.7 Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB) Collecting MarkupSafe>=0.23 Downloading https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl Collecting certifi>=2017.4.17 Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl (125kB) Collecting idna<2.9,>=2.5 Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) Collecting chardet<3.1.0,>=3.0.2 Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting pyparsing>=2.0.2 Downloading https://files.pythonhosted.org/packages/5d/bc/1e58593167fade7b544bfe9502a26dc860940a79ab306e651e7f13be68c2/pyparsing-2.4.6-py2.py3-none-any.whl (67kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-cp36-none-any.whl size=23755 sha256=40b4d55dd6120a0ef4f033ad1af24866f40bed0e3f10ffce86496f3802c53e12 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-cp36-none-any.whl size=491058 sha256=89e8ee6dcd68ffa65c89228f13901e4537775163e6f5bfdbbb0e7bd19137b4a0 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e Successfully built mock future Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, certifi, urllib3, idna, chardet, requests, sphinxcontrib-websupport, six, pyparsing, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.2.0 mock-1.0.1 packaging-20.0 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.7 [rtd-command-info] start-time: 2020-01-20T18:35:28.404062Z, end-time: 2020-01-20T18:36:06.864569Z, duration: 38, 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 Collecting anndata>=0.6.22.post1 Downloading https://files.pythonhosted.org/packages/2b/72/87196c15f68d9865c31a43a10cf7c50bcbcedd5607d09f9aada0b3963103/anndata-0.6.22.post1-py3-none-any.whl (47kB) Collecting matplotlib==3.0.* Downloading https://files.pythonhosted.org/packages/e9/69/f5e05f578585ed9935247be3788b374f90701296a70c8871bcd6d21edb00/matplotlib-3.0.3-cp36-cp36m-manylinux1_x86_64.whl (13.0MB) Collecting pandas>=0.21 Downloading https://files.pythonhosted.org/packages/52/3f/f6a428599e0d4497e1595030965b5ba455fd8ade6e977e3c819973c4b41d/pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4MB) Collecting scipy>=1.3 Downloading https://files.pythonhosted.org/packages/dc/29/162476fd44203116e7980cfbd9352eef9db37c49445d1fec35509022f6aa/scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1MB) Collecting seaborn Downloading https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl (208kB) Collecting h5py!=2.10.0 Downloading https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl (2.8MB) Collecting tables Downloading https://files.pythonhosted.org/packages/ed/c3/8fd9e3bb21872f9d69eb93b3014c86479864cca94e625fd03713ccacec80/tables-3.6.1-cp36-cp36m-manylinux1_x86_64.whl (4.3MB) Collecting tqdm Downloading https://files.pythonhosted.org/packages/72/c9/7fc20feac72e79032a7c8138fd0d395dc6d8812b5b9edf53c3afd0b31017/tqdm-4.41.1-py2.py3-none-any.whl (56kB) Collecting importlib_metadata>=0.7 Downloading https://files.pythonhosted.org/packages/d7/31/74dcb59a601b95fce3b0334e8fc9db758f78e43075f22aeb3677dfb19f4c/importlib_metadata-1.4.0-py2.py3-none-any.whl Collecting scikit-learn>=0.21.2 Downloading https://files.pythonhosted.org/packages/d1/48/e9fa9e252abcd1447eff6f9257636af31758a6e46fd5ce5d3c879f6907cb/scikit_learn-0.22.1-cp36-cp36m-manylinux1_x86_64.whl (7.0MB) Collecting statsmodels>=0.10.0rc2 Downloading https://files.pythonhosted.org/packages/a8/17/44a9f61db85d7adb3b84a381a7ca6493385ea2734eb3e38ef78faadcfa16/statsmodels-0.11.0rc2-cp36-cp36m-manylinux1_x86_64.whl (8.7MB) Collecting patsy Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl (231kB) Collecting networkx Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl (1.6MB) Collecting natsort Downloading https://files.pythonhosted.org/packages/e5/d1/3e509d47e393f16ef3b469cae76daf5eca0a4089b13ff41d7c378ba8179f/natsort-7.0.0-py3-none-any.whl Collecting joblib Downloading https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl (294kB) Collecting numba>=0.41.0 Downloading https://files.pythonhosted.org/packages/f8/7d/f2b5ea8d5952115351e303d1aadbdd1c5b08f479d76456d43a5d7a3a8c88/numba-0.47.0-cp36-cp36m-manylinux1_x86_64.whl (3.7MB) Collecting umap-learn>=0.3.10 Downloading