Read the Docs build information Build id: 1955747 Project: icb-scanpy Version: 2815 Commit: b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e Date: 2024-01-17T16:42:58.469534Z State: finished Success: True [rtd-command-info] start-time: 2024-01-17T16:42:59.594067Z, end-time: 2024-01-17T16:43:02.183342Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-01-17T16:43:02.248422Z, end-time: 2024-01-17T16:43:02.933403Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/2815/head:external-2815 From https://github.com/scverse/scanpy * [new ref] refs/pull/2815/head -> external-2815 [rtd-command-info] start-time: 2024-01-17T16:43:03.060772Z, end-time: 2024-01-17T16:43:03.274191Z, duration: 0, exit-code: 0 git checkout --force b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e Note: switching to 'b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e'. 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 b24d1c4 (fix): change `tol` again for violin plots [rtd-command-info] start-time: 2024-01-17T16:43:03.355576Z, end-time: 2024-01-17T16:43:03.414627Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-01-17T16:43:03.482876Z, end-time: 2024-01-17T16:43:03.546561Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-20.04 tools: python: '3.11' sphinx: fail_on_warning: true # do not change or you will be fired configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - leiden [rtd-command-info] start-time: 2024-01-17T16:43:12.415177Z, end-time: 2024-01-17T16:43:13.804519Z, duration: 1, exit-code: 0 asdf global python 3.11.6 [rtd-command-info] start-time: 2024-01-17T16:43:14.827390Z, end-time: 2024-01-17T16:43:16.991778Z, duration: 2, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.6.final.0-64 in 742ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2815, 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==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-01-17T16:43:17.075067Z, end-time: 2024-01-17T16:43:28.433650Z, duration: 11, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2815/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-23.3.2-py3-none-any.whl (2.1 MB) 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filename=scanpy-0.1.dev57+gb24d1c4-py3-none-any.whl size=2060678 sha256=dc5d901f54f609321888379f4bd6bfbfc7fd59b3db4bc9d8a633ab1786c510bd Stored in directory: /tmp/pip-ephem-wheel-cache-cibrab2x/wheels/e7/ae/80/1389594619e95a02a6c6aa08e39f797be80fe9a0e2866f9fce Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.5-py3-none-any.whl size=86836 sha256=8c5dde201cafd01601a337bf6a12544f3cde57e4f5dd4501729cc66b0b78f0c6 Stored in directory: /tmp/pip-ephem-wheel-cache-cibrab2x/wheels/de/07/2e/814a6ee82e37528f2044a609a431028375b149bc31f03c0e27 Building wheel for sam-algorithm (setup.py): started Building wheel for sam-algorithm (setup.py): finished with status 'done' Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34578 sha256=3e87e1d6032399e4174d8a792a4ae02b692254f03d01eb53ac6f91f7d6faf47a Stored in directory: /tmp/pip-ephem-wheel-cache-cibrab2x/wheels/0c/4e/72/438a6a71defb1c2ba8e15e371bbdc31e5c9ea3ae0084a38911 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=8024 sha256=3b6d00f00568d293f90fe934fc3010c6eef6113bc9a9162dec4d6525f77f8f21 Stored in directory: /tmp/pip-ephem-wheel-cache-cibrab2x/wheels/4e/56/35/a748fc57279a4b84d0b332879445fed1ad8478e7257986b015 Building wheel for hnswlib (pyproject.toml): started Building wheel for hnswlib (pyproject.toml): finished with status 'done' Created wheel for hnswlib: filename=hnswlib-0.8.0-cp311-cp311-linux_x86_64.whl size=2261459 sha256=8a4f4cc09ea31bbb2bbf81f3d7a8093c06605deacff82973b10f9ec43e457274 Stored in directory: /tmp/pip-ephem-wheel-cache-cibrab2x/wheels/ea/4e/27/39aebca9958719776e36fada290845a7ef10f053ad70e22ceb Successfully built scanpy umap-learn sam-algorithm session-info hnswlib Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, llvmlite, legacy-api-wrap, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fonttools, executing, dill, defusedxml, decorator, debugpy, cycler, click, attrs, array-api-compat, accessible-pygments, sqlalchemy, session-info, scipy, referencing, python-dateutil, patsy, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, statsmodels, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb Successfully installed accessible-pygments-0.0.4 anndata-0.10.4 array-api-compat-1.4 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.2 bleach-6.1.0 click-8.1.7 comm-0.2.1 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.7 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.47.2 greenlet-3.0.3 h5py-3.10.0 harmonypy-0.0.9 hnswlib-0.8.0 igraph-0.10.8 importlib_metadata-7.0.1 ipykernel-6.29.0 ipython-8.20.0 jedi-0.19.1 joblib-1.3.2 jsonschema-4.21.0 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 legacy-api-wrap-1.4 leidenalg-0.10.1 llvmlite-0.41.1 markdown-it-py-3.0.0 matplotlib-3.8.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.0.0 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.9.0 nbconvert-7.14.2 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.9 networkx-3.2.1 numba-0.58.1 numpy-1.26.3 pandas-2.1.4 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.6 pexpect-4.9.0 pillow-10.2.0 platformdirs-4.1.0 prompt-toolkit-3.0.43 psutil-5.9.7 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.1 pynndescent-0.5.11 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.32.1 rpds-py-0.17.1 sam-algorithm-1.0.2 scanpy-0.1.dev57+gb24d1c4 scanpydoc-0.13.4 scikit-learn-1.3.2 scipy-1.11.4 seaborn-0.13.1 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-1.25.2 sphinx-book-theme-1.1.0 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.25 stack-data-0.6.3 statsmodels-0.14.1 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.2.0 tinycss2-1.2.1 tornado-6.4 tqdm-4.66.1 traitlets-5.14.1 typing-extensions-4.9.0 tzdata-2023.4 umap-learn-0.5.