Read the Docs build information Build id: 1166890 Project: icb-scanpy Version: latest Commit: d7e13025b931ad4afd03b4344ef5ff4a46f78b2b Date: 2022-11-03T13:52:25.633502Z State: finished Success: True [rtd-command-info] start-time: 2022-11-03T13:53:30.916132Z, end-time: 2022-11-03T13:53:34.267586Z, 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: 2022-11-03T13:53:34.551999Z, end-time: 2022-11-03T13:53:34.781666Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. 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 d7e13025 [pre-commit.ci] pre-commit autoupdate (#2347) [rtd-command-info] start-time: 2022-11-03T13:53:34.968373Z, end-time: 2022-11-03T13:53:35.051848Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-11-03T13:53:40.384976Z, end-time: 2022-11-03T13:53:40.472494Z, duration: 0, exit-code: 0 asdf global python 3.9.13 [rtd-command-info] start-time: 2022-11-03T13:53:41.038719Z, end-time: 2022-11-03T13:53:42.022590Z, duration: 0, exit-code: 0 python -mvirtualenv created virtual environment CPython3.9.13.final.0-64 in 653ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, 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: 2022-11-03T13:53:42.249109Z, end-time: 2022-11-03T13:53:53.042097Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.3-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/latest/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-22.3 setuptools-58.2.0 [rtd-command-info] start-time: 2022-11-03T13:53:53.272434Z, end-time: 2022-11-03T13:54:00.140733Z, duration: 6, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 Collecting pillow Downloading Pillow-9.3.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 70.1 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 277.3 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 Downloading 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/tmp/pip-ephem-wheel-cache-aqle562m/wheels/95/5a/42/6d69898ad0ccd6d30cf1ea4ae71db699e0c7bef2294dc557a5 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.11.0 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-9.3.0 pyparsing-3.0.9 pytz-2022.6 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 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 urllib3-1.26.12 [rtd-command-info] start-time: 2022-11-03T13:54:00.373929Z, end-time: 2022-11-03T13:55:16.651760Z, duration: 76, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest 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 patsy Downloading patsy-0.5.3-py2.py3-none-any.whl (233 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.8/233.8 kB 9.7 MB/s eta 0:00:00 Collecting pandas>=1.0 Downloading pandas-1.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 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texttable-1.6.4-py2.py3-none-any.whl (10 kB) Building wheels for collected packages: umap-learn, scanpy, session-info, pynndescent, python-igraph 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-0.5.3-py3-none-any.whl size=82830 sha256=3313fc564814931a0a465e99105e3c730cc44ca37355bd58f497fbb58b700f53 Stored in directory: /tmp/pip-ephem-wheel-cache-g30v9r_7/wheels/fb/99/10/ed2f3bc57ea29f540470eb43570929e30ae911b2d8353b2ee4 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.dev26+gd7e13025-py3-none-any.whl size=11485248 sha256=ad8f512ca6bf799364644993214fb29586cd84e2da89ee99cded6fd69867bc8d Stored in directory: /tmp/pip-ephem-wheel-cache-g30v9r_7/wheels/2c/ca/a8/b038e303156487f1950e65fb14990e1642cd81a73929959d71 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=2b2e604092b5b894ced27a83f7d41f399c37effe8ba8647a76577ae93dbc7834 Stored in directory: /tmp/pip-ephem-wheel-cache-g30v9r_7/wheels/10/95/8e/0027616beb8c496d40470a655c3fbb5699aec17e5004258617 Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55511 sha256=d34f076ce1b9d6f41ca490578fd5083679fc029eda138e03b9903cac70e0e8de Stored in directory: /tmp/pip-ephem-wheel-cache-g30v9r_7/wheels/8d/ca/f1/f60e041b5c82ae83173373a8991be5419647bdcf64026fd91f Building wheel for python-igraph (setup.py): started Building wheel for python-igraph (setup.py): finished with status 'done' Created wheel for python-igraph: filename=python_igraph-0.10.2-py3-none-any.whl size=9074 sha256=8e53ee0f14b645d1ea1a2c938eaa7b202507127f1bdc073e3f849d7e9c44c83c Stored in directory: /tmp/pip-ephem-wheel-cache-g30v9r_7/wheels/08/72/27/96ba6f06c4e05bc7424baf1a314ac172dd996683e50bd2d0b5 Successfully built umap-learn scanpy session-info pynndescent python-igraph Installing collected packages: texttable, stdlib_list, zipp, typing-extensions, tqdm, threadpoolctl, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, session-info, pyyaml, python-dateutil, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, Jinja2, igraph, fonttools, cycler, scipy, python-igraph, patsy, pandas, numba, markdown-it-py, importlib-metadata, h5py, dunamai, contourpy, statsmodels, sphinx, scikit-learn, mdit-py-plugins, matplotlib, get_version, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, myst-parser, umap-learn, scanpy Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed Jinja2-3.1.2 anndata-0.8.0 contourpy-1.0.6 cycler-0.11.0 dunamai-1.13.2 fonttools-4.38.0 get_version-3.5.4 h5py-3.7.0 igraph-0.10.2 importlib-metadata-5.0.0 joblib-1.2.0 kiwisolver-1.4.4 llvmlite-0.39.1 markdown-it-py-2.1.0 matplotlib-3.6.2 mdit-py-plugins-0.3.1 mdurl-0.1.2 myst-parser-0.18.1 natsort-8.2.0 networkx-2.8.8 numba-0.56.3 numpy-1.23.4 pandas-1.5.1 patsy-0.5.3 pynndescent-0.5.8 python-dateutil-2.8.2 python-igraph-0.10.2 pyyaml-6.0 scanpy-1.10.0.dev26+gd7e13025 scanpydoc-0.7.7 scikit-learn-1.1.3 scipy-1.9.3 seaborn-0.12.1 session-info-1.0.0 setuptools-65.5.0 sphinx-5.3.0 sphinx-autodoc-typehints-1.19.5 sphinx-rtd-theme-1.1.