https://files.pythonhosted.org/packages/ad/92/36bac74962b424870026cb0b42cec3d5b6f4afa37d81818475d8762f9255/umap-learn-0.3.10.tar.gz (40kB) Collecting legacy-api-wrap Downloading https://files.pythonhosted.org/packages/a4/68/da997bc56bb69dcdcee4054f0bc42266909307b905389fbc54c9158f42da/legacy_api_wrap-1.2-py3-none-any.whl Collecting setuptools_scm Downloading https://files.pythonhosted.org/packages/b4/23/17dbdfa1202cdb33d7df245b55d4c7b3bce9109d297cccca21c22500aebb/setuptools_scm-3.4.2-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 -r docs/../requirements.txt (line 21)) (20.0) 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 Downloading https://files.pythonhosted.org/packages/c4/bb/64c45dd915150952feda858a112a13dc43fb24df2f397d82cdbd4db274b6/Sphinx-2.3.1-py3-none-any.whl (2.7MB) Collecting sphinx-autodoc-typehints Downloading https://files.pythonhosted.org/packages/00/83/87b8890a93b3994b49960716009c1effb6f7a1fef3a1ec553fda2a7c84de/sphinx_autodoc_typehints-1.10.3-py3-none-any.whl Collecting scanpydoc>=0.4.5 Downloading https://files.pythonhosted.org/packages/5f/61/55b773fdfc34808275d0d3a1de6434b1fe5116be569ee18ee9f8de6b1ee4/scanpydoc-0.4.5-py3-none-any.whl Collecting typing_extensions Downloading https://files.pythonhosted.org/packages/03/92/705fe8aca27678e01bbdd7738173b8e7df0088a2202c80352f664630d638/typing_extensions-3.7.4.1-py3-none-any.whl Collecting numpy~=1.14 Downloading https://files.pythonhosted.org/packages/62/20/4d43e141b5bc426ba38274933ef8e76e85c7adea2c321ecf9ebf7421cedf/numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl (20.1MB) Collecting cycler>=0.10 Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.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==3.0.*->-r docs/../requirements.txt (line 3)) (2.4.6) Collecting python-dateutil>=2.1 Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB) Collecting kiwisolver>=1.0.1 Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB) 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 4)) (2019.3) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from h5py!=2.10.0->-r docs/../requirements.txt (line 7)) (1.14.0) Collecting numexpr>=2.6.2 Downloading https://files.pythonhosted.org/packages/36/ed/eac5f6123f54a61cd13b7e89826b97edea54adf76d9f8e9fa2ce70e2fdf8/numexpr-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (162kB) Collecting zipp>=0.5 Downloading https://files.pythonhosted.org/packages/45/d8/f1e05f399573d2b4723dae1c1f1487dd2e7871c79ed32da741f49faaa226/zipp-2.0.0-py3-none-any.whl Collecting decorator>=4.3.0 Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-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 numba>=0.41.0->-r docs/../requirements.txt (line 17)) (41.0.1) Collecting llvmlite>=0.31.0dev0 Downloading https://files.pythonhosted.org/packages/ad/bb/60d4033d56c9da36490af19caa6c794b72b8aef6f792fdfa8cb95d11e419/llvmlite-0.31.0-cp36-cp36m-manylinux1_x86_64.whl (20.2MB) Collecting get-version>=2.0.4 Downloading https://files.pythonhosted.org/packages/23/48/7610e884e62fff2183e7bc8592397c39a020267fb5147905fcd3f9cc820c/get_version-2.1-py3-none-any.whl (43kB) Collecting sphinxcontrib-qthelp Downloading https://files.pythonhosted.org/packages/ce/5b/4747c3ba98b3a3e21a66faa183d8f79b9ded70e74212a7988d236a6eb78a/sphinxcontrib_qthelp-1.0.2-py2.py3-none-any.whl (90kB) Collecting sphinxcontrib-jsmath Downloading https://files.pythonhosted.org/packages/c2/42/4c8646762ee83602e3fb3fbe774c2fac12f317deb0b5dbeeedd2d3ba4b77/sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl Collecting sphinxcontrib-applehelp Downloading https://files.pythonhosted.org/packages/13/9a/4428b3114d654cb1cd34d90d5e6fab938d5436f94a571155187ea1dd78b4/sphinxcontrib_applehelp-1.0.1-py2.py3-none-any.whl (121kB) 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 3)) (2.8.0) 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 3)) (2.3.1) Collecting sphinxcontrib-serializinghtml Downloading https://files.pythonhosted.org/packages/57/b3/3648e48fa5682e61e9839d62de4e23af1795ceb738d68d73bd974257a95c/sphinxcontrib_serializinghtml-1.1.3-py2.py3-none-any.whl (89kB) 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 