Read the Docs build information Build id: 2335128 Project: icb-scanpy Version: 3148 Commit: 72125841fac84fdd4e906ffd4c85c9c4dce9b949 Date: 2024-07-08T17:47:59.895459Z State: finished Success: True [rtd-command-info] start-time: 2024-07-08T17:48:01.018464Z, end-time: 2024-07-08T17:48:03.241141Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-07-08T17:48:03.313673Z, end-time: 2024-07-08T17:48:04.095166Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/3148/head:external-3148 From https://github.com/scverse/scanpy * [new ref] refs/pull/3148/head -> external-3148 [rtd-command-info] start-time: 2024-07-08T17:48:04.214908Z, end-time: 2024-07-08T17:48:04.429644Z, duration: 0, exit-code: 0 git checkout --force 72125841fac84fdd4e906ffd4c85c9c4dce9b949 Note: switching to '72125841fac84fdd4e906ffd4c85c9c4dce9b949'. 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 7212584 [pre-commit.ci] pre-commit autoupdate [rtd-command-info] start-time: 2024-07-08T17:48:04.492688Z, end-time: 2024-07-08T17:48:04.545150Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 submodules: include: all build: os: ubuntu-20.04 tools: python: '3.12' 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: 2024-07-08T17:48:04.687070Z, end-time: 2024-07-08T17:48:05.114565Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-07-08T17:48:05.185065Z, end-time: 2024-07-08T17:48:22.032934Z, duration: 16, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/notebooks'... Submodule path 'notebooks': checked out '02c4946e0be47e033355ef84b2a4909b302d2513' [rtd-command-info] start-time: 2024-07-08T17:48:29.495894Z, end-time: 2024-07-08T17:48:30.927771Z, duration: 1, exit-code: 0 asdf global python 3.12.3 [rtd-command-info] start-time: 2024-07-08T17:48:32.070759Z, end-time: 2024-07-08T17:48:34.672087Z, duration: 2, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.3.final.0-64 in 852ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3148, 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: 2024-07-08T17:48:34.751259Z, end-time: 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readthedocs-sphinx-ext Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-0.7.16 babel-2.15.0 certifi-2024.7.4 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.7 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-7.3.7 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.2 [rtd-command-info] start-time: 2024-07-08T17:49:03.220411Z, end-time: 2024-07-08T17:50:52.375133Z, duration: 109, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,leiden] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148 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 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Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: scanpy, sam-algorithm, session-info, hnswlib Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-0.1.dev50+g7212584-py3-none-any.whl size=2084786 sha256=0d993bbea27ff24fbaff5efbf87a04e4406f9b8bca781d50d425137f6c1e36e6 Stored in directory: /tmp/pip-ephem-wheel-cache-52rs3_ht/wheels/13/e6/08/290cbf38434692d1c1da4d0bfc195bec11c5030de43461f66a 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=34573 sha256=2e0a593dc7d126744a9690f1d3abaa1af0197ce99ca70afc6e7ce905e42231b2 Stored in directory: /tmp/pip-ephem-wheel-cache-52rs3_ht/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed 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=8023 sha256=fff7003ba2925cd813b92effba1feaddc59ece541732c3c9007653424449c2ca Stored in directory: /tmp/pip-ephem-wheel-cache-52rs3_ht/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d 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-cp312-cp312-linux_x86_64.whl size=2314148 sha256=32351c25388bb60460144010f69c3e4cebe4ae31a36f04ed7a3f172826510fc2 Stored in directory: /tmp/pip-ephem-wheel-cache-52rs3_ht/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e Successfully built scanpy sam-algorithm session-info hnswlib Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, array-api-compat, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, 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, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fsspec, fonttools, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, attrs, accessible-pygments, sqlalchemy, session-info, scipy, referencing, python-dateutil, pybtex, patsy, partd, 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, pybtex-docutils, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, statsmodels, sphinxcontrib-bibtex, 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-0.0.5 anndata-0.10.8 array-api-compat-1.7.1 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 click-8.1.7 cloudpickle-3.0.0 comm-0.2.2 contourpy-1.2.1 cycler-0.12.1 dask-2024.7.0 debugpy-1.8.2 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 executing-2.0.1 fastjsonschema-2.20.0 fonttools-4.53.1 fsspec-2024.6.1 greenlet-3.0.3 h5py-3.11.0 harmonypy-0.0.10 hnswlib-0.8.0 igraph-0.11.5 importlib_metadata-8.0.0 ipykernel-6.29.5 ipython-8.26.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 latexcodec-3.0.0 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.43.