Read the Docs build information Build id: 980893 Project: icb-scanpy Version: 2277 Commit: 9dcf5e41c9047f5ebeabec064610a44679e1e208 Date: 2022-06-15T22:08:46.174756Z State: finished Success: True [rtd-command-info] start-time: 2022-06-15T22:09:50.591059Z, end-time: 2022-06-15T22:09:53.245867Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2022-06-15T22:09:53.469939Z, end-time: 2022-06-15T22:09:54.026585Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2277/head:external-2277 From https://github.com/scverse/scanpy * [new ref] refs/pull/2277/head -> external-2277 [rtd-command-info] start-time: 2022-06-15T22:09:54.214727Z, end-time: 2022-06-15T22:09:54.410053Z, duration: 0, exit-code: 0 git checkout --force 9dcf5e41c9047f5ebeabec064610a44679e1e208 Note: switching to '9dcf5e41c9047f5ebeabec064610a44679e1e208'. 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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 9dcf5e41 Revert conditional spacing changes for multipanel plots [rtd-command-info] start-time: 2022-06-15T22:09:54.627154Z, end-time: 2022-06-15T22:09:54.706355Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-06-15T22:09:59.860998Z, end-time: 2022-06-15T22:09:59.955728Z, duration: 0, exit-code: 0 asdf global python 3.9.13 [rtd-command-info] start-time: 2022-06-15T22:10:00.461485Z, end-time: 2022-06-15T22:10:01.512917Z, duration: 1, exit-code: 0 python -mvirtualenv created virtual environment CPython3.9.13.final.0-64 in 726ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2277, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2022-06-15T22:10:01.706817Z, end-time: 2022-06-15T22:10:12.779511Z, duration: 11, 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/2277/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.1.2-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2277/lib/python3.9/site-packages (57.4.0) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 57.4.0 Uninstalling setuptools-57.4.0: Successfully uninstalled setuptools-57.4.0 Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-22.1.2 setuptools-58.2.0 [rtd-command-info] start-time: 2022-06-15T22:10:12.974836Z, end-time: 2022-06-15T22:10:45.278316Z, duration: 32, 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 jinja2<3.1.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 26.3 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 146.3 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing 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0:00:00 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=47f1f14d069fba3bec6faf4913e782e7f03acff3b14ce2c7c79997b9b6ca4e23 Stored in directory: /tmp/pip-ephem-wheel-cache-v8n0ipt4/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f 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-cp39-cp39-linux_x86_64.whl size=1361234 sha256=283c6bd8ef34b8363e3767b28e2563bae8ddcc763a125b8f2b1087bd99cfa629 Stored in directory: /tmp/pip-ephem-wheel-cache-v8n0ipt4/wheels/d3/de/21/f0ad1b0453288616d3f4d2ce28431aa7a2adde8f27c9b7a0af 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=e0700876757c73e42ec4ecaa367231043c5023e7bfa1fe8027c941ff7b0e888f Stored in directory: /tmp/pip-ephem-wheel-cache-v8n0ipt4/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.2 certifi-2022.6.15 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.0 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 urllib3-1.26.9 [rtd-command-info] start-time: 2022-06-15T22:10:45.515245Z, end-time: 2022-06-15T22:12:03.026704Z, duration: 77, 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/2277 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 anndata>=0.7.4 Downloading anndata-0.8.0-py3-none-any.whl (96 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.1/96.1 kB 8.3 MB/s eta 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pynndescent>=0.5 Downloading pynndescent-0.5.7.tar.gz (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 193.1 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pyyaml Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 661.8/661.8 kB 277.2 MB/s eta 0:00:00 Collecting markdown-it-py<3.0.0,>=1.0.0 Downloading markdown_it_py-2.1.0-py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 229.3 MB/s eta 0:00:00 Collecting typing-extensions Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB) Collecting mdit-py-plugins~=0.3.0 Downloading mdit_py_plugins-0.3.0-py3-none-any.whl (43 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.7/43.7 kB 205.8 MB/s eta 0:00:00 Collecting python-igraph Downloading python-igraph-0.9.11.tar.gz (9.5 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting stdlib_list Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.5/63.5 kB 213.0 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2277/lib/python3.9/site-packages (from Jinja2>=2.3->sphinx>=4.4->scanpy==1.10.0.dev14+g9dcf5e41) (2.1.1) Collecting mdurl~=0.1 Downloading mdurl-0.1.1-py3-none-any.whl (10 kB) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2277/lib/python3.9/site-packages (from requests>=2.5.0->sphinx>=4.4->scanpy==1.10.0.dev14+g9dcf5e41) (2.0.12) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2277/lib/python3.9/site-packages (from 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umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82830 sha256=d8a30ce43ab39b2e90d921403542915fe7f235bcecd20028745a21374d13936a Stored in directory: /tmp/pip-ephem-wheel-cache-vew8q9hq/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9 Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.10.0.dev14+g9dcf5e41-py3-none-any.whl size=11479886 sha256=c34180a3f8292b6591a512119a26e4800dae30d6ef3457f17f8c702e7347316b Stored in directory: /tmp/pip-ephem-wheel-cache-vew8q9hq/wheels/0b/92/70/4fc82ea05044d50005ed850295a215c7a120d3985bac1986ac Building wheel for session-info (setup.py): started Building wheel for session-info (setup.py): finished with status 