3)) (2.10.3) 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 3)) (0.7.12) 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 3)) (0.14) 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 3)) (1.2.0) Collecting sphinxcontrib-devhelp Downloading https://files.pythonhosted.org/packages/b0/a3/fea98741f0b2f2902fbf6c35c8e91b22cd0dd13387291e81d457f9a93066/sphinxcontrib_devhelp-1.0.1-py2.py3-none-any.whl (84kB) 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 3)) (2.0.0) Collecting sphinxcontrib-htmlhelp Downloading https://files.pythonhosted.org/packages/e4/35/80a67cc493f4a8a9634ab203a77aaa1b84d79ccb1c02eca72cb084d2c7f7/sphinxcontrib_htmlhelp-1.0.2-py2.py3-none-any.whl (96kB) 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 3)) (2.22.0) Collecting more-itertools Downloading https://files.pythonhosted.org/packages/bc/e2/3206a70758a21f9878fcf9478282bb68fbc66a5564718f9ed724c3f2bb52/more_itertools-8.1.0-py3-none-any.whl (41kB) 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 3)) (1.1.1) 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 3)) (1.25.7) 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 3)) (3.0.4) 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 3)) (2019.11.28) 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 3)) (2.8) Building wheels for collected packages: umap-learn Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.3.10-cp36-none-any.whl size=38881 sha256=1f63e392afa437c0bf11b31ce320499b9fa73b364f03a8406383cff01ea728ea Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/d0/f8/d5/8e3af3ee957feb9b403a060ebe72f7561887fef9dea658326e Successfully built umap-learn Installing collected packages: numpy, scipy, natsort, python-dateutil, pandas, h5py, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, tqdm, more-itertools, zipp, importlib-metadata, joblib, scikit-learn, patsy, statsmodels, decorator, networkx, llvmlite, numba, umap-learn, get-version, legacy-api-wrap, setuptools-scm, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinx, sphinx-autodoc-typehints, scanpydoc, typing-extensions Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed anndata-0.6.22.post1 cycler-0.10.0 decorator-4.4.1 get-version-2.1 h5py-2.9.0 importlib-metadata-1.4.0 joblib-0.14.1 kiwisolver-1.1.0 legacy-api-wrap-1.2 llvmlite-0.31.0 matplotlib-3.0.3 more-itertools-8.1.0 natsort-7.0.0 networkx-2.4 numba-0.47.0 numexpr-2.7.1 numpy-1.18.1 pandas-0.25.3 patsy-0.5.1 python-dateutil-2.8.1 scanpydoc-0.4.5 scikit-learn-0.22.1 scipy-1.4.1 seaborn-0.9.0 setuptools-scm-3.4.2 sphinx-2.3.1 sphinx-autodoc-typehints-1.10.3 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 statsmodels-0.11.0rc2 tables-3.6.1 tqdm-4.41.1 typing-extensions-3.7.4.1 umap-learn-0.3.10 zipp-2.0.0 [rtd-command-info] start-time: 2020-01-20T18:36:07.631689Z, end-time: 2020-01-20T18:36:07.848490Z, 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[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '2.0' # Nicer param docs suppress_warnings = ['ref.citation'] # 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', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('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/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_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_BrightFG.svg' def setup(app): app.warningiserror = on_rtd app.add_stylesheet('css/custom.css') # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric" } 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'), ] ########################################################################### # 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/"), ("1.4.4.post1", "/en/1.4.4.post1/"), ("1.1", "/en/1.1/"), ], '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', 'proxied_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': '9dd2e948', } 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: 2020-01-20T18:36:07.937696Z, end-time: 2020-01-20T18:37:49.929445Z, duration: 101, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v2.3.1 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/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, _links.rst, api/index.rst, api/plotting.