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.13.5 stdlib_list-0.8.0 texttable-1.6.4 threadpoolctl-3.1.0 tqdm-4.64.1 typing-extensions-4.4.0 umap-learn-0.5.3 zipp-3.10.0 [rtd-command-info] start-time: 2022-11-03T13:55:18.484240Z, end-time: 2022-11-03T13:55:18.545651Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa from packaging.version import parse as parse_version # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '2.0' # Nicer param docs suppress_warnings = [ 'ref.citation', 'myst.header', # https://github.com/executablebooks/MyST-Parser/issues/262 ] # General information project = 'Scanpy' author = 'Scanpy development team' copyright = f'{datetime.now():%Y}, the Scanpy development team.' version = scanpy.__version__.replace('.dirty', '') # Bumping the version updates all docs, so don't do that if parse_version(version).is_devrelease: parsed = parse_version(version) version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev" release = version # default settings templates_path = ['_templates'] master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'myst_parser', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', # 'scanpydoc', # scanpydoc.elegant_typehints causes full doc rebuilds 'scanpydoc.rtd_github_links', 'scanpydoc.theme', 'scanpydoc.definition_list_typed_field', 'scanpydoc.autosummary_generate_imported', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images typehints_defaults = 'braces' scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('https://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/stable/', None), networkx=('https://networkx.org/documentation/stable/', None), numpy=('https://numpy.org/doc/stable/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), pytest=('https://docs.pytest.org/en/latest/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'scanpydoc' html_theme_options = dict( navigation_depth=4, logo_only=True, docsearch_index='scanpy', docsearch_key='fa4304eb95d2134997e3729553a674b2', ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.warningiserror = on_rtd # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", # If the docs are built with an old version of numpy, this will make it work: "numpy.random.RandomState": "numpy.random.mtrand.RandomState", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", "pandas.core.series.Series": "pandas.Series", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.plotting._utils._AxesSubplot'), ('py:class', 'scanpy._utils.Empty'), ('py:class', 'numpy.random.mtrand.RandomState'), # Will work once scipy 1.8 is released ('py:class', 'scipy.sparse.base.spmatrix'), ('py:class', 'scipy.sparse.csr.csr_matrix'), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy.readthedocs.io/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': 'd7e13025', } # 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 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1166890/' 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: 2022-11-03T13:55:18.731014Z, end-time: 2022-11-03T13:57:30.604904Z, duration: 131, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v5.3.0 making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv... loading intersphinx inventory from https://docs.h5py.org/en/stable/objects.inv... loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, api.md, basic_usage.md, community.md, contributors.md, dev/ci.md, dev/code.md, dev/documentation.md, dev/external-tools.md, dev/getting-set-up.md, ..., release-notes/1.8.0.md, release-notes/1.8.1.md, release-notes/1.8.2.md, release-notes/1.9.0.md, release-notes/1.9.1.md, release-notes/1.9.2.md, release-notes/index.md, release-notes/release-latest.md, tutorials.md, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 63 source files that are out of date updating environment: [new config] 318 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 0%] api reading sources... [ 0%] basic_usage reading sources... [ 1%] community reading sources... [ 1%] contributors reading sources... [ 1%] dev/ci reading sources... [ 2%] dev/code reading sources... [ 2%] dev/documentation reading sources... [ 2%] dev/external-tools reading sources... [ 3%] dev/getting-set-up reading sources... [ 3%] dev/index reading sources... [ 3%] dev/release reading sources... [ 4%] dev/testing reading sources... [ 4%] dev/versioning reading sources... [ 4%] ecosystem reading sources... [ 5%] external reading sources... [ 5%] generated/classes/scanpy.pl.DotPlot reading sources... [ 5%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 5%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT reading sources... [ 8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING reading sources... [ 9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.add_dendrogram reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.add_totals reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.get_axes reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.getdoc reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.legend reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.make_figure reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.savefig reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.show reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.style reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.swap_axes reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.add_dendrogram reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_totals reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.get_axes reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.getdoc reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.legend reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.make_figure reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.savefig reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.show reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.swap_axes reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... 