Read the Docs build information Build id: 570676 Project: icb-scanpy Version: latest Commit: cf2e5671bc235b18754ca8d9cf70ae84b6182f1c Date: 2021-02-23T19:03:46.383937Z State: finished Success: True [rtd-command-info] start-time: 2021-02-23T19:03:47.871540Z, end-time: 2021-02-23T19:03:50.992545Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2021-02-23T19:03:51.430031Z, end-time: 2021-02-23T19:03:51.605019Z, 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 cf2e5671 Drop passing of **kwds (#1655) [rtd-command-info] start-time: 2021-02-23T19:03:51.709564Z, end-time: 2021-02-23T19:03:51.770002Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-02-23T19:03:52.851287Z, end-time: 2021-02-23T19:04:11.035759Z, duration: 18, exit-code: 0 python3.8 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.8 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: 2021-02-23T19:04:11.160935Z, end-time: 2021-02-23T19:04:12.757942Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools==41.0.1 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (21.0.1) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 53.0.0 Uninstalling setuptools-53.0.0: Successfully uninstalled setuptools-53.0.0 Successfully installed setuptools-41.0.1 [rtd-command-info] start-time: 2021-02-23T19:04:12.912782Z, end-time: 2021-02-23T19:04:45.599115Z, duration: 32, exit-code: 0 python -m pip install --upgrade --no-cache-dir docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.3-py2.py3-none-any.whl (11 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Pygments>=2.0 Downloading Pygments-2.8.0-py3-none-any.whl (983 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx<2) (41.0.1) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux2010_x86_64.whl (32 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.3-py2.py3-none-any.whl (137 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Building wheels for collected packages: mock, pillow, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=3911297208d1fa7d002adf85e0afc6635ea7e29ea7ef570d81c9ad854c2a3dd7 Stored in directory: /tmp/pip-ephem-wheel-cache-qg6e594z/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1259960 sha256=87953b0239724bb909451103330bc8c2f701dda70c916635dee70f8de3cca412 Stored in directory: /tmp/pip-ephem-wheel-cache-qg6e594z/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=12f479ba4dcb7a2ffe3dd2e8cbac1ff63b53d4ebeae30cba3b6fa2e1fbd0afa9 Stored in directory: /tmp/pip-ephem-wheel-cache-qg6e594z/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.0 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.3 recommonmark-0.5.0 requests-2.25.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.3 [rtd-command-info] start-time: 2021-02-23T19:04:45.733950Z, end-time: 2021-02-23T19:05:25.596374Z, duration: 39, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting numba>=0.41.0 Downloading numba-0.52.0-cp38-cp38-manylinux2014_x86_64.whl (3.2 MB) Collecting patsy Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting joblib Downloading joblib-1.0.1-py3-none-any.whl (303 kB) Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl (9.4 MB) Collecting tables Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB) Collecting networkx>=2.3 Downloading networkx-2.5-py3-none-any.whl (1.6 MB) Collecting h5py>=2.10.0 Downloading h5py-3.1.0-cp38-cp38-manylinux1_x86_64.whl (4.4 MB) Collecting natsort Downloading natsort-7.1.1-py3-none-any.whl (35 kB) Collecting scikit-learn>=0.21.2 Downloading scikit_learn-0.24.1-cp38-cp38-manylinux2010_x86_64.whl (24.9 MB) Collecting sinfo Downloading sinfo-0.3.1.tar.gz (23 kB) Collecting pandas>=0.21 Downloading pandas-1.2.2-cp38-cp38-manylinux1_x86_64.whl (9.7 MB) Collecting legacy-api-wrap Downloading legacy_api_wrap-1.2-py3-none-any.whl (37 kB) Collecting anndata>=0.7.4 Downloading anndata-0.7.5-py3-none-any.whl (119 kB) Collecting numpy>=1.17.0 Downloading numpy-1.20.1-cp38-cp38-manylinux2010_x86_64.whl (15.4 MB) Collecting scipy>=1.4 Downloading scipy-1.6.1-cp38-cp38-manylinux1_x86_64.whl (27.3 MB) Collecting matplotlib>=3.1.2 Downloading matplotlib-3.3.4-cp38-cp38-manylinux1_x86_64.whl (11.6 MB) Collecting tqdm Downloading tqdm-4.57.0-py2.py3-none-any.whl (72 kB) Collecting umap-learn>=0.3.10 Downloading umap-learn-0.5.1.tar.gz (80 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from scanpy==1.8.0.dev34+gcf2e5671) (20.9) Collecting seaborn Downloading seaborn-0.11.1-py3-none-any.whl (285 kB) Requirement already satisfied: sphinx-rtd-theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from scanpy==1.8.0.dev34+gcf2e5671) (0.4.3) Collecting sphinx-rtd-theme>=0.3.1 Downloading sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl (2.8 MB) Collecting sphinx-autodoc-typehints Downloading sphinx_autodoc_typehints-1.11.1-py3-none-any.whl (8.7 kB) Collecting scanpydoc>=0.5 Downloading scanpydoc-0.5.6-py3-none-any.whl (28 kB) Collecting sphinx>=3.2 Downloading Sphinx-3.5.1-py3-none-any.whl (2.8 MB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from matplotlib>=3.1.2->scanpy==1.8.0.dev34+gcf2e5671) (2.4.7) Collecting python-dateutil>=2.