Read the Docs build information Build id: 473145 Project: icb-scanpy Version: 959 Commit: 6b971113bc96814fbd3cb90b6a5da2725645848c Date: 2020-11-06T20:28:38.328767Z State: finished Success: False [rtd-command-info] start-time: 2020-11-06T20:28:40.971829Z, end-time: 2020-11-06T20:28:43.395745Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2020-11-06T20:28:43.504165Z, end-time: 2020-11-06T20:28:44.112651Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/959/head:external-959 From https://github.com/theislab/scanpy * [new ref] refs/pull/959/head -> external-959 [rtd-command-info] start-time: 2020-11-06T20:28:45.241998Z, end-time: 2020-11-06T20:28:45.426254Z, duration: 0, exit-code: 0 git checkout --force 6b971113bc96814fbd3cb90b6a5da2725645848c Note: checking out '6b971113bc96814fbd3cb90b6a5da2725645848c'. 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 6b97111 Merge branch 'master' into score_layers [rtd-command-info] start-time: 2020-11-06T20:28:46.412109Z, end-time: 2020-11-06T20:28:46.464049Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-11-06T20:28:48.436735Z, end-time: 2020-11-06T20:28:52.721375Z, duration: 4, exit-code: 0 python3.6 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.6.12' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-11-06T20:28:52.837963Z, end-time: 2020-11-06T20:28:53.596898Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (20.2.4) [rtd-command-info] start-time: 2020-11-06T20:28:53.992323Z, end-time: 2020-11-06T20:29:02.660048Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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<2.2 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 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-2.1.1-py2.py3-none-any.whl (13 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.2-py3-none-any.whl (948 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 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) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2020.4-py2.py3-none-any.whl (509 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=6987211c5fd5ef300bf2e3195acec024e3c73fd159ccb6fb7c5db3dec1ebbfa5 Stored in directory: /tmp/pip-ephem-wheel-cache-1s28avns/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b 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=2fb43ea38b0d4a53078b7c77d1be618f22d6618379a2026ce3a271ce89bb6f51 Stored in directory: /tmp/pip-ephem-wheel-cache-1s28avns/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, chardet, urllib3, certifi, idna, requests, six, pyparsing, packaging, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, Pygments, snowballstemmer, imagesize, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.2 Uninstalling setuptools-50.3.2: Successfully uninstalled setuptools-50.3.2 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.11 [rtd-command-info] start-time: 2020-11-06T20:29:02.915048Z, end-time: 2020-11-06T20:29:35.388920Z, duration: 32, 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/959 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-0.51.2-cp36-cp36m-manylinux2014_x86_64.whl (3.1 MB) Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from scanpy==0.1.dev149+g6b97111) (20.4) Collecting legacy-api-wrap Downloading legacy_api_wrap-1.2-py3-none-any.whl (37 kB) Collecting joblib Downloading joblib-0.17.0-py3-none-any.whl (301 kB) Collecting networkx>=2.3 Downloading networkx-2.5-py3-none-any.whl (1.6 MB) Collecting patsy Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting tqdm Downloading tqdm-4.51.0-py2.py3-none-any.whl (70 kB) Collecting tables Downloading tables-3.6.1-cp36-cp36m-manylinux1_x86_64.whl (4.3 MB) Collecting h5py>=2.10.0 Downloading h5py-3.1.0-cp36-cp36m-manylinux1_x86_64.whl (4.0 MB) Collecting matplotlib>=3.1.2 Downloading matplotlib-3.3.2-cp36-cp36m-manylinux1_x86_64.whl (11.6 MB) Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.12.1-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB) Collecting anndata>=0.7 Downloading anndata-0.7.4-py3-none-any.whl (118 kB) Collecting umap-learn>=0.3.10 Downloading umap-learn-0.4.6.tar.gz (69 kB) Collecting sinfo Downloading sinfo-0.3.1.tar.gz (23 kB) Collecting scipy>=1.4 Downloading scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB) Collecting