'done' Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8045 sha256=9e6a2721e0d802099e7838d9551c49208aac081dacad0f607272f9be1587e3cf Stored in directory: /tmp/pip-ephem-wheel-cache-vew8q9hq/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6 Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.7-py3-none-any.whl size=54287 sha256=4caa440acc869fbc347d6516ecc7d71faa385c7ca97cf9d9ccac6f89e11dd728 Stored in directory: /tmp/pip-ephem-wheel-cache-vew8q9hq/wheels/5b/f5/6e/aac11d69fe2115d9ac871d6c148b361f0d3f8a35ed7354fa03 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-0.9.11-py3-none-any.whl size=9076 sha256=fa641050682349640b24974a6ba38652eafa3ce766f3fbb78860555ca57e6385 Stored in directory: /tmp/pip-ephem-wheel-cache-vew8q9hq/wheels/ec/a8/eb/80bcf5c6a4defe501353cf37f0751ae11d4d6854aa39fefc19 Successfully built umap-learn scanpy session-info pynndescent python-igraph Installing collected packages: texttable, stdlib_list, zipp, typing-extensions, tqdm, threadpoolctl, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, session-info, pyyaml, python-dateutil, pillow, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, Jinja2, igraph, fonttools, cycler, scipy, python-igraph, patsy, pandas, numba, matplotlib, markdown-it-py, importlib-metadata, h5py, dunamai, statsmodels, sphinx, seaborn, scikit-learn, mdit-py-plugins, get_version, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpydoc, pynndescent, myst-parser, umap-learn, scanpy 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: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 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 Jinja2-3.1.2 anndata-0.8.0 cycler-0.11.0 dunamai-1.12.0 fonttools-4.33.3 get_version-3.5.4 h5py-3.7.0 igraph-0.9.11 importlib-metadata-4.11.4 joblib-1.1.0 kiwisolver-1.4.3 llvmlite-0.38.1 markdown-it-py-2.1.0 matplotlib-3.5.2 mdit-py-plugins-0.3.0 mdurl-0.1.1 myst-parser-0.18.0 natsort-8.1.0 networkx-2.8.4 numba-0.55.2 numpy-1.22.4 pandas-1.4.2 patsy-0.5.2 pillow-9.1.1 pynndescent-0.5.7 python-dateutil-2.8.2 python-igraph-0.9.11 pyyaml-6.0 scanpy-1.10.0.dev14+g9dcf5e41 scanpydoc-0.7.7 scikit-learn-1.1.1 scipy-1.8.1 seaborn-0.11.2 session-info-1.0.0 setuptools-62.4.0 sphinx-5.0.1 sphinx-autodoc-typehints-1.18.3 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-0.13.2 stdlib_list-0.8.0 texttable-1.6.4 threadpoolctl-3.1.0 tqdm-4.64.0 typing-extensions-4.2.0 umap-learn-0.5.3 zipp-3.8.0 [rtd-command-info] start-time: 2022-06-15T22:12:04.619724Z, end-time: 2022-06-15T22:12:04.685033Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa from packaging.version import parse as parse_version # 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', 'myst.header', # https://github.com/executablebooks/MyST-Parser/issues/262 ] # General information project = 'Scanpy' author = 'Scanpy development team' copyright = f'{datetime.now():%Y}, the Scanpy development team.' version = scanpy.__version__.replace('.dirty', '') # Bumping the version updates all docs, so don't do that if parse_version(version).is_devrelease: parsed = parse_version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # default settings templates_path = ['_templates'] master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'myst_parser', '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', # scanpydoc.elegant_typehints causes full doc rebuilds 'scanpydoc.rtd_github_links', 'scanpydoc.theme', 'scanpydoc.definition_list_typed_field', 'scanpydoc.autosummary_generate_imported', *[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 typehints_defaults = 'braces' 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=('https://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/stable/', None), networkx=('https://networkx.org/documentation/stable/', None), numpy=('https://numpy.org/doc/stable/', 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/', 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/main/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': "2277", 'version_slug': "2277", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", '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': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': '9dcf5e41c9047f5ebeabec064610a44679e1e208', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '9dcf5e41c9047f5ebeabec064610a44679e1e208', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '9dcf5e41c9047f5ebeabec064610a44679e1e208', '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': '9dcf5e41', } # 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 'external' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'https://github.com/scverse/scanpy/pull/2277' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/980893/' 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: 2022-06-15T22:12:04.869425Z, end-time: 2022-06-15T22:14:05.438502Z, duration: 120, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v5.0.1 making output directory... done myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') 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 https://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/stable/objects.inv... loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/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/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, api.md, basic_usage.md, community.md, contributors.md, dev/ci.md, dev/code.md, dev/documentation.md, dev/external-tools.md, dev/getting-set-up.md, ..., release-notes/1.8.0.md, release-notes/1.8.1.md, release-notes/1.8.2.md, release-notes/1.9.0.md, release-notes/1.9.1.md, release-notes/1.9.2.md, release-notes/index.md, release-notes/release-latest.md, tutorials.md, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2277/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 63 source files that are out of date updating environment: [new config] 318 added, 0 changed, 0 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