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting pillow>=6.2.0 Downloading Pillow-8.1.0-cp38-cp38-manylinux1_x86_64.whl (2.2 MB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from cycler>=0.10->matplotlib>=3.1.2->scanpy==1.8.0.dev34+gcf2e5671) (1.15.0) Collecting decorator>=4.3.0 Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from numba>=0.41.0->scanpy==1.8.0.dev34+gcf2e5671) (41.0.1) Collecting setuptools Downloading setuptools-53.0.0-py3-none-any.whl (784 kB) Collecting llvmlite<0.36,>=0.35.0 Downloading llvmlite-0.35.0-cp38-cp38-manylinux2010_x86_64.whl (25.3 MB) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from pandas>=0.21->scanpy==1.8.0.dev34+gcf2e5671) (2021.1) Collecting get_version Downloading get_version-2.1-py3-none-any.whl (43 kB) Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (2.8.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (2.1.0) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (2.9.0) Requirement already satisfied: Jinja2>=2.3 in 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sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (1.1.4) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (0.14) Collecting docutils>=0.12 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (1.1.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (1.26.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (2020.12.5) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (2.10) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev34+gcf2e5671) (4.0.0) Collecting pynndescent>=0.5 Downloading pynndescent-0.5.2.tar.gz (1.1 MB) Collecting stdlib_list Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB) Collecting numexpr>=2.6.2 Downloading numexpr-2.7.2-cp38-cp38-manylinux2010_x86_64.whl (472 kB) Building wheels for collected packages: scanpy, umap-learn, pynndescent, sinfo Building wheel for scanpy (PEP 517): started Building wheel for scanpy (PEP 517): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.8.0.dev34+gcf2e5671-py3-none-any.whl size=10260058 sha256=6d26d93677d8fe4194f3ff8ae409e894e2670ef4f497efd0607393b4b46f677c Stored in directory: /tmp/pip-ephem-wheel-cache-cutfyg0t/wheels/3b/59/52/933b5c7bcaabc49289abbc1d71f859ce119211165023059b98 Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.1-py3-none-any.whl size=76566 sha256=728ccb7243871dd723cd180635d48de369792ccf042ac593d9c3f7cccbed526e Stored in directory: /tmp/pip-ephem-wheel-cache-cutfyg0t/wheels/95/85/b7/b4b7040e49367b6d1505d7e8fb57e3e79b22fa6ac26f72520b Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.2-py3-none-any.whl size=51347 sha256=6aa867c6f6c8e05bc5fbef4c98f6e1865e69dfb69969e9a4671ea605369bca77 Stored in directory: /tmp/pip-ephem-wheel-cache-cutfyg0t/wheels/bb/81/5d/c78c8f15f3c815197129f91ec435d8ae0bb0a7a856d962c3ce Building wheel for sinfo (setup.py): started Building wheel for sinfo (setup.py): finished with status 'done' Created wheel for sinfo: filename=sinfo-0.3.1-py3-none-any.whl size=7016 sha256=4debe0e79610b79f475adbf01d14010016c22e3a7f98efa1ff46dc59fc0f5968 Stored in directory: /tmp/pip-ephem-wheel-cache-cutfyg0t/wheels/b0/57/9c/707469c51dbe9a69ad875a1a3faca170da471308c1e4c22ce0 Successfully built scanpy umap-learn pynndescent sinfo Installing collected packages: numpy, threadpoolctl, setuptools, scipy, llvmlite, joblib, scikit-learn, python-dateutil, pillow, numba, kiwisolver, cycler, stdlib-list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pynndescent, patsy, pandas, numexpr, natsort, matplotlib, h5py, get-version, docutils, decorator, umap-learn, tqdm, tables, statsmodels, sphinx, sinfo, seaborn, networkx, legacy-api-wrap, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpydoc, scanpy Attempting uninstall: setuptools Found existing installation: setuptools 41.0.1 Uninstalling setuptools-41.0.1: Successfully uninstalled setuptools-41.0.1 Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: docutils Found existing installation: docutils 0.14 Uninstalling docutils-0.14: Successfully uninstalled docutils-0.14 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed anndata-0.7.5 cycler-0.10.0 decorator-4.4.2 docutils-0.16 get-version-2.1 h5py-3.1.0 joblib-1.0.1 kiwisolver-1.3.1 legacy-api-wrap-1.2 llvmlite-0.35.0 matplotlib-3.3.4 natsort-7.1.1 networkx-2.5 numba-0.52.0 numexpr-2.7.2 numpy-1.20.1 pandas-1.2.2 patsy-0.5.1 pillow-8.1.0 pynndescent-0.5.2 python-dateutil-2.8.1 scanpy-1.8.0.dev34+gcf2e5671 scanpydoc-0.5.6 scikit-learn-0.24.1 scipy-1.6.1 seaborn-0.11.1 setuptools-53.0.0 sinfo-0.3.1 sphinx-3.5.1 sphinx-autodoc-typehints-1.11.1 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.12.2 stdlib-list-0.8.0 tables-3.6.1 threadpoolctl-2.1.0 tqdm-4.57.0 umap-learn-0.5.1 [rtd-command-info] start-time: 2021-02-23T19:05:26.492750Z, end-time: 2021-02-23T19:05:26.550787Z, 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', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('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), pytest=('https://docs.pytest.org/en/latest/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'scanpydoc' html_theme_options = dict(navigation_depth=4, logo_only=True) # 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 # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", # If the docs are built with an old version of numpy, this will make it work: "numpy.random.RandomState": "numpy.random.mtrand.RandomState", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.plotting._utils._AxesSubplot'), ('py:class', 'scanpy._utils.Empty'), ('py:class', 'numpy.random.mtrand.RandomState'), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # 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://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("1.7.0rc1", "/en/1.7.0rc1/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy.readthedocs.io/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'cf2e5671', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/570676/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-02-23T19:05:26.680243Z, end-time: 2021-02-23T19:08:12.279937Z, duration: 165, exit-code: 0 python -m sphinx -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.5.1 Matplotlib is building the font cache; this may take a moment. 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.pytest.org/en/latest/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... intersphinx inventory has moved: https://networkx.github.io/documentation/networkx-1.10/objects.inv -> https://networkx.org/documentation/networkx-1.10/objects.inv loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... intersphinx inventory has moved: http://docs.h5py.org/en/stable/objects.inv -> https://docs.h5py.org/en/stable/objects.inv loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv [autosummary] generating autosummary for: _key_contributors.rst, api/index.rst, api/plotting.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, contributors.rst, dev/ci.rst, dev/code.rst, dev/documentation.rst, ..., release-notes/1.5.0.rst, release-notes/1.5.1.rst, release-notes/1.6.0.rst, release-notes/1.7.0.rst, release-notes/1.7.1.rst, release-notes/1.8.0.rst, release-notes/index.rst, release-notes/release-latest.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.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.harmony_timeseries.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.palantir_results.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.sam.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, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.wishbone.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.pl.StackedViolin.add_dendrogram.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.add_totals.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.get_axes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.legend.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.make_figure.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.savefig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.show.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.style.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.StackedViolin.swap_axes.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 58 source files that are out of date updating environment: [new config] 307 added, 0 changed, 0 removed reading sources... 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