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[ 29%] generated/classes/scanpy.pl.StackedViolin.get_axes reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.getdoc reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.legend reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.make_figure reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.savefig reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.show reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.swap_axes reading sources... [ 32%] generated/scanpy.Neighbors reading sources... [ 32%] generated/scanpy.Neighbors.compute_eigen reading sources... [ 32%] generated/scanpy.Neighbors.compute_neighbors reading sources... [ 33%] generated/scanpy.Neighbors.compute_transitions reading sources... [ 33%] generated/scanpy.Neighbors.connectivities reading sources... 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[ 38%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.figdir reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.file_format_figs reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.logfile reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.logpath reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.max_memory reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.n_jobs reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.plot_suffix reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.set_figure_params reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.verbosity reading sources... 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[ 46%] generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 46%] generated/scanpy.external.exporting.cellbrowser reading sources... [ 46%] generated/scanpy.external.exporting.spring_project reading sources... [ 47%] generated/scanpy.external.pl.phate reading sources... [ 47%] generated/scanpy.external.pl.sam reading sources... [ 47%] generated/scanpy.external.pl.scrublet_score_distribution reading sources... [ 48%] generated/scanpy.external.pl.trimap reading sources... [ 48%] generated/scanpy.external.pl.wishbone_marker_trajectory reading sources... [ 48%] generated/scanpy.external.pp.bbknn reading sources... [ 49%] generated/scanpy.external.pp.dca reading sources... [ 49%] generated/scanpy.external.pp.harmony_integrate reading sources... [ 49%] generated/scanpy.external.pp.hashsolo reading sources... [ 50%] generated/scanpy.external.pp.magic reading sources... [ 50%] generated/scanpy.external.pp.mnn_correct reading sources... [ 50%] generated/scanpy.external.pp.scanorama_integrate reading sources... [ 50%] generated/scanpy.external.pp.scrublet reading sources... [ 51%] generated/scanpy.external.pp.scrublet_simulate_doublets reading sources... [ 51%] generated/scanpy.external.tl.cyclone reading sources... [ 51%] generated/scanpy.external.tl.harmony_timeseries reading sources... [ 52%] generated/scanpy.external.tl.palantir reading sources... [ 52%] generated/scanpy.external.tl.palantir_results reading sources... [ 52%] generated/scanpy.external.tl.phate reading sources... [ 53%] generated/scanpy.external.tl.phenograph reading sources... [ 53%] generated/scanpy.external.tl.sam reading sources... [ 53%] generated/scanpy.external.tl.sandbag reading sources... [ 54%] generated/scanpy.external.tl.trimap reading sources... [ 54%] generated/scanpy.external.tl.wishbone reading sources... [ 54%] generated/scanpy.get.obs_df reading sources... [ 55%] generated/scanpy.get.rank_genes_groups_df reading sources... [ 55%] generated/scanpy.get.var_df reading sources... [ 55%] generated/scanpy.logging.print_header reading sources... [ 55%] generated/scanpy.logging.print_versions reading sources... [ 56%] generated/scanpy.metrics.confusion_matrix reading sources... [ 56%] generated/scanpy.metrics.gearys_c reading sources... [ 56%] generated/scanpy.metrics.morans_i reading sources... [ 57%] generated/scanpy.pl.clustermap reading sources... [ 57%] generated/scanpy.pl.dendrogram reading sources... [ 57%] generated/scanpy.pl.diffmap /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( reading sources... [ 58%] 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. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:749: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored dot_ax.scatter(x, y, **kwds) 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 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:749: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored dot_ax.scatter(x, y, **kwds) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:749: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored dot_ax.scatter(x, y, **kwds) reading sources... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 58%] generated/scanpy.pl.dpt_timeseries reading sources... [ 59%] 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`). /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( reading sources... [ 59%] generated/scanpy.pl.embedding reading sources... [ 59%] generated/scanpy.pl.embedding_density reading sources... [ 60%] generated/scanpy.pl.filter_genes_dispersion reading sources... [ 60%] generated/scanpy.pl.heatmap /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. obs_tidy.index.value_counts(sort=False).iteritems() reading sources... [ 60%] generated/scanpy.pl.highest_expr_genes reading sources... [ 61%] generated/scanpy.pl.highly_variable_genes reading sources... [ 61%] 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... [ 61%] generated/scanpy.pl.paga 0%| | 0.00/23.5M [00:00