Read the Docs build information Build id: 787793 Project: icb-scanpy Version: latest Commit: 16e62d1336a95966238113cdb5ab50f7d9f880ce Date: 2021-12-01T18:05:04.189554Z State: finished Success: True [rtd-command-info] start-time: 2021-12-01T18:05:05.586804Z, end-time: 2021-12-01T18:05:08.658809Z, 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: 2021-12-01T18:05:08.820685Z, end-time: 2021-12-01T18:05:09.032640Z, 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 16e62d13 [pre-commit.ci] pre-commit autoupdate (#2056) [rtd-command-info] start-time: 2021-12-01T18:05:09.154140Z, end-time: 2021-12-01T18:05:09.222462Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-12-01T18:05:10.237668Z, end-time: 2021-12-01T18:05:14.409412Z, duration: 4, 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: 2021-12-01T18:05:14.528610Z, end-time: 2021-12-01T18:05:16.242637Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (21.3.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 59.4.0 Uninstalling setuptools-59.4.0: Successfully uninstalled setuptools-59.4.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2021-12-01T18:05:16.364832Z, end-time: 2021-12-01T18:05:41.896620Z, duration: 25, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' 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-1.8.6-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-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 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) (58.2.0) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.8-py3-none-any.whl (39 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.6-py3-none-any.whl (97 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 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=23772 sha256=c87a658a67367c4a5637fc4af73b417ee12da3268a4b897df2de933eb39678aa Stored in directory: /tmp/pip-ephem-wheel-cache-b92ze0gz/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=1259953 sha256=d8033f36fdd4c3e766e1797d19499fc4e20e480ad14b704a19ca530a150cef48 Stored in directory: /tmp/pip-ephem-wheel-cache-b92ze0gz/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=491070 sha256=74bfa1685c9e9e6b161cd6ec2601583428b3c1a6c784f96a5fdcc29ec23cead6 Stored in directory: /tmp/pip-ephem-wheel-cache-b92ze0gz/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, 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 Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.8 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.6 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-12-01T18:05:42.023604Z, end-time: 2021-12-01T18:07:03.777678Z, duration: 81, 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' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy>=1.17.0 Downloading numpy-1.21.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting tables Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB) Collecting tqdm Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB) Collecting umap-learn>=0.3.10 Downloading umap-learn-0.5.2.tar.gz (86 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from scanpy==1.9.0.dev36+g16e62d13) (21.3) Collecting pandas>=0.21 Downloading pandas-1.3.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB) Collecting h5py>=2.10.0 Downloading h5py-3.6.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting matplotlib>=3.1.2 Downloading matplotlib-3.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.3 MB) Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.13.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB) Collecting joblib Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB) Collecting natsort Downloading natsort-8.0.0-py3-none-any.whl (37 kB) Collecting patsy Downloading patsy-0.5.2-py2.py3-none-any.whl (233 kB) Collecting anndata>=0.7.4 Downloading anndata-0.7.8-py3-none-any.whl (91 kB) Collecting scikit-learn>=0.22 Downloading scikit_learn-1.0.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (25.9 MB) Collecting networkx>=2.3 Downloading networkx-2.6.3-py3-none-any.whl (1.9 MB) Collecting scipy>=1.4 Downloading scipy-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 MB) Collecting sinfo Downloading sinfo-0.3.4.tar.gz (24 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting numba>=0.41.0 Downloading numba-0.54.