Read the Docs build information Build id: 256807 Project: icb-scanpy Version: latest Commit: 02008143e1cda86970d7d2fe420ab76c75023e3c Date: 2019-11-06T10:36:25.110478Z State: finished Success: True [rtd-command-info] start-time: 2019-11-06T10:36:25.883768Z, end-time: 2019-11-06T10:36:25.901770Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy.git [rtd-command-info] start-time: 2019-11-06T10:36:25.979273Z, end-time: 2019-11-06T10:36:26.521076Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy 19d7cd2..0200814 master -> origin/master [rtd-command-info] start-time: 2019-11-06T10:36:27.134316Z, end-time: 2019-11-06T10:36:27.155455Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 19d7cd2 remove text box border HEAD is now at 0200814 Allow specifying chromosome name when retrieving mitochondrial genes. (#902) [rtd-command-info] start-time: 2019-11-06T10:36:27.253054Z, end-time: 2019-11-06T10:36:27.276038Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-11-06T10:36:28.456190Z, end-time: 2019-11-06T10:36:32.386228Z, 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 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-11-06T10:36:32.483012Z, end-time: 2019-11-06T10:36:33.738886Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (19.3.1) [rtd-command-info] start-time: 2019-11-06T10:36:33.820663Z, end-time: 2019-11-06T10:36:37.692884Z, duration: 3, 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 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.3.1) 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) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.0) Collecting sphinx<2 Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.0) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: 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) (2.7.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.13.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: 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) (1.1.1) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) Requirement already satisfied, skipping upgrade: 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>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: 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>=2.0.0->sphinx<2) (1.25.6) sphinx-autodoc-typehints 1.10.2 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible. Installing collected packages: sphinx Found existing installation: Sphinx 2.2.1 Uninstalling Sphinx-2.2.1: Successfully uninstalled Sphinx-2.2.1 Successfully installed sphinx-1.8.5 [rtd-command-info] start-time: 2019-11-06T10:36:37.783268Z, end-time: 2019-11-06T10:36:41.973195Z, duration: 4, 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: anndata>=0.6.22rc1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 1)) (0.6.22.post1) Requirement already satisfied: matplotlib==3.0.* in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 3)) (3.0.3) Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 4)) (0.25.3) Requirement already satisfied: scipy>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 5)) (1.3.1) Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 6)) (0.9.0) Requirement already satisfied: h5py!=2.10.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 7)) (2.9.0) Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 8)) (3.6.1) Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 9)) (4.37.0) Requirement already satisfied: importlib_metadata>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 10)) (0.23) Requirement already satisfied: scikit-learn>=0.21.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 11)) (0.21.3) Requirement already satisfied: statsmodels>=0.10.0rc2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 12)) (0.10.1) Requirement already satisfied: patsy in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 13)) (0.5.1) Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 14)) (2.4) Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 15)) (6.0.0) Requirement already satisfied: joblib in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 16)) (0.14.0) Requirement already satisfied: numba>=0.41.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 17)) (0.46.0) Requirement already satisfied: umap-learn>=0.