seaborn Downloading seaborn-0.11.0-py3-none-any.whl (283 kB) Collecting numpy>=1.17.0 Downloading numpy-1.19.4-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB) Collecting pandas>=0.21 Downloading pandas-1.1.4-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB) Collecting importlib-metadata>=0.7; python_version < "3.8" Downloading importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB) Collecting natsort Downloading natsort-7.0.1-py3-none-any.whl (33 kB) Collecting scikit-learn>=0.21.2 Downloading scikit_learn-0.23.2-cp36-cp36m-manylinux1_x86_64.whl (6.8 MB) Collecting sphinx-autodoc-typehints; extra == "doc" Downloading sphinx_autodoc_typehints-1.11.1-py3-none-any.whl (8.7 kB) Collecting scanpydoc>=0.5; extra == "doc" Downloading scanpydoc-0.5.5-py3-none-any.whl (28 kB) Collecting sphinx<3.1,>3; extra == "doc" Downloading Sphinx-3.0.4-py3-none-any.whl (2.8 MB) Collecting sphinx-rtd-theme>=0.3.1; extra == "doc" Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB) Collecting typing-extensions; python_version < "3.8" and extra == "doc" Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB) Collecting llvmlite<0.35,>=0.34.0.dev0 Downloading llvmlite-0.34.0-cp36-cp36m-manylinux2010_x86_64.whl (24.6 MB) Collecting setuptools Downloading setuptools-50.3.2-py3-none-any.whl (785 kB) Requirement already up-to-date: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from packaging->scanpy==0.1.dev149+g6b97111) (1.15.0) Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from packaging->scanpy==0.1.dev149+g6b97111) (2.4.7) Collecting get-version>=2.0.4 Downloading get_version-2.1-py3-none-any.whl (43 kB) Collecting decorator>=4.3.0 Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting numexpr>=2.6.2 Downloading numexpr-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (162 kB) Collecting cached-property; python_version < "3.8" Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting pillow>=6.2.0 Downloading Pillow-8.0.1-cp36-cp36m-manylinux1_x86_64.whl (2.2 MB) 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) Requirement already up-to-date: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from matplotlib>=3.1.2->scanpy==0.1.dev149+g6b97111) (2020.6.20) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Collecting stdlib_list Downloading stdlib_list-0.7.0-py3-none-any.whl (60 kB) Requirement already up-to-date: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from pandas>=0.21->scanpy==0.1.dev149+g6b97111) (2020.4) Collecting zipp>=0.5 Downloading zipp-3.4.0-py3-none-any.whl (5.2 kB) Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (2.11.2) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already up-to-date: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (1.1.4) Collecting docutils>=0.12 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already up-to-date: Pygments>=2.0 in 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sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (2.24.0) Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (1.2.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (1.1.1) Requirement already up-to-date: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (2.10) Requirement already up-to-date: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (1.25.11) Requirement already up-to-date: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev149+g6b97111) (3.0.4) Building wheels for collected packages: scanpy, umap-learn, sinfo Building wheel for scanpy (PEP 517): started Building wheel for scanpy (PEP 517): finished with status 'done' Created wheel for scanpy: filename=scanpy-0.1.dev149+g6b97111-py3-none-any.whl size=10143526 sha256=a520344bb010178239740a1091bf942db9a5a3a3650f23479d67d28a69e17929 Stored in directory: /tmp/pip-ephem-wheel-cache-jqr6jhs9/wheels/70/9b/ae/5a6b637c58fbf64fa5fa9054813e89d533d4b3dcbf151d14ef 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-0.4.6-py3-none-any.whl size=67950 sha256=fd80d96fc50420643be54bd6ee811329411f154f090b86eaef20cd091592ba83 Stored in directory: /tmp/pip-ephem-wheel-cache-jqr6jhs9/wheels/22/ce/3d/75f6600b4d93c851021aceeec51b7b330c0ad4d9692e69be6a 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=e3ab30a09832ca34ed424382480ee2593d336d6fc47e0b2b533754b511a3cb83 