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB) Collecting seaborn Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) Requirement already satisfied: sphinx-rtd-theme>=0.3.1 in 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requests>=2.5.0->sphinx<4.2,>=4.1->scanpy==1.9.0.dev36+g16e62d13) (3.3) Collecting tomli>=1.0.0 Downloading tomli-1.2.2-py3-none-any.whl (12 kB) Collecting dunamai Downloading dunamai-1.7.0-py3-none-any.whl (16 kB) Building wheels for collected packages: umap-learn, python-igraph, scanpy, sinfo, pynndescent 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-0.5.2-py3-none-any.whl size=82709 sha256=ad228c06f8ca7838b9fc21d05e117276c6fd99ff5e663f61683b00d11765c7c4 Stored in directory: /tmp/pip-ephem-wheel-cache-jn0jwtiy/wheels/f2/64/75/df601da9514261c8cb0830b9515d2b94b5a51f09ddeae92b9e Building wheel for python-igraph (setup.py): started Building wheel for python-igraph (setup.py): finished with status 'done' Created wheel for python-igraph: filename=python_igraph-0.9.8-py3-none-any.whl size=9070 sha256=b1d6b3e33467a5053c375bd8e71edf281c4ee9e844e6d5c46c56f8aa1a803869 Stored in directory: /tmp/pip-ephem-wheel-cache-jn0jwtiy/wheels/f9/14/00/acd6e2e744895a9833123220e47f6f947a423f26e66fc9e4fd Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.9.0.dev36+g16e62d13-py3-none-any.whl size=11404848 sha256=3aa8011b3aa893b5b3cb7858372e9674775917a80b3a394ab5882d42bc65f64a Stored in directory: /tmp/pip-ephem-wheel-cache-jn0jwtiy/wheels/3b/59/52/933b5c7bcaabc49289abbc1d71f859ce119211165023059b98 Building wheel for sinfo (setup.py): started Building wheel for sinfo (setup.py): finished with status 'done' Created wheel for sinfo: filename=sinfo-0.3.4-py3-none-any.whl size=7899 sha256=ae807a89d9282191efd35d925d00509535131764ea55081b9c12116cb2e957e8 Stored in directory: /tmp/pip-ephem-wheel-cache-jn0jwtiy/wheels/0e/63/be/1333921ddb5d249efe6db671c36608e46593e018994c3be11d Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.5-py3-none-any.whl size=52603 sha256=008828364cca30c654eea06400fd3f34b4ab312d949b2d35b04bd7cff7bc560e Stored in directory: /tmp/pip-ephem-wheel-cache-jn0jwtiy/wheels/e4/0e/b5/07c0c231aacb04e5d1046fe7459bb27ea79f95b5edbe88e435 Successfully built umap-learn python-igraph scanpy sinfo pynndescent Installing collected packages: numpy, tomli, threadpoolctl, setuptools, scipy, llvmlite, joblib, setuptools-scm, scikit-learn, python-dateutil, pillow, numba, kiwisolver, fonttools, cycler, xlrd, tqdm, texttable, stdlib-list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pynndescent, patsy, pandas, numexpr, natsort, matplotlib, h5py, dunamai, umap-learn, tables, statsmodels, sphinx, sinfo, seaborn, networkx, igraph, get-version, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpydoc, scanpy, python-igraph Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 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-0.7.8 cycler-0.11.0 dunamai-1.7.0 fonttools-4.28.2 get-version-3.5.3 h5py-3.6.0 igraph-0.9.8 joblib-1.1.0 kiwisolver-1.3.2 llvmlite-0.37.0 matplotlib-3.5.0 natsort-8.0.0 networkx-2.6.3 numba-0.54.1 numexpr-2.7.3 numpy-1.20.3 pandas-1.3.4 patsy-0.5.2 pillow-8.4.0 pynndescent-0.5.5 python-dateutil-2.8.2 python-igraph-0.9.8 scanpy-1.9.0.dev36+g16e62d13 scanpydoc-0.7.3 scikit-learn-1.0.1 scipy-1.7.3 seaborn-0.11.2 setuptools-59.4.0 setuptools-scm-6.3.2 sinfo-0.3.4 sphinx-4.1.2 sphinx-autodoc-typehints-1.12.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.13.1 stdlib-list-0.8.0 tables-3.6.1 texttable-1.6.4 threadpoolctl-3.0.0 tomli-1.2.2 tqdm-4.62.3 umap-learn-0.5.2 xlrd-1.2.0 [rtd-command-info] start-time: 2021-12-01T18:07:04.750167Z, end-time: 2021-12-01T18:07:04.820423Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[: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, docsearch_index='scanpy', docsearch_key='fa4304eb95d2134997e3729553a674b2', ) 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", "pandas.core.series.Series": "pandas.Series", } 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'), # Will work once scipy 1.8 is released ('py:class', 'scipy.sparse.base.spmatrix'), ('py:class', 'scipy.sparse.csr.csr_matrix'), ] # 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 # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring 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/"), ], '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': '16e62d13', } # 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/787793/' 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: 2021-12-01T18:07:04.925915Z, end-time: 2021-12-01T18:09:43.922090Z, duration: 158, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.1.2 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... 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://docs.scipy.org/doc/scipy/reference/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://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, api.rst, basic_usage.rst, community.rst, contributors.rst, dev/ci.rst, dev/code.rst, dev/documentation.rst, dev/external-tools.rst, dev/getting-set-up.rst, ..., release-notes/1.7.2.rst, release-notes/1.8.0.rst, release-notes/1.8.1.rst, release-notes/1.8.2.rst, release-notes/1.8.3.rst, release-notes/1.9.0.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/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 61 source files that are out of date updating environment: [new config] 312 added, 0 changed, 0 removed reading sources... 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