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 18)) (0.3.10) Requirement already satisfied: legacy-api-wrap in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 19)) (1.2) Requirement already satisfied: setuptools_scm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 20)) (3.3.3) 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 3)) Using cached https://files.pythonhosted.org/packages/1d/58/a547b02946af1cf337c701cafcf3267065c1c83d6e701f540961f4907b5d/Sphinx-2.2.1-py3-none-any.whl Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 4)) (1.10.2) Requirement already satisfied: scanpydoc>=0.4.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 5)) (0.4.4) Requirement already satisfied: typing_extensions in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (3.7.4.1) Requirement already satisfied: numpy~=1.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from anndata>=0.6.22rc1->-r docs/../requirements.txt (line 1)) (1.17.3) 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)) (2.4.4) Requirement already satisfied: cycler>=0.10 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)) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 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)) (1.1.0) Requirement already satisfied: python-dateutil>=2.1 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)) (2.8.1) 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)) (1.13.0) Requirement already satisfied: numexpr>=2.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from tables->-r docs/../requirements.txt (line 8)) (2.7.0) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from importlib_metadata>=0.7->-r docs/../requirements.txt (line 10)) (0.6.0) Requirement already satisfied: decorator>=4.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from networkx->-r docs/../requirements.txt (line 14)) (4.4.1) Requirement already satisfied: llvmlite>=0.30.0dev0 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)) (0.30.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from legacy-api-wrap->-r docs/../requirements.txt (line 19)) (41.0.1) Requirement already satisfied: get-version>=2.0.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from legacy-api-wrap->-r docs/../requirements.txt (line 19)) (2.1) Requirement already satisfied: sphinxcontrib-jsmath 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)) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp 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)) (1.0.2) 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: 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)) (2.7.0) 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: sphinxcontrib-applehelp 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)) (1.0.1) 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) 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)) (1.1.0) 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: 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) 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 3)) (19.2) Requirement already satisfied: sphinxcontrib-qthelp 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)) (1.0.2) Requirement already satisfied: sphinxcontrib-devhelp 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)) (1.0.1) 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) Requirement already satisfied: sphinxcontrib-serializinghtml 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)) (1.1.3) Requirement already satisfied: more-itertools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from zipp>=0.5->importlib_metadata>=0.7->-r docs/../requirements.txt (line 10)) (7.2.0) 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: 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) 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)) (1.25.6) 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)) (2019.9.11) 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) Installing collected packages: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed sphinx-2.2.1 [rtd-command-info] start-time: 2019-11-06T10:36:44.430128Z, end-time: 2019-11-06T10:36:44.756538Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys import warnings from pathlib import Path from datetime import datetime import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import scanpy # noqa with warnings.catch_warnings(): warnings.filterwarnings('ignore', category=FutureWarning) import scanpy.api