Read the Docs build information Build id: 908950 Project: icb-scanpy Version: 2220 Commit: f54da0f37df187aeee999935c92d2648d6cf0d09 Date: 2022-04-06T17:15:27.977148Z State: finished Success: True [rtd-command-info] start-time: 2022-04-06T17:15:29.850611Z, end-time: 2022-04-06T17:15:33.529756Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2022-04-06T17:15:33.690468Z, end-time: 2022-04-06T17:15:34.287807Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2220/head:external-2220 From https://github.com/scverse/scanpy * [new ref] refs/pull/2220/head -> external-2220 [rtd-command-info] start-time: 2022-04-06T17:15:34.512246Z, end-time: 2022-04-06T17:15:34.711407Z, duration: 0, exit-code: 0 git checkout --force f54da0f37df187aeee999935c92d2648d6cf0d09 Note: switching to 'f54da0f37df187aeee999935c92d2648d6cf0d09'. 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 f54da0f3 update colors [rtd-command-info] start-time: 2022-04-06T17:15:34.898781Z, end-time: 2022-04-06T17:15:34.967447Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-04-06T17:15:35.211710Z, end-time: 2022-04-06T17:15:36.119136Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2022-04-06T17:15:36.442203Z, end-time: 2022-04-06T17:15:48.493635Z, duration: 12, exit-code: 0 git submodule update --init --force docs/tutorials Submodule 'docs/tutorials' (https://github.com/scverse/scanpy-tutorials.git) registered for path 'docs/tutorials' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/tutorials'... Submodule path 'docs/tutorials': checked out 'b52a0cf74d76506dd1a0cc542c4012f9a15ef021' [rtd-command-info] start-time: 2022-04-06T17:15:53.828808Z, end-time: 2022-04-06T17:15:54.405366Z, duration: 0, exit-code: 0 asdf global python 3.9.7 [rtd-command-info] start-time: 2022-04-06T17:15:55.164822Z, end-time: 2022-04-06T17:15:56.686830Z, duration: 1, exit-code: 0 python -mvirtualenv /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220 created virtual environment CPython3.9.7.final.0-64 in 726ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220, 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: 2022-04-06T17:15:56.886901Z, end-time: 2022-04-06T17:16:08.101624Z, duration: 11, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/bin/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/2220/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.0.4-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/2220/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-22.0.4 setuptools-58.2.0 [rtd-command-info] start-time: 2022-04-06T17:16:08.428521Z, end-time: 2022-04-06T17:16:52.450554Z, duration: 44, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/bin/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 26.0 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 121.3 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 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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=1b896fae2f1093064e072d7015147a19c0efcef92b085ba96c5aa80682da2187 Stored in directory: /tmp/pip-ephem-wheel-cache-u2_v7alk/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=1361178 sha256=2d413a4b52eef0a7871e5d9476d51cfcb522bb2fa3876cd1f93ac470f5df31ca Stored in directory: /tmp/pip-ephem-wheel-cache-u2_v7alk/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=183188843a9771aa7127774db7dfa06cf93317a550f555c46d9cd0f29a5a8ddf Stored in directory: /tmp/pip-ephem-wheel-cache-u2_v7alk/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 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-3.0.7 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 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: 2022-04-06T17:16:52.634387Z, end-time: 2022-04-06T17:18:30.095539Z, duration: 97, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220 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 statsmodels>=0.10.0rc2 Downloading 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sha256=f7b5b1cc9038e3e647559f939a4ac945448625833090bba707a66d1ff0eb74a0 Stored in directory: /tmp/pip-ephem-wheel-cache-djlc5fb3/wheels/4a/66/81/205d77bd58539a1d07fb8b795fcea0b17f4d59912c0f4202b7 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.dev45+gf54da0f3-py3-none-any.whl size=11482403 sha256=4310afe1db68a13a740f7eff996748e13a1b237a9a49a49705f8b38b6c07d58b Stored in directory: /tmp/pip-ephem-wheel-cache-djlc5fb3/wheels/4c/03/a0/77944ec6cc08b06fab4866f161f6fd9ef0ff1c566a783e415f 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=f3f3871fcbcfd62c3ecd50f70dcb5d60ea4af45d1f2a7df3a0b91fec3c5e247c Stored in directory: /tmp/pip-ephem-wheel-cache-djlc5fb3/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-0.5.6-py3-none-any.whl