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.17.0 [rtd-command-info] start-time: 2024-01-17T16:45:10.025189Z, end-time: 2024-01-17T16:45:10.094560Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from pathlib import Path from typing import TYPE_CHECKING 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 if TYPE_CHECKING: from sphinx.application import Sphinx # -- 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" repository_url = "https://github.com/scverse/scanpy" 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", "**.ipynb_checkpoints"] extensions = [ "myst_nb", "sphinx_copybutton", "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx.ext.extlinks", "matplotlib.sphinxext.plot_directive", "sphinx_autodoc_typehints", # needs to be after napoleon "git_ref", # needs to be before scanpydoc.rtd_github_links "scanpydoc", # needs to be before sphinx.ext.linkcode "sphinx.ext.linkcode", "sphinx_design", "sphinx_search.extension", "sphinxext.opengraph", *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}], ] # 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 = [ "amsmath", "colon_fence", "deflist", "dollarmath", "html_image", "html_admonition", ] myst_url_schemes = ("http", "https", "mailto") nb_output_stderr = "remove" nb_execution_mode = "off" nb_merge_streams = True 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" 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), cuml=("https://docs.rapids.ai/api/cuml/stable/", None), cycler=("https://matplotlib.org/cycler/", None), dask=("https://docs.dask.org/en/stable/", None), dask_ml=("https://ml.dask.org/", None), h5py=("https://docs.h5py.org/en/stable/", None), ipython=("https://ipython.readthedocs.io/en/stable/", None), igraph=("https://python.igraph.org/en/stable/api/", 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), pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None), pytest=("https://docs.pytest.org/en/latest/", None), python=("https://docs.python.org/3", None), rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None), scipy=("https://docs.scipy.org/doc/scipy/", None), seaborn=("https://seaborn.pydata.org/", None), sklearn=("https://scikit-learn.org/stable/", None), tutorials=("https://scanpy-tutorials.readthedocs.io/en/latest/", None), ) # -- Options for HTML output ---------------------------------------------- # The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search html_theme = "scanpydoc" html_theme_options = { "repository_url": repository_url, "use_repository_button": True, } html_static_path = ["_static"] html_show_sphinx = False html_logo = "_static/img/Scanpy_Logo_BrightFG.svg" html_title = "scanpy" def setup(app: Sphinx): """App setup hook.""" app.add_config_value( "recommonmark_config", { "auto_toc_tree_section": "Contents", "enable_auto_toc_tree": True, "enable_math": True, "enable_inline_math": False, "enable_eval_rst": True, }, True, ) # -- 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.metrics.DistanceMetric", "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 = [ # Technical issues ("py:class", "numpy.int64"), # documented as “attribute” # Will probably be documented ("py:class", "scanpy._settings.Verbosity"), ("py:class", "scanpy.neighbors.OnFlySymMatrix"), ("py:class", "scanpy.plotting._baseplot_class.BasePlot"), # Currently undocumented # https://github.com/mwaskom/seaborn/issues/1810 ("py:class", "seaborn.matrix.ClusterGrid"), ("py:class", "samalg.SAM"), # Won’t be documented ("py:class", "scanpy.plotting._utils._AxesSubplot"), ("py:class", "scanpy._utils.Empty"), ("py:class", "numpy.random.mtrand.RandomState"), ("py:class", "scanpy.neighbors._types.KnnTransformerLike"), # 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 # extlinks config extlinks = { "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"), "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"), } ########################################################################### # 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') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "2815", 'version_slug': "2815", '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/"), ("1.9.x", "/en/1.9.x/"), ("1.8.x", "/en/1.8.x/"), ("1.7.x", "/en/1.7.x/"), ("1.6.x", "/en/1.6.x/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', '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': 'b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'b24d1c4f4926c7c923dcb5de7233f4d4a48e0b3e', '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': 'b24d1c4f', } # 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(): for key in context: if key not in html_context: html_context[key] = context[key] 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/2815' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1955747/' 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: 2024-01-17T16:45:10.168376Z, end-time: 2024-01-17T16:49:12.096089Z, duration: 241, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.2.6 Matplotlib is building the font cache; this may take a moment. making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'deflist', 'dollarmath', 'amsmath', 'html_admonition', 'colon_fence', 'html_image'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) myst-nb v1.0.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/_readthedocs/.jupyter_cache 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://docs.rapids.ai/api/cuml/stable/objects.inv... loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv... loading intersphinx inventory from https://docs.dask.org/en/stable/objects.inv... loading intersphinx inventory from https://ml.dask.org/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://python.igraph.org/en/stable/api/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://pynndescent.readthedocs.io/en/latest/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://rapids-singlecell.readthedocs.io/en/latest/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: _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, api/preprocessing.md, ..., release-notes/1.9.0.md, release-notes/1.9.1.md, release-notes/1.9.2.md, release-notes/1.9.3.md, release-notes/1.9.4.md, release-notes/1.9.5.md, release-notes/1.9.6.md, release-notes/1.9.7.md, release-notes/index.md, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2815/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492 building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 81 source files that are out of date updating environment: [new config] 336 added, 0 changed, 0 removed [2Kreading sources... [ 0%] _tutorials [2Kreading sources... [ 1%] api/classes [2Kreading sources... [ 1%] api/datasets [2Kreading sources... [ 1%] api/deprecated [2Kreading sources... [ 1%] api/experimental [2Kreading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot [2Kreading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT [2Kreading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH [2Kreading sources... 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