on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links needs_sphinx = '2.0' # Nicer param docs suppress_warnings = ['ref.citation'] # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('http://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), scvelo=('https://scvelo.readthedocs.io/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=( 'https://scanpy-tutorials.readthedocs.io/en/latest', None, ), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=4, logo_only=True # Only show the logo ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map( html_context ) def setup(app): app.warningiserror = on_rtd app.add_stylesheet('css/custom.css') app.connect('autodoc-process-docstring', insert_function_images) app.connect('build-finished', show_param_warnings) app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}')) # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Images for plot functions ------------------------------------------------- def insert_function_images(app, what, name, obj, options, lines): path = Path(__file__).parent / 'api' / f'{name}.png' if what != 'function' or not path.is_file(): return lines[0:0] = [ f'.. image:: {path.name}', ' :width: 200', ' :align: right', '', ] # -- GitHub links -------------------------------------------------------------- def autolink(url_template, title_template='{}'): from docutils import nodes def role(name, rawtext, text, lineno, inliner, options={}, content=[]): url = url_template.format(text) title = title_template.format(text) node = nodes.reference(rawtext, title, refuri=url, **options) return [node], [] return role # -- Test for new scanpydoc functionality -------------------------------------- import re from sphinx.ext.napoleon import NumpyDocstring def process_return(lines): for line in lines: m = re.fullmatch(r'(?P\w+)\s+:\s+(?P[\w.]+)', line) if m: # Once this is in scanpydoc, we can use the fancy hover stuff yield f'**{m["param"]}** : :class:`~{m["type"]}`' else: yield line def scanpy_parse_returns_section(self, section): lines_raw = list( process_return(self._dedent(self._consume_to_next_section())) ) lines = self._format_block(':returns: ', lines_raw) if lines and lines[-1]: lines.append('') return lines NumpyDocstring._parse_returns_section = scanpy_parse_returns_section # -- Warn for non-annotated params --------------------------------------------- _format_docutils_params_orig = NumpyDocstring._format_docutils_params param_warnings = {} def scanpy_log_param_types(self, fields, field_role='param', type_role='type'): for _name, _type, _desc in fields: if ( not _type or not self._obj.__module__.startswith('scanpy') or self._name.startswith('scanpy.api') ): continue w_list = param_warnings.setdefault((self._name, self._obj), []) if (_name, _type) not in w_list: w_list.append((_name, _type)) return _format_docutils_params_orig(self, fields, field_role, type_role) def show_param_warnings(app, exception): import inspect for (fname, fun), params in param_warnings.items(): _, line = inspect.getsourcelines(fun) file_name = inspect.getsourcefile(fun) params_str = '\n'.join(f'\t{n}: {t}' for n, t in params) warnings.warn_explicit( f'\nParameters in `{fname}` have types in docstring.\n' f'Replace them with type annotations.\n{params_str}', UserWarning, file_name, line, ) if param_warnings: raise RuntimeError('Encountered text parameter type. Use annotations.') NumpyDocstring._format_docutils_params = scanpy_log_param_types # -- Debug code ---------------------------------------------------------------- # Just do the following to see the rst of a function: # rm -f _build/doctrees/api/scanpy..doctree; DEBUG=1 make html import os if os.environ.get('DEBUG') is not None: import sphinx.ext.napoleon pd = sphinx.ext.napoleon._process_docstring def pd_new(app, what, name, obj, options, lines): pd(app, what, name, obj, options, lines) print(*lines, sep='\n') sphinx.ext.napoleon._process_docstring = pd_new # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric" } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.readwrite.Empty'), ] for mod_name in [ 'pp', 'tl', 'pl', 'queries', 'logging', 'datasets', 'export_to', None, ]: if mod_name is None: mod = scanpy.api mod_name = 'scanpy.api' else: mod = getattr(scanpy.api, mod_name) mod_name = f'scanpy.api.