size=53945 sha256=0e43943a41012f7a468b5e056c673872239e549bff2886d8fb1cb4162bd699be Stored in directory: /tmp/pip-ephem-wheel-cache-djlc5fb3/wheels/c0/f0/1d/20aa0dcee54ef40c179a4a4f57fad413437864a67757013a99 Successfully built umap-learn scanpy session-info pynndescent Installing collected packages: webencodings, wcwidth, stdlib_list, pure-eval, ptyprocess, pickleshare, mistune, fastjsonschema, executing, backcall, zipp, typing-extensions, traitlets, tqdm, tornado, threadpoolctl, testpath, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, setuptools, session-info, pyzmq, pyyaml, python-dateutil, pyrsistent, prompt-toolkit, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mdurl, llvmlite, kiwisolver, jupyterlab-pygments, joblib, Jinja2, fonttools, entrypoints, defusedxml, decorator, cycler, attrs, asttokens, stack-data, scipy, patsy, pandas, numba, matplotlib-inline, matplotlib, markdown-it-py, jupyter-core, jsonschema, jedi, importlib-metadata, h5py, dunamai, bleach, beautifulsoup4, statsmodels, sphinx, seaborn, scikit-learn, nbformat, mdit-py-plugins, jupyter-client, ipython, get_version, anndata, sphinxext-opengraph, sphinx-design, sphinx-autodoc-typehints, scanpydoc, pynndescent, nbclient, myst-parser, furo, umap-learn, nbconvert, scanpy, nbsphinx 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 Successfully installed Jinja2-3.1.1 anndata-0.8.0 asttokens-2.0.5 attrs-21.4.0 backcall-0.2.0 beautifulsoup4-4.10.0 bleach-4.1.0 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 dunamai-1.11.1 entrypoints-0.4 executing-0.8.3 fastjsonschema-2.15.3 fonttools-4.31.2 furo-2022.3.4 get_version-3.5.4 h5py-3.6.0 importlib-metadata-4.11.3 ipython-8.2.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.4.0 jupyter-client-7.2.1 jupyter-core-4.9.2 jupyterlab-pygments-0.1.2 kiwisolver-1.4.2 llvmlite-0.38.0 markdown-it-py-2.0.1 matplotlib-3.5.1 matplotlib-inline-0.1.3 mdit-py-plugins-0.3.0 mdurl-0.1.0 mistune-0.8.4 myst-parser-0.17.0 natsort-8.1.0 nbclient-0.5.13 nbconvert-6.4.5 nbformat-5.3.0 nbsphinx-0.8.8 nest-asyncio-1.5.5 networkx-2.7.1 numba-0.55.1 numpy-1.21.5 pandas-1.4.2 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.1.0 prompt-toolkit-3.0.29 ptyprocess-0.7.0 pure-eval-0.2.2 pynndescent-0.5.6 pyrsistent-0.18.1 python-dateutil-2.8.2 pyyaml-6.0 pyzmq-22.3.0 scanpy-1.10.0.dev45+gf54da0f3 scanpydoc-0.7.7 scikit-learn-1.0.2 scipy-1.8.0 seaborn-0.11.2 session-info-1.0.0 setuptools-62.0.0 soupsieve-2.3.2 sphinx-4.5.0 sphinx-autodoc-typehints-1.17.0 sphinx-design-0.0.13 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 sphinxext-opengraph-0.6.3 stack-data-0.2.0 statsmodels-0.13.2 stdlib_list-0.8.0 testpath-0.6.0 threadpoolctl-3.1.0 tornado-6.1 tqdm-4.64.0 traitlets-5.1.1 typing-extensions-4.1.1 umap-learn-0.5.2 wcwidth-0.2.5 webencodings-0.5.1 zipp-3.8.0 [rtd-command-info] start-time: 2022-04-06T17:18:31.610272Z, end-time: 2022-04-06T17:18:31.677967Z, 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 = '4.0' # 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'] extensions = [ 'myst_parser', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', 'sphinx.ext.viewcode', # '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.definition_list_typed_field', 'scanpydoc.autosummary_generate_imported', "sphinx_design", "sphinxext.opengraph", "nbsphinx", *[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 myst_enable_extensions = [ "colon_fence", "dollarmath", "amsmath", ] # nbsphinx specific settings exclude_patterns = ["_build", "**.ipynb_checkpoints"] nbsphinx_execute = "never" ogp_site_url = "https://scanpy.readthedocs.io/en/stable/" ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg" typehints_defaults = 'braces' scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' pygments_style = "default" pygments_dark_style = "native" 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 = "furo" html_theme_options = { "sidebar_hide_name": True, "light_css_variables": { "color-brand-primary": "#2b8cee", "color-brand-content": "#368ce2", "admonition-font-size": "var(--font-size-normal)", "admonition-title-font-size": "var(--font-size-normal)", "code-font-size": "var(--font-size--small)", }, } html_static_path = ['_static'] html_css_files = ["css/override.css"] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' html_title = "scanpy" # def setup(app): # app.warningiserror = on_rtd nbsphinx_prolog = r""" .. raw:: html {{% set docname = env.doc2path(env.docname, base=None).split("/")[-1] %}} .. raw:: html .. raw:: html

Note

This page was generated from {docname}. Interactive online version: Colab badge. Some tutorial content may look better in light mode.