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.9.1 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.1 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.1.1 myst-parser-3.0.1 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.4 nest-asyncio-1.6.0 networkx-3.3 numba-0.60.0 numpy-2.0.0 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-10.4.0 platformdirs-4.2.2 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.2 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.1.2 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.1 pyzmq-26.0.3 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.19.0 sam-algorithm-1.0.2 scanpy-0.1.dev50+g7212584 scanpydoc-0.13.4 scikit-learn-1.5.1 scipy-1.14.0 seaborn-0.13.2 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.2.2 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.0 sphinxcontrib-bibtex-2.6.2 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.31 stack-data-0.6.3 statsmodels-0.14.2 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-0.12.1 tornado-6.4.1 tqdm-4.66.4 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.1 umap-learn-0.5.6 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.19.2 [rtd-command-info] start-time: 2024-07-08T17:50:52.968178Z, end-time: 2024-07-08T17:50:53.021544Z, 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 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 = [ "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 Version(version).is_devrelease: parsed = Version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # Bibliography settings bibtex_bibfiles = ["references.bib"] bibtex_reference_style = "author_year" # 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", "sphinxcontrib.bibtex", "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", "ftp") 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), ) # -- 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", "numpy.bool_": "numpy.bool", # Since numpy 2, numpy.bool is the canonical dtype } nitpick_ignore = [ # Technical issues ("py:class", "numpy.int64"), # documented as “attribute” ("py:class", "numpy._typing._dtype_like._SupportsDType"), ("py:class", "numpy._typing._dtype_like._DTypeDict"), # 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': "3148", 'version_slug': "3148", '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/"), ("1.10.x", "/en/1.10.x/"), ("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': '72125841fac84fdd4e906ffd4c85c9c4dce9b949', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '72125841fac84fdd4e906ffd4c85c9c4dce9b949', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '72125841fac84fdd4e906ffd4c85c9c4dce9b949', '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': '72125841', } # 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/3148' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/2335128/' 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: 2024-07-08T17:50:53.118743Z, end-time: 2024-07-08T17:55:27.915247Z, duration: 274, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.3.7 Matplotlib is building the font cache; this may take a moment. making output directory... done checking bibtex cache... out of date parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/references.bib... parsed 66 entries myst v3.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'deflist', 'html_admonition', 'colon_fence', 'html_image', 'dollarmath'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) myst-nb v1.1.1: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/3148/_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... [autosummary] generating autosummary for: 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, api/queries.md, ..., tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/index.md, tutorials/spatial/integration-scanorama.ipynb, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3148/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 104 source files that are out of date updating environment: [new config] 360 added, 0 changed, 0 removed reading sources... [ 0%] api/classes reading sources... [ 1%] api/datasets reading sources... [ 1%] api/deprecated reading sources... [ 1%] api/experimental reading sources... [ 1%] 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... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... 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[ 14%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.legend reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.savefig reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.show reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.add_totals reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.get_axes reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.getdoc reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.legend reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.make_figure reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.savefig reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.show reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes reading sources... [ 25%] api/generated/scanpy.pl.diffmap reading sources... [ 25%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 26%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 26%] 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... [ 26%] api/generated/scanpy.pl.embedding reading sources... [ 26%] api/generated/scanpy.pl.embedding_density :65: (ERROR/3) no path specified :75: (ERROR/3) no path specified :82: (ERROR/3) no path specified reading sources... [ 27%] api/generated/scanpy.pl.filter_genes_dispersion reading sources... [ 27%] api/generated/scanpy.pl.highest_expr_genes reading sources... [ 27%] api/generated/scanpy.pl.highly_variable_genes reading sources... [ 28%] api/generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00