{mod_name}' for name, item in vars(mod).items(): if not callable(item): continue for kind in ['func', 'obj']: nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}')) ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("inherit-requirements", "/en/inherit-requirements/"), ("contributors", "/en/contributors/"), ], 'downloads': [ ("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '02008143', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-11-06T10:36:44.856729Z, end-time: 2019-11-06T10:38:48.217304Z, duration: 123, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v2.2.1 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: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 155 source files that are out of date updating environment: [new config] 155 added, 0 changed, 0 removed reading sources... [ 0%] api/index reading sources... [ 1%] api/plotting reading sources... [ 1%] api/scanpy.Neighbors reading sources... [ 2%] api/scanpy.Neighbors.compute_eigen reading sources... [ 3%] api/scanpy.Neighbors.compute_neighbors reading sources... [ 3%] api/scanpy.Neighbors.compute_transitions reading sources... [ 4%] api/scanpy.Neighbors.connectivities reading sources... [ 5%] api/scanpy.Neighbors.distances reading sources... [ 5%] api/scanpy.Neighbors.distances_dpt reading sources... [ 6%] api/scanpy.Neighbors.eigen_basis reading sources... [ 7%] api/scanpy.Neighbors.eigen_values reading sources... [ 7%] api/scanpy.Neighbors.getdoc reading sources... [ 8%] api/scanpy.Neighbors.rp_forest reading sources... [ 9%] api/scanpy.Neighbors.to_igraph reading sources... [ 9%] api/scanpy.Neighbors.transitions reading sources... [ 10%] api/scanpy.Neighbors.transitions_sym reading sources... [ 10%] api/scanpy._settings.ScanpyConfig reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.autosave reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.cache_compression reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.figdir reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 16%] 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... [ 18%] 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... [ 21%] api/scanpy._settings.ScanpyConfig.writedir reading sources... [ 22%] api/scanpy.api reading sources... [ 23%] api/scanpy.datasets.blobs reading sources... [ 23%] api/scanpy.datasets.ebi_expression_atlas reading sources... [ 24%] api/scanpy.datasets.krumsiek11 reading sources... [ 25%] api/scanpy.datasets.moignard15 reading sources... [ 25%] api/scanpy.datasets.paul15 reading sources... [ 26%] api/scanpy.datasets.pbmc3k reading sources... [ 27%] api/scanpy.datasets.pbmc68k_reduced reading sources... [ 27%] api/scanpy.datasets.toggleswitch reading sources... [ 28%] api/scanpy.external reading sources... [ 29%] api/scanpy.get.obs_df reading sources... [ 29%] api/scanpy.get.rank_genes_groups_df reading sources... [ 30%] api/scanpy.get.var_df reading sources... [ 30%] api/scanpy.logging.print_versions reading sources... [ 31%] api/scanpy.pl.clustermap reading sources... [ 32%] api/scanpy.pl.dendrogram reading sources... [ 32%] api/scanpy.pl.diffmap reading sources... [ 33%] api/scanpy.pl.dotplot reading sources... [ 34%] api/scanpy.pl.dpt_groups_pseudotime reading sources... [ 34%] api/scanpy.pl.dpt_timeseries reading sources... [ 35%] api/scanpy.pl.draw_graph reading sources... [ 36%] api/scanpy.pl.embedding reading sources... [ 36%] api/scanpy.pl.embedding_density reading sources... [ 37%] api/scanpy.pl.filter_genes_dispersion reading sources... [ 38%] api/scanpy.pl.heatmap reading sources... [ 38%] api/scanpy.pl.highest_expr_genes reading sources... [ 39%] api/scanpy.pl.highly_variable_genes reading sources... [ 40%] api/scanpy.pl.matrixplot reading sources... [ 40%] api/scanpy.pl.paga reading sources... [ 41%] api/scanpy.pl.paga_compare reading sources... [ 41%] api/scanpy.pl.paga_path reading sources... [ 42%] api/scanpy.pl.pca reading sources... [ 43%] api/scanpy.pl.pca_loadings reading sources... [ 43%] api/scanpy.pl.pca_overview reading sources... [ 44%] api/scanpy.pl.pca_variance_ratio reading sources... [ 45%] api/scanpy.pl.rank_genes_groups reading sources... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot reading sources... [ 46%] api/scanpy.pl.rank_genes_groups_heatmap reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_matrixplot reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin reading sources... [ 48%] api/scanpy.pl.rank_genes_groups_tracksplot reading sources... [ 49%] api/scanpy.pl.rank_genes_groups_violin reading sources... [ 49%] api/scanpy.pl.ranking reading sources... [ 50%] api/scanpy.pl.scatter reading sources... [ 50%] api/scanpy.pl.sim reading sources... [ 51%] api/scanpy.pl.stacked_violin reading sources... [ 52%] api/scanpy.pl.tracksplot reading sources... [ 52%] api/scanpy.pl.tsne reading sources... [ 53%] api/scanpy.pl.umap reading sources... [ 54%] api/scanpy.pl.violin reading sources... [ 54%] api/scanpy.plotting reading sources... [ 55%] api/scanpy.pp.calculate_qc_metrics reading sources... [ 56%] api/scanpy.pp.combat reading sources... [ 56%] api/scanpy.pp.downsample_counts reading sources... [ 57%] api/scanpy.pp.filter_cells reading sources... [ 58%] api/scanpy.pp.filter_genes reading sources... [ 58%] api/scanpy.pp.filter_genes_dispersion reading sources... [ 59%] api/scanpy.pp.highly_variable_genes reading sources... [ 60%] api/scanpy.pp.log1p reading sources... [ 60%] api/scanpy.pp.neighbors reading sources... [ 61%] api/scanpy.pp.normalize_per_cell reading sources... [ 61%] api/scanpy.pp.normalize_total reading sources... [ 62%] api/scanpy.pp.pca reading sources... [ 63%] api/scanpy.pp.recipe_seurat reading sources... [ 63%] api/scanpy.pp.recipe_weinreb17 reading sources... [ 64%] api/scanpy.pp.recipe_zheng17 reading sources... [ 65%] api/scanpy.pp.regress_out reading sources... [ 65%] api/scanpy.pp.scale reading sources... [ 66%] api/scanpy.pp.subsample reading sources... [ 67%] api/scanpy.queries.biomart_annotations reading sources... [ 67%] api/scanpy.queries.enrich reading sources... [ 68%] api/scanpy.queries.gene_coordinates reading sources... [ 69%] api/scanpy.queries.mitochondrial_genes reading sources... [ 69%] api/scanpy.read reading sources... [ 70%] api/scanpy.read_10x_h5 reading sources... [ 70%] api/scanpy.read_10x_mtx reading sources... [ 71%] api/scanpy.read_csv reading sources... [ 72%] api/scanpy.read_excel reading sources... [ 72%] api/scanpy.read_h5ad reading sources... [ 73%] api/scanpy.read_hdf reading sources... [ 74%] api/scanpy.read_loom reading sources... [ 74%] api/scanpy.read_mtx reading sources... [ 75%] api/scanpy.read_text reading sources... [ 76%] api/scanpy.read_umi_tools reading sources... [ 76%] api/scanpy.set_figure_params reading sources... [ 77%] api/scanpy.tl.dendrogram reading sources... [ 78%] api/scanpy.tl.diffmap reading sources... [ 78%] api/scanpy.tl.dpt reading sources... [ 79%] api/scanpy.tl.draw_graph reading sources... [ 80%] api/scanpy.tl.filter_rank_genes_groups reading sources... [ 80%] api/scanpy.tl.leiden reading sources... [ 81%] api/scanpy.tl.louvain reading sources... [ 81%] api/scanpy.tl.marker_gene_overlap reading sources... [ 82%] api/scanpy.tl.paga reading sources... [ 83%] api/scanpy.tl.pca reading sources... [ 83%] api/scanpy.tl.rank_genes_groups reading sources... [ 84%] api/scanpy.tl.score_genes reading sources... [ 85%] api/scanpy.tl.score_genes_cell_cycle reading sources... [ 85%] api/scanpy.tl.sim reading sources... [ 86%] api/scanpy.tl.tsne reading sources... [ 87%] api/scanpy.tl.umap reading sources... [ 87%] basic_usage reading sources... [ 88%] examples reading sources... [ 89%] external/index reading sources... [ 89%] external/scanpy.external.exporting.cellbrowser reading sources... [ 90%] external/scanpy.external.exporting.spring_project reading sources... [ 90%] external/scanpy.external.pl.phate reading sources... [ 91%] external/scanpy.external.pp.bbknn reading sources... [ 92%] external/scanpy.external.pp.dca reading sources... [ 92%] external/scanpy.external.pp.magic reading sources... [ 93%] external/scanpy.external.pp.mnn_correct reading sources... [ 94%] external/scanpy.external.tl.cyclone reading sources... [ 94%] external/scanpy.external.tl.palantir reading sources... [ 95%] external/scanpy.external.tl.phate reading sources... [ 96%] external/scanpy.external.tl.phenograph reading sources... [ 96%] external/scanpy.external.tl.sandbag reading sources... [ 97%] index reading sources... [ 98%] installation reading sources... [ 98%] references reading sources... [ 99%] release_notes reading sources... [100%] tutorials looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 0%] api/index writing output... [ 1%] api/plotting writing output... [ 1%] api/scanpy.Neighbors writing output... [ 2%] api/scanpy.Neighbors.compute_eigen