""".format( docname="{{ docname|e }}" ) # -- 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': "2220", 'version_slug': "2220", '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': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': 'f54da0f37df187aeee999935c92d2648d6cf0d09', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'f54da0f37df187aeee999935c92d2648d6cf0d09', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'f54da0f37df187aeee999935c92d2648d6cf0d09', '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': 'f54da0f3', } # 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/2220' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/908950/' 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: 2022-04-06T17:18:31.926329Z, end-time: 2022-04-06T17:23:40.999508Z, duration: 309, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/bin/python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.5.0 Matplotlib is building the font cache; this may take a moment. loading translations [en]... done making output directory... done myst v0.17.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'amsmath'], 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', 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, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200) 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, _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, ..., tutorials/scanpy_workshop/day2_01_DE_Colabs.ipynb, tutorials/scanpy_workshop/day2_01_DifferentialExpression.ipynb, tutorials/scanpy_workshop/day2_02_GSEA_Colabs.ipynb, tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis.ipynb, tutorials/scanpy_workshop/day2_03_RNAvelocity.ipynb, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/integration-scanorama.ipynb, tutorials/tutorial_pearson_residuals.ipynb, tutorials/visualizing-marker-genes.rst, usage-principles.md WARNING: [autosummary] failed to import Neighbors. Possible hints: * ModuleNotFoundError: No module named 'Neighbors' * KeyError: 'Neighbors' * ValueError: not enough values to unpack (expected 2, got 1) WARNING: [autosummary] failed to import _settings.ScanpyConfig. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings WARNING: [autosummary] failed to import logging.print_header. Possible hints: * ImportError: * AttributeError: module 'logging' has no attribute 'print_header' * ModuleNotFoundError: No module named 'logging.print_header' WARNING: [autosummary] failed to import logging.print_versions. Possible hints: * ImportError: * ModuleNotFoundError: No module named 'logging.print_versions' * AttributeError: module 'logging' has no attribute 'print_versions' WARNING: [autosummary] failed to import read. Possible hints: * ModuleNotFoundError: No module named 'read' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read' WARNING: [autosummary] failed to import read_10x_h5. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_10x_h5' * ModuleNotFoundError: No module named 'read_10x_h5' WARNING: [autosummary] failed to import read_10x_mtx. Possible hints: * ModuleNotFoundError: No module named 'read_10x_mtx' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_10x_mtx' WARNING: [autosummary] failed to import read_csv. Possible hints: * ModuleNotFoundError: No module named 'read_csv' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_csv' WARNING: [autosummary] failed to import read_excel. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_excel' * KeyError: 'read_excel' WARNING: [autosummary] failed to import read_h5ad. Possible hints: * ModuleNotFoundError: No module named 'read_h5ad' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_h5ad' WARNING: [autosummary] failed to import read_hdf. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_hdf' * KeyError: 'read_hdf' WARNING: [autosummary] failed to import read_loom. Possible hints: * KeyError: 'read_loom' * ModuleNotFoundError: No module named 'read_loom' * ValueError: not enough values to unpack (expected 2, got 1) WARNING: [autosummary] failed to import read_mtx. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_mtx' * ModuleNotFoundError: No module named 'read_mtx' WARNING: [autosummary] failed to import read_text. Possible hints: * ModuleNotFoundError: No module named 'read_text' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_text' WARNING: [autosummary] failed to import read_umi_tools. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_umi_tools' * KeyError: 'read_umi_tools' WARNING: [autosummary] failed to import read_visium. Possible hints: * ModuleNotFoundError: No module named 'read_visium' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_visium' WARNING: [autosummary] failed to import set_figure_params. Possible hints: * KeyError: 'set_figure_params' * ModuleNotFoundError: No module named 'set_figure_params' * ValueError: not enough values to unpack (expected 2, got 1) [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.datasets.pbmc3k_processed.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/generated/scanpy.external.tl.wishbone.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.add_totals.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.get_axes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.legend.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.make_figure.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.savefig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.show.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.style.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/classes/scanpy.pl.StackedViolin.swap_axes.