Read the Docs build information Build id: 2104682 Project: icb-scanpy Version: 2946 Commit: 745e79ef47a8cc41082b066736f2519fdedf6a5e Date: 2024-03-22T13:53:07.094754Z State: cancelled Success: False [rtd-command-info] start-time: 2024-03-22T13:53:08.275907Z, end-time: 2024-03-22T13:53:09.482916Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-03-22T13:53:09.547202Z, end-time: 2024-03-22T13:53:10.735015Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/2946/head:external-2946 From https://github.com/scverse/scanpy * [new ref] refs/pull/2946/head -> external-2946 * [new tag] 1.10.0rc1 -> 1.10.0rc1 [rtd-command-info] start-time: 2024-03-22T13:53:10.865041Z, end-time: 2024-03-22T13:53:11.076349Z, duration: 0, exit-code: 0 git checkout --force 745e79ef47a8cc41082b066736f2519fdedf6a5e Note: switching to '745e79ef47a8cc41082b066736f2519fdedf6a5e'. 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 745e79e Linting [rtd-command-info] start-time: 2024-03-22T13:53:11.140635Z, end-time: 2024-03-22T13:53:11.211943Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-22T13:53:11.276565Z, end-time: 2024-03-22T13:53:11.335922Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 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: 2024-03-22T13:53:17.451567Z, end-time: 2024-03-22T13:53:17.535322Z, duration: 0, exit-code: 0 asdf global python 3.12.0 [rtd-command-info] start-time: 2024-03-22T13:53:17.949594Z, end-time: 2024-03-22T13:53:19.190752Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.0.final.0-64 in 882ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2946, 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: 2024-03-22T13:53:19.264578Z, end-time: 2024-03-22T13:53:33.412636Z, duration: 14, 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/2946/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 39.3 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Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: scanpy, umap-learn, 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-1.10.0rc2.dev23+g745e79e-py3-none-any.whl size=2076891 sha256=1a210aaaf5d8466763a78cf1b1c9067bb75f5676c07e03681aee419d9132b980 Stored in directory: /tmp/pip-ephem-wheel-cache-o6n6to1e/wheels/d8/11/67/e0ec72168831690a939d6809df913e29b0836a8dc8ebbc1e56 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=ddfa79e06f55d51173f9a72cb9f36aef0dd7e05d1bcc8614034ed27e19ff629a Stored in directory: /tmp/pip-ephem-wheel-cache-o6n6to1e/wheels/3b/a7/91/c110129e07039fd4ae51fd2d857035b20d1e298c165e936f91 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=be787498a2f322a3125da758a95dec08b07a474914830637d12ca713cdbe2f76 Stored in directory: /tmp/pip-ephem-wheel-cache-o6n6to1e/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=8024 sha256=9270b2d1a70751f92153bffd6fd1fac5e0bb75b097e8dd8ff5cb76bb11c2d8d9 Stored in directory: /tmp/pip-ephem-wheel-cache-o6n6to1e/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=2275395 sha256=8da9a68c01cdbfb0f075aec5127eccd419c7a115e40027781af576a88f505482 Stored in directory: /tmp/pip-ephem-wheel-cache-o6n6to1e/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e 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, 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, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fsspec, fonttools, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, attrs, array-api-compat, accessible-pygments, sqlalchemy, session-info, scipy, referencing, python-dateutil, 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, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, 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-0.10.6 array-api-compat-1.5.1 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-1.2.0 cycler-0.12.1 dask-2024.3.1 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.50.0 fsspec-2024.3.1 greenlet-3.0.3 h5py-3.10.0 harmonypy-0.0.9 hnswlib-0.8.0 igraph-0.11.4 importlib_metadata-7.1.0 ipykernel-6.29.3 ipython-8.22.2 jedi-0.19.1 joblib-1.3.2 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.1 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.42.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.8.3 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-0.10.0 nbconvert-7.16.3 nbformat-5.10.3 nbsphinx-0.9.3 nest-asyncio-1.6.0 networkx-3.2.1 numba-0.59.1 numpy-1.26.4 pandas-2.2.1 pandocfilters-1.5.1 parso-0.8.3 partd-1.4.1 patsy-0.5.6 pexpect-4.9.0 pillow-10.2.0 platformdirs-4.2.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 pynndescent-0.5.11 pyparsing-3.1.2 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.34.0 rpds-py-0.18.0 sam-algorithm-1.0.2 scanpy-1.10.0rc2.dev23+g745e79e scanpydoc-0.13.4 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.0 sphinx-book-theme-1.1.2 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.28 stack-data-0.6.3 statsmodels-0.14.1 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.4.0 tinycss2-1.2.1 toolz-0.12.1 tornado-6.4 tqdm-4.66.2 traitlets-5.14.2 typing-extensions-4.10.0 tzdata-2024.1 umap-learn-0.5.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.18.1 [rtd-command-info] start-time: 2024-03-22T13:55:23.789688Z, end-time: 2024-03-22T13:55:23.855040Z, 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 # 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': "2946", 'version_slug': "2946", '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': '745e79ef47a8cc41082b066736f2519fdedf6a5e', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '745e79ef47a8cc41082b066736f2519fdedf6a5e', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '745e79ef47a8cc41082b066736f2519fdedf6a5e', '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': '745e79ef', } # 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/2946' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/2104682/' 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'])