writing output... [ 3%] api/scanpy.Neighbors.compute_neighbors writing output... [ 3%] api/scanpy.Neighbors.compute_transitions writing output... [ 4%] api/scanpy.Neighbors.connectivities writing output... [ 5%] api/scanpy.Neighbors.distances writing output... [ 5%] api/scanpy.Neighbors.distances_dpt writing output... [ 6%] api/scanpy.Neighbors.eigen_basis writing output... [ 7%] api/scanpy.Neighbors.eigen_values writing output... [ 7%] api/scanpy.Neighbors.getdoc writing output... [ 8%] api/scanpy.Neighbors.rp_forest writing output... [ 9%] api/scanpy.Neighbors.to_igraph writing output... [ 9%] api/scanpy.Neighbors.transitions writing output... [ 10%] api/scanpy.Neighbors.transitions_sym writing output... [ 10%] api/scanpy._settings.ScanpyConfig writing output... [ 11%] api/scanpy._settings.ScanpyConfig.autosave writing output... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow writing output... [ 12%] api/scanpy._settings.ScanpyConfig.cache_compression writing output... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir writing output... [ 14%] api/scanpy._settings.ScanpyConfig.categories_to_ignore writing output... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir writing output... [ 15%] api/scanpy._settings.ScanpyConfig.figdir writing output... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_data writing output... [ 16%] 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... [ 18%] 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... [ 21%] api/scanpy._settings.ScanpyConfig.writedir writing output... [ 22%] api/scanpy.api writing output... [ 23%] api/scanpy.datasets.blobs writing output... [ 23%] api/scanpy.datasets.ebi_expression_atlas writing output... [ 24%] api/scanpy.datasets.krumsiek11 writing output... [ 25%] api/scanpy.datasets.moignard15 writing output... [ 25%] api/scanpy.datasets.paul15 writing output... [ 26%] api/scanpy.datasets.pbmc3k writing output... [ 27%] api/scanpy.datasets.pbmc68k_reduced writing output... [ 27%] api/scanpy.datasets.toggleswitch writing output... [ 28%] api/scanpy.external writing output... [ 29%] api/scanpy.get.obs_df writing output... [ 29%] api/scanpy.get.rank_genes_groups_df writing output... [ 30%] api/scanpy.get.var_df writing output... [ 30%] api/scanpy.logging.print_versions writing output... [ 31%] api/scanpy.pl.clustermap writing output... [ 32%] api/scanpy.pl.dendrogram writing output... [ 32%] api/scanpy.pl.diffmap writing output... [ 33%] api/scanpy.pl.dotplot writing output... [ 34%] api/scanpy.pl.dpt_groups_pseudotime writing output... [ 34%] api/scanpy.pl.dpt_timeseries writing output... [ 35%] api/scanpy.pl.draw_graph writing output... [ 36%] api/scanpy.pl.embedding writing output... [ 36%] api/scanpy.pl.embedding_density writing output... [ 37%] api/scanpy.pl.filter_genes_dispersion writing output... [ 38%] api/scanpy.pl.heatmap writing output... [ 38%] api/scanpy.pl.highest_expr_genes writing output... [ 39%] api/scanpy.pl.highly_variable_genes writing output... [ 40%] api/scanpy.pl.matrixplot writing output... [ 40%] api/scanpy.pl.paga writing output... [ 41%] api/scanpy.pl.paga_compare writing output... [ 41%] api/scanpy.pl.paga_path writing output... [ 42%] api/scanpy.pl.pca writing output... [ 43%] api/scanpy.pl.pca_loadings writing output... [ 43%] api/scanpy.pl.pca_overview writing output... [ 44%] api/scanpy.pl.pca_variance_ratio writing output... [ 45%] api/scanpy.pl.rank_genes_groups writing output... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot writing output... [ 46%] api/scanpy.pl.rank_genes_groups_heatmap writing output... [ 47%] api/scanpy.pl.rank_genes_groups_matrixplot writing output... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin writing output... [ 48%] api/scanpy.pl.rank_genes_groups_tracksplot writing output... [ 49%] api/scanpy.pl.rank_genes_groups_violin writing output... [ 49%] api/scanpy.pl.ranking writing output... [ 50%] api/scanpy.pl.scatter writing output... [ 50%] api/scanpy.pl.sim writing output... [ 51%] api/scanpy.pl.stacked_violin writing output... [ 52%] api/scanpy.pl.tracksplot writing output... [ 52%] api/scanpy.pl.tsne writing output... [ 53%] api/scanpy.pl.umap writing output... [ 54%] api/scanpy.pl.violin writing output... [ 54%] api/scanpy.plotting writing output... [ 55%] api/scanpy.pp.calculate_qc_metrics writing