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 98 source files that are out of date updating environment: [new config] 306 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 0%] _tutorials reading sources... [ 0%] api/classes reading sources... [ 1%] api/datasets reading sources... [ 1%] api/deprecated reading sources... [ 1%] api/experimental reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX reading sources... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT reading sources... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE reading sources... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT reading sources... [ 9%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram reading sources... [ 9%] api/generated/classes/scanpy.pl.DotPlot.add_totals reading sources... [ 9%] api/generated/classes/scanpy.pl.DotPlot.get_axes reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.getdoc reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.legend reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.make_figure reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.savefig reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.show reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.style reading sources... [ 12%] api/generated/classes/scanpy.pl.DotPlot.swap_axes reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.legend reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.savefig reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.show reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 19%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.add_totals reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.get_axes reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.getdoc reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.legend reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.make_figure reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.savefig reading sources... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.show reading sources... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes reading sources... [ 30%] api/generated/scanpy.datasets.blobs reading sources... [ 30%] api/generated/scanpy.datasets.ebi_expression_atlas reading sources... [ 30%] api/generated/scanpy.datasets.krumsiek11 reading sources... [ 31%] api/generated/scanpy.datasets.moignard15 reading sources... [ 31%] api/generated/scanpy.datasets.paul15 reading sources... [ 31%] api/generated/scanpy.datasets.pbmc3k reading sources... [ 32%] api/generated/scanpy.datasets.pbmc3k_processed reading sources... [ 32%] api/generated/scanpy.datasets.pbmc68k_reduced reading sources... [ 32%] api/generated/scanpy.datasets.toggleswitch reading sources... [ 33%] api/generated/scanpy.datasets.visium_sge reading sources... [ 33%] api/generated/scanpy.experimental.pp.highly_variable_genes reading sources... [ 33%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals reading sources... [ 33%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca reading sources... [ 34%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 34%] api/generated/scanpy.get.obs_df reading sources... [ 34%] api/generated/scanpy.get.rank_genes_groups_df reading sources... [ 35%] api/generated/scanpy.get.var_df reading sources... [ 35%] api/generated/scanpy.metrics.confusion_matrix reading sources... [ 35%] api/generated/scanpy.metrics.gearys_c reading sources... [ 36%] api/generated/scanpy.metrics.morans_i reading sources... [ 36%] api/generated/scanpy.pl.clustermap reading sources... [ 36%] api/generated/scanpy.pl.dendrogram reading sources... [ 37%] api/generated/scanpy.pl.diffmap reading sources... [ 37%] api/generated/scanpy.pl.dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 37%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 38%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 38%] api/generated/scanpy.pl.draw_graph WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`). reading sources... [ 38%] api/generated/scanpy.pl.embedding reading sources... [ 39%] api/generated/scanpy.pl.embedding_density reading sources... [ 39%] api/generated/scanpy.pl.filter_genes_dispersion reading sources... [ 39%] api/generated/scanpy.pl.heatmap reading sources... [ 40%] api/generated/scanpy.pl.highest_expr_genes reading sources... [ 40%] api/generated/scanpy.pl.highly_variable_genes reading sources... [ 40%] api/generated/scanpy.pl.matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 41%] api/generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00", line 3, in File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/tools/_draw_graph.py", line 167, in draw_graph g = _utils.get_igraph_from_adjacency(adjacency) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/_utils/__init__.py", line 209, in get_igraph_from_adjacency import igraph as ig ModuleNotFoundError: No module named 'igraph' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:120: WARNING: Exception occurred in plotting scanpy-pl-paga-1 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.pl.paga.rst: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/lib/python3.9/site-packages/matplotlib/sphinxext/plot_directive.py", line 517, in _run_code exec(code, ns) File "", line 3, in File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/tools/_paga.py", line 124, in paga paga.compute_connectivities() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/tools/_paga.py", line 159, in compute_connectivities return self._compute_connectivities_v1_2() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/tools/_paga.py", line 168, in _compute_connectivities_v1_2 import igraph ModuleNotFoundError: No module named 'igraph' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:130: WARNING: Exception occurred in plotting scanpy-pl-paga-2 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/generated/scanpy.pl.paga.rst: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2220/lib/python3.9/site-packages/matplotlib/sphinxext/plot_directive.py", line 517, in _run_code exec(code, ns) File "", line 1, in File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/plotting/_tools/paga.py", line 481, in paga groups_key = adata.uns['paga']['groups'] KeyError: 'groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.spatial:192: ERROR: Unknown interpreted text role "tutorial". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/preprocessing/_simple.py:docstring of scanpy.preprocessing._simple.regress_out:3: ERROR: Unknown interpreted text role "issue". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/scanpy/tools/_ingest.py:docstring of scanpy.tools._ingest.ingest:3: ERROR: Unknown interpreted text role "tutorial". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/plotting.md:14: ERROR: Unknown interpreted text role "tutorial". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:12: WARNING: autosummary: failed to import read. Possible hints: * ModuleNotFoundError: No module named 'read' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:22: WARNING: autosummary: failed to import read_10x_h5. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_10x_h5' * ModuleNotFoundError: No module named 'read_10x_h5' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:22: WARNING: autosummary: failed to import read_10x_mtx. Possible hints: * ModuleNotFoundError: No module named 'read_10x_mtx' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_10x_mtx' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:22: WARNING: autosummary: failed to import read_visium. Possible hints: * ModuleNotFoundError: No module named 'read_visium' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_visium' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_h5ad. Possible hints: * ModuleNotFoundError: No module named 'read_h5ad' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_h5ad' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_csv. Possible hints: * ModuleNotFoundError: No module named 'read_csv' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_csv' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_excel. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_excel' * KeyError: 'read_excel' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_hdf. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_hdf' * KeyError: 'read_hdf' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_loom. Possible hints: * KeyError: 'read_loom' * ModuleNotFoundError: No module named 'read_loom' * ValueError: not enough values to unpack (expected 2, got 1) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_mtx. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_mtx' * ModuleNotFoundError: No module named 'read_mtx' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_text. Possible hints: * ModuleNotFoundError: No module named 'read_text' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'read_text' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/reading.md:34: WARNING: autosummary: failed to import read_umi_tools. Possible hints: * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'read_umi_tools' * KeyError: 'read_umi_tools' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:9: WARNING: autosummary: failed to import set_figure_params. Possible hints: * KeyError: 'set_figure_params' * ModuleNotFoundError: No module named 'set_figure_params' * ValueError: not enough values to unpack (expected 2, got 1) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:19: WARNING: autosummary: failed to import _settings.ScanpyConfig. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:34: WARNING: autosummary: failed to import _settings.ScanpyConfig.autoshow. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:34: WARNING: autosummary: failed to import _settings.ScanpyConfig.autosave. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:44: WARNING: autosummary: failed to import _settings.ScanpyConfig.figdir. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:44: WARNING: autosummary: failed to import _settings.ScanpyConfig.cachedir. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:44: WARNING: autosummary: failed to import _settings.ScanpyConfig.datasetdir. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:57: WARNING: autosummary: failed to import _settings.ScanpyConfig.verbosity. Possible hints: * ModuleNotFoundError: No module named '_settings' * KeyError: '_settings' * ImportError: no module named _settings.ScanpyConfig /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:66: WARNING: autosummary: failed to import logging.print_header. Possible hints: * ImportError: * AttributeError: module 'logging' has no attribute 'print_header' * ModuleNotFoundError: No module named 'logging.print_header' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/api/settings.md:66: WARNING: autosummary: failed to import logging.print_versions. Possible hints: * ImportError: * ModuleNotFoundError: No module named 'logging.print_versions' * AttributeError: module 'logging' has no attribute 'print_versions' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/release-notes/1.9.1.md:8: ERROR: Unknown interpreted text role "pr". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/release-notes/1.9.1.md:9: ERROR: Unknown interpreted text role "pr". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/release-notes/1.9.0.md:7: ERROR: Unknown interpreted text role "tutorial". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/release-notes/1.9.0.md:13: ERROR: Unknown interpreted text role "pr". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2220/docs/release-notes/1.9.0.md:23: ERROR: Unknown interpreted text role "pr". 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