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, ecosystem.rst, external/index.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.pbmc3k_processed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.pbmc68k_reduced.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.bbknn.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.dca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.magic.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.mnn_correct.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.trimap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_eigen.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.rp_forest.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 16 source files that are out of date updating environment: [new config] 163 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 1%] _links reading sources... [ 1%] api/index reading sources... [ 2%] api/plotting reading sources... [ 3%] api/scanpy.Neighbors reading sources... [ 3%] api/scanpy.Neighbors.compute_eigen reading sources... [ 4%] api/scanpy.Neighbors.compute_neighbors reading sources... [ 4%] api/scanpy.Neighbors.compute_transitions reading sources... [ 5%] api/scanpy.Neighbors.connectivities reading sources... [ 6%] api/scanpy.Neighbors.distances reading sources... [ 6%] api/scanpy.Neighbors.distances_dpt reading sources... [ 7%] api/scanpy.Neighbors.eigen_basis reading sources... [ 7%] api/scanpy.Neighbors.eigen_values reading sources... [ 8%] api/scanpy.Neighbors.getdoc reading sources... [ 9%] api/scanpy.Neighbors.rp_forest reading sources... [ 9%] api/scanpy.Neighbors.to_igraph reading sources... [ 10%] api/scanpy.Neighbors.transitions reading sources... [ 11%] api/scanpy.Neighbors.transitions_sym reading sources... [ 11%] api/scanpy._settings.ScanpyConfig reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.autosave reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.cache_compression reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.cachedir reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.figdir reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 17%] api/scanpy._settings.ScanpyConfig.file_format_figs reading sources... [ 17%] api/scanpy._settings.ScanpyConfig.logfile reading sources... [ 18%] api/scanpy._settings.ScanpyConfig.logpath reading sources... [ 19%] api/scanpy._settings.ScanpyConfig.max_memory reading sources... [ 19%] api/scanpy._settings.ScanpyConfig.n_jobs reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.plot_suffix reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params reading sources... [ 21%] api/scanpy._settings.ScanpyConfig.verbosity reading sources... [ 22%] api/scanpy._settings.ScanpyConfig.writedir reading sources... [ 22%] api/scanpy.datasets.blobs reading sources... [ 23%] api/scanpy.datasets.ebi_expression_atlas reading sources... [ 23%] api/scanpy.datasets.krumsiek11 reading sources... [ 24%] api/scanpy.datasets.moignard15 reading sources... [ 25%] api/scanpy.datasets.paul15 reading sources... [ 25%] api/scanpy.datasets.pbmc3k reading sources... [ 26%] api/scanpy.datasets.pbmc3k_processed 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... [ 31%] api/scanpy.pl.dendrogram reading sources... [ 32%] api/scanpy.pl.diffmap reading sources... [ 33%] api/scanpy.pl.dotplot reading sources... [ 33%] api/scanpy.pl.dpt_groups_pseudotime reading sources... [ 34%] api/scanpy.pl.dpt_timeseries reading sources... [ 34%] api/scanpy.pl.draw_graph reading sources... [ 35%] api/scanpy.pl.embedding reading sources... [ 36%] api/scanpy.pl.embedding_density reading sources... [ 36%] api/scanpy.pl.filter_genes_dispersion reading sources... [ 37%] api/scanpy.pl.heatmap reading sources... [ 38%] 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... [ 42%] 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... [ 44%] 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... [ 46%] api/scanpy.pl.rank_genes_groups_stacked_violin reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_violin reading sources... [ 48%] api/scanpy.pl.ranking reading