output... [ 56%] api/scanpy.pp.combat writing output... [ 56%] api/scanpy.pp.downsample_counts writing output... [ 57%] api/scanpy.pp.filter_cells writing output... [ 58%] api/scanpy.pp.filter_genes writing output... [ 58%] api/scanpy.pp.filter_genes_dispersion writing output... [ 59%] api/scanpy.pp.highly_variable_genes writing output... [ 60%] api/scanpy.pp.log1p writing output... [ 60%] api/scanpy.pp.neighbors writing output... [ 61%] api/scanpy.pp.normalize_per_cell writing output... [ 61%] api/scanpy.pp.normalize_total writing output... [ 62%] api/scanpy.pp.pca writing output... [ 63%] api/scanpy.pp.recipe_seurat writing output... [ 63%] api/scanpy.pp.recipe_weinreb17 writing output... [ 64%] api/scanpy.pp.recipe_zheng17 writing output... [ 65%] api/scanpy.pp.regress_out writing output... [ 65%] api/scanpy.pp.scale writing output... [ 66%] api/scanpy.pp.subsample writing output... [ 67%] api/scanpy.queries.biomart_annotations writing output... [ 67%] api/scanpy.queries.enrich writing output... [ 68%] api/scanpy.queries.gene_coordinates writing output... [ 69%] api/scanpy.queries.mitochondrial_genes writing output... [ 69%] api/scanpy.read writing output... [ 70%] api/scanpy.read_10x_h5 writing output... [ 70%] api/scanpy.read_10x_mtx writing output... [ 71%] api/scanpy.read_csv writing output... [ 72%] api/scanpy.read_excel writing output... [ 72%] api/scanpy.read_h5ad writing output... [ 73%] api/scanpy.read_hdf writing output... [ 74%] api/scanpy.read_loom writing output... [ 74%] api/scanpy.read_mtx writing output... [ 75%] api/scanpy.read_text writing output... [ 76%] api/scanpy.read_umi_tools writing output... [ 76%] api/scanpy.set_figure_params writing output... [ 77%] api/scanpy.tl.dendrogram writing output... [ 78%] api/scanpy.tl.diffmap writing output... [ 78%] api/scanpy.tl.dpt writing output... [ 79%] api/scanpy.tl.draw_graph writing output... [ 80%] api/scanpy.tl.filter_rank_genes_groups writing output... [ 80%] api/scanpy.tl.leiden writing output... [ 81%] api/scanpy.tl.louvain writing output... [ 81%] api/scanpy.tl.marker_gene_overlap writing output... [ 82%] api/scanpy.tl.paga writing output... [ 83%] api/scanpy.tl.pca writing output... [ 83%] api/scanpy.tl.rank_genes_groups writing output... [ 84%] api/scanpy.tl.score_genes writing output... [ 85%] api/scanpy.tl.score_genes_cell_cycle writing output... [ 85%] api/scanpy.tl.sim writing output... [ 86%] api/scanpy.tl.tsne writing output... [ 87%] api/scanpy.tl.umap writing output... [ 87%] basic_usage writing output... [ 88%] examples writing output... [ 89%] external/index writing output... [ 89%] external/scanpy.external.exporting.cellbrowser writing output... [ 90%] external/scanpy.external.exporting.spring_project writing output... [ 90%] external/scanpy.external.pl.phate writing output... [ 91%] external/scanpy.external.pp.bbknn writing output... [ 92%] external/scanpy.external.pp.dca writing output... [ 92%] external/scanpy.external.pp.magic writing output... [ 93%] external/scanpy.external.pp.mnn_correct writing output... [ 94%] external/scanpy.external.tl.cyclone writing output... [ 94%] external/scanpy.external.tl.palantir writing output... [ 95%] external/scanpy.external.tl.phate writing output... [ 96%] external/scanpy.external.tl.phenograph writing output... [ 96%] external/scanpy.external.tl.sandbag writing output... [ 97%] index writing output... [ 98%] installation writing output... [ 98%] references writing output... [ 99%] release_notes writing output... [100%] tutorials generating indices... genindex py-modindexdone writing additional pages... searchdone copying images... [ 11%] api/scanpy.pl.dotplot.png copying images... [ 22%] api/scanpy.pl.heatmap.png copying images... [ 33%] api/scanpy.pl.matrixplot.png copying images... [ 44%] api/scanpy.pl.rank_genes_groups_dotplot.png copying images... [ 55%] api/scanpy.pl.rank_genes_groups_heatmap.png copying images... [ 66%] api/scanpy.pl.rank_genes_groups_matrixplot.png copying images... [ 77%] api/scanpy.pl.rank_genes_groups_stacked_violin.png copying images... [ 88%] api/scanpy.pl.stacked_violin.png copying images... [100%] api/scanpy.pl.violin.png copying static files... ... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors warnings.warn('"%s" is shallow and may cause errors' % (wd.path,)) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a