Stored in directory: /tmp/pip-ephem-wheel-cache-jqr6jhs9/wheels/f3/57/7c/26afb068dd34e984706ae3b99ef4145c76afcdb8070b4f1244 Successfully built scanpy umap-learn sinfo Installing collected packages: llvmlite, numpy, setuptools, numba, get-version, legacy-api-wrap, joblib, decorator, networkx, patsy, tqdm, numexpr, tables, cached-property, h5py, pillow, python-dateutil, cycler, kiwisolver, matplotlib, pandas, scipy, statsmodels, zipp, importlib-metadata, natsort, anndata, threadpoolctl, scikit-learn, umap-learn, stdlib-list, sinfo, seaborn, sphinxcontrib-devhelp, docutils, sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinx, sphinx-autodoc-typehints, scanpydoc, sphinx-rtd-theme, typing-extensions, 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-0.7.4 cached-property-1.5.2 cycler-0.10.0 decorator-4.4.2 docutils-0.16 get-version-2.1 h5py-3.1.0 importlib-metadata-2.0.0 joblib-0.17.0 kiwisolver-1.3.1 legacy-api-wrap-1.2 llvmlite-0.34.0 matplotlib-3.3.2 natsort-7.0.1 networkx-2.5 numba-0.51.2 numexpr-2.7.1 numpy-1.19.4 pandas-1.1.4 patsy-0.5.1 pillow-8.0.1 python-dateutil-2.8.1 scanpy-0.1.dev149+g6b97111 scanpydoc-0.5.5 scikit-learn-0.23.2 scipy-1.5.4 seaborn-0.11.0 setuptools-50.3.2 sinfo-0.3.1 sphinx-3.0.4 sphinx-autodoc-typehints-1.11.1 sphinx-rtd-theme-0.5.0 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-0.12.1 stdlib-list-0.7.0 tables-3.6.1 threadpoolctl-2.1.0 tqdm-4.51.0 typing-extensions-3.7.4.3 umap-learn-0.4.6 zipp-3.4.0 [rtd-command-info] start-time: 2020-11-06T20:29:36.862619Z, end-time: 2020-11-06T20:29:36.932823Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys import warnings from pathlib import Path from datetime import datetime import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '2.0' # Nicer param docs suppress_warnings = ['ref.citation'] # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('http://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), scvelo=('https://scvelo.readthedocs.io/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = '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'), ] ########################################################################### # 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': "959", 'version_slug': "959", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("1.4.4.post1", "/en/1.4.4.post1/"), ("1.1", "/en/1.1/"), ], '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': '6b971113bc96814fbd3cb90b6a5da2725645848c', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '6b971113bc96814fbd3cb90b6a5da2725645848c', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '6b971113bc96814fbd3cb90b6a5da2725645848c', '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': '6b971113', } 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 'external' == '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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-11-06T20:29:37.199790Z, end-time: 2020-11-06T20:29:43.339024Z, duration: 6, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.0.4 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/config.py", line 319, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile_ exec(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/959/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/959/scanpy/__init__.py", line 11, in from . import tools as tl File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/959/scanpy/tools/__init__.py", line 18, in from ._score_genes import score_genes, score_genes_cell_cycle File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/959/scanpy/tools/_score_genes.py", line 146 else: ^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/cmd/build.py", line 279, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/application.py", line 218, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/config.py", line 174, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/959/lib/python3.6/site-packages/sphinx/config.py", line 322, in eval_config_file raise ConfigError(msg % err) sphinx.errors.ConfigError: There is a syntax error in your configuration file: invalid syntax (_score_genes.py, line 146) Configuration error: There is a syntax error in your configuration file: invalid syntax (_score_genes.py, line 146)