sources... [ 49%] api/scanpy.pl.scatter reading sources... [ 49%] api/scanpy.pl.sim reading sources... [ 50%] api/scanpy.pl.stacked_violin reading sources... [ 50%] api/scanpy.pl.tracksplot reading sources... [ 51%] api/scanpy.pl.tsne reading sources... [ 52%] api/scanpy.pl.umap reading sources... [ 52%] api/scanpy.pl.violin reading sources... [ 53%] api/scanpy.plotting reading sources... [ 53%] api/scanpy.pp.calculate_qc_metrics reading sources... [ 54%] api/scanpy.pp.combat reading sources... [ 55%] api/scanpy.pp.downsample_counts reading sources... [ 55%] api/scanpy.pp.filter_cells reading sources... [ 56%] api/scanpy.pp.filter_genes reading sources... [ 57%] api/scanpy.pp.filter_genes_dispersion reading sources... [ 57%] api/scanpy.pp.highly_variable_genes reading sources... [ 58%] api/scanpy.pp.log1p reading sources... [ 58%] api/scanpy.pp.neighbors reading sources... [ 59%] api/scanpy.pp.normalize_per_cell reading sources... [ 60%] api/scanpy.pp.normalize_total reading sources... [ 60%] api/scanpy.pp.pca reading sources... [ 61%] api/scanpy.pp.recipe_seurat reading sources... [ 61%] api/scanpy.pp.recipe_weinreb17 reading sources... [ 62%] api/scanpy.pp.recipe_zheng17 reading sources... [ 63%] api/scanpy.pp.regress_out reading sources... [ 63%] api/scanpy.pp.scale reading sources... [ 64%] api/scanpy.pp.subsample reading sources... [ 65%] api/scanpy.queries.biomart_annotations reading sources... [ 65%] api/scanpy.queries.enrich reading sources... [ 66%] api/scanpy.queries.gene_coordinates reading sources... [ 66%] api/scanpy.queries.mitochondrial_genes reading sources... [ 67%] api/scanpy.read reading sources... [ 68%] api/scanpy.read_10x_h5 reading sources... [ 68%] api/scanpy.read_10x_mtx reading sources... [ 69%] api/scanpy.read_csv reading sources... [ 69%] api/scanpy.read_excel reading sources... [ 70%] api/scanpy.read_h5ad reading sources... [ 71%] api/scanpy.read_hdf reading sources... [ 71%] api/scanpy.read_loom reading sources... [ 72%] api/scanpy.read_mtx reading sources... [ 73%] api/scanpy.read_text reading sources... [ 73%] api/scanpy.read_umi_tools reading sources... [ 74%] api/scanpy.set_figure_params reading sources... [ 74%] api/scanpy.tl.dendrogram reading sources... [ 75%] api/scanpy.tl.diffmap reading sources... [ 76%] api/scanpy.tl.dpt reading sources... [ 76%] api/scanpy.tl.draw_graph reading sources... [ 77%] api/scanpy.tl.embedding_density reading sources... [ 77%] api/scanpy.tl.filter_rank_genes_groups reading sources... [ 78%] api/scanpy.tl.ingest reading sources... [ 79%] api/scanpy.tl.leiden reading sources... [ 79%] api/scanpy.tl.louvain reading sources... [ 80%] api/scanpy.tl.marker_gene_overlap reading sources... [ 80%] api/scanpy.tl.paga reading sources... [ 81%] api/scanpy.tl.pca reading sources... [ 82%] api/scanpy.tl.rank_genes_groups reading sources... [ 82%] api/scanpy.tl.score_genes reading sources... [ 83%] api/scanpy.tl.score_genes_cell_cycle reading sources... [ 84%] api/scanpy.tl.sim reading sources... [ 84%] api/scanpy.tl.tsne reading sources... [ 85%] api/scanpy.tl.umap reading sources... [ 85%] basic_usage reading sources... [ 86%] ecosystem reading sources... [ 87%] external/index reading sources... [ 87%] external/scanpy.external.exporting.cellbrowser reading sources... [ 88%] external/scanpy.external.exporting.spring_project reading sources... [ 88%] external/scanpy.external.pl.phate reading sources... [ 89%] external/scanpy.external.pl.trimap reading sources... [ 90%] external/scanpy.external.pp.bbknn reading sources... [ 90%] external/scanpy.external.pp.dca reading sources... [ 91%] external/scanpy.external.pp.magic reading sources... [ 92%] external/scanpy.external.pp.mnn_correct reading sources... [ 92%] external/scanpy.external.tl.cyclone reading sources... [ 93%] external/scanpy.external.tl.palantir reading sources... [ 93%] external/scanpy.external.tl.phate reading sources... [ 94%] external/scanpy.external.tl.phenograph reading sources... [ 95%] external/scanpy.external.tl.sandbag reading sources... [ 95%] external/scanpy.external.tl.trimap reading sources... [ 96%] index reading sources... [ 96%] installation reading sources... [ 97%] references reading sources... [ 98%] release-latest reading sources... [ 98%] release-notes reading sources... [ 99%] tutorials reading sources... [100%] usage-principles looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 0%] _key_contributors writing output... [ 1%] _links writing output... [ 1%] api/index writing output... [ 2%] api/plotting writing output... [ 3%] api/scanpy.Neighbors writing output... [ 3%] api/scanpy.Neighbors.compute_eigen writing output... [ 4%] api/scanpy.Neighbors.compute_neighbors writing output... [ 4%] api/scanpy.Neighbors.compute_transitions writing output... [ 5%] api/scanpy.Neighbors.connectivities writing output... [ 6%] api/scanpy.Neighbors.distances writing output... [ 6%] api/scanpy.Neighbors.distances_dpt writing output... [ 7%] api/scanpy.Neighbors.eigen_basis writing output... [ 7%] api/scanpy.Neighbors.eigen_values writing output... [ 8%] api/scanpy.Neighbors.getdoc writing output... [ 9%] api/scanpy.Neighbors.rp_forest writing output... [ 9%] api/scanpy.Neighbors.to_igraph writing output... [ 10%] api/scanpy.Neighbors.transitions writing output... [ 11%] api/scanpy.Neighbors.transitions_sym writing output... [ 11%] api/scanpy._settings.ScanpyConfig writing output... [ 12%] api/scanpy._settings.ScanpyConfig.autosave writing output... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow writing output... [ 13%] api/scanpy._settings.ScanpyConfig.cache_compression writing output... [ 14%] api/scanpy._settings.ScanpyConfig.cachedir writing output... [ 14%] api/scanpy._settings.ScanpyConfig.categories_to_ignore writing output... [ 15%] api/scanpy._settings.ScanpyConfig.datasetdir writing output... [ 15%] api/scanpy._settings.ScanpyConfig.figdir writing output... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_data writing output... [ 17%] api/scanpy._settings.ScanpyConfig.file_format_figs writing output... [ 17%] api/scanpy._settings.ScanpyConfig.logfile writing output... [ 18%] api/scanpy._settings.ScanpyConfig.logpath writing output... [ 19%] api/scanpy._settings.ScanpyConfig.max_memory writing output... [ 19%] api/scanpy._settings.ScanpyConfig.n_jobs writing output... [ 20%] api/scanpy._settings.ScanpyConfig.plot_suffix writing output... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params writing output... [ 21%] api/scanpy._settings.ScanpyConfig.verbosity writing output... [ 22%] api/scanpy._settings.ScanpyConfig.writedir writing output... [ 22%] api/scanpy.datasets.blobs writing output... [ 23%] api/scanpy.datasets.ebi_expression_atlas writing output... [ 23%] api/scanpy.datasets.krumsiek11 writing output... [ 24%] api/scanpy.datasets.moignard15 writing output... [ 25%] api/scanpy.datasets.paul15 writing output... [ 25%] api/scanpy.datasets.pbmc3k writing output... [ 26%] api/scanpy.datasets.pbmc3k_processed 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... [ 31%] api/scanpy.pl.dendrogram writing output... [ 32%] api/scanpy.pl.diffmap writing output... [ 33%] api/scanpy.pl.dotplot writing output... [ 33%] api/scanpy.pl.dpt_groups_pseudotime writing output... [ 34%] api/scanpy.pl.dpt_timeseries writing output... [ 34%] api/scanpy.pl.draw_graph writing output... [ 35%] api/scanpy.pl.embedding writing output... [ 36%] api/scanpy.pl.embedding_density writing output... [ 36%] api/scanpy.pl.filter_genes_dispersion writing output... [ 37%] api/scanpy.pl.heatmap writing output... [ 38%] 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... [ 42%] 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... [ 44%] 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... [ 46%] api/scanpy.pl.rank_genes_groups_stacked_violin writing output... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot writing output... [ 47%] api/scanpy.pl.rank_genes_groups_violin writing output... [ 48%] api/scanpy.pl.ranking writing output... [ 49%] api/scanpy.pl.scatter writing output... [ 49%] api/scanpy.pl.sim writing output... [ 50%] api/scanpy.pl.stacked_violin writing output... [ 50%] api/scanpy.pl.tracksplot writing output... [ 51%] api/scanpy.pl.tsne writing output... [ 52%] api/scanpy.pl.umap writing output... [ 52%] api/scanpy.pl.violin writing output... [ 53%] api/scanpy.plotting writing output... [ 53%] api/scanpy.pp.calculate_qc_metrics writing output... [ 54%] api/scanpy.pp.combat writing output... [ 55%] api/scanpy.pp.downsample_counts writing output... [ 55%] api/scanpy.pp.filter_cells writing output... [ 56%] api/scanpy.pp.filter_genes writing output... [ 57%] api/scanpy.pp.filter_genes_dispersion writing output... [ 57%] api/scanpy.pp.highly_variable_genes writing output... [ 58%] api/scanpy.pp.log1p writing output... [ 58%] api/scanpy.pp.neighbors writing output... [ 59%] api/scanpy.pp.normalize_per_cell writing output... [ 60%] api/scanpy.pp.normalize_total writing output... [ 60%] api/scanpy.pp.pca writing output... [ 61%] api/scanpy.pp.recipe_seurat writing output... [ 61%] api/scanpy.pp.recipe_weinreb17 writing output... [ 62%] api/scanpy.pp.recipe_zheng17 writing output... [ 63%] api/scanpy.pp.regress_out writing output... [ 63%] api/scanpy.pp.scale writing output... [ 64%] api/scanpy.pp.subsample writing output... [ 65%] api/scanpy.queries.biomart_annotations writing output... [ 65%] api/scanpy.queries.enrich writing output... [ 66%] api/scanpy.queries.gene_coordinates writing output... [ 66%] api/scanpy.queries.mitochondrial_genes writing output... [ 67%] api/scanpy.read writing output... [ 68%] api/scanpy.read_10x_h5 writing output... [ 68%] api/scanpy.read_10x_mtx writing output... [ 69%] api/scanpy.read_csv writing output... [ 69%] api/scanpy.read_excel writing output... [ 70%] api/scanpy.read_h5ad writing output... [ 71%] api/scanpy.read_hdf writing output... [ 71%] api/scanpy.read_loom writing output... [ 72%] api/scanpy.read_mtx writing output... [ 73%] api/scanpy.read_text writing output... [ 73%] api/scanpy.read_umi_tools writing output... [ 74%] api/scanpy.set_figure_params writing output... [ 74%] api/scanpy.tl.dendrogram writing output... [ 75%] api/scanpy.tl.diffmap writing output... [ 76%] api/scanpy.tl.dpt writing output... [ 76%] api/scanpy.tl.draw_graph writing output... [ 77%] api/scanpy.tl.embedding_density writing output... [ 77%] api/scanpy.tl.filter_rank_genes_groups writing output... [ 78%] api/scanpy.tl.ingest writing output... [ 79%] api/scanpy.tl.leiden writing output... [ 79%] api/scanpy.tl.louvain writing output... [ 80%] api/scanpy.tl.marker_gene_overlap writing output... [ 80%] api/scanpy.tl.paga writing output... [ 81%] api/scanpy.tl.pca writing output... [ 82%] api/scanpy.tl.rank_genes_groups writing output... [ 82%] api/scanpy.tl.score_genes writing output... [ 83%] api/scanpy.tl.score_genes_cell_cycle writing output... [ 84%] api/scanpy.tl.sim writing output... [ 84%] api/scanpy.tl.tsne writing output... [ 85%] api/scanpy.tl.umap writing output... [ 85%] basic_usage writing output... [ 86%] ecosystem writing output... [ 87%] external/index writing output... [ 87%] external/scanpy.external.exporting.cellbrowser writing output... [ 88%] external/scanpy.external.exporting.spring_project writing output... [ 88%] external/scanpy.external.pl.phate writing output... [ 89%] external/scanpy.external.pl.trimap writing output... [ 90%] external/scanpy.external.pp.bbknn writing output... [ 90%] external/scanpy.external.pp.dca writing output... [ 91%] external/scanpy.external.pp.magic writing output... [ 92%] external/scanpy.external.pp.mnn_correct writing output... [ 92%] external/scanpy.external.tl.cyclone writing output... [ 93%] external/scanpy.external.tl.palantir writing output... [ 93%] external/scanpy.external.tl.phate writing output... [ 94%] external/scanpy.external.tl.phenograph writing output... [ 95%] external/scanpy.external.tl.sandbag writing output... [ 95%] external/scanpy.external.tl.trimap writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] references writing output... [ 98%] release-latest writing output... [ 98%] release-notes writing output... [ 99%] tutorials writing output... [100%] usage-principles 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('"{}" is shallow and may cause errors'.format(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