Read the Docs build information Build id: 196225 Project: icb-scanpy Version: stable Commit: bc87c15a5482dcec5380965b990b6c6126ba8e8d Date: 2019-03-29T08:54:17.041313Z State: finished Success: True [rtd-command-info] start-time: 2019-03-29T08:54:17.574593Z, end-time: 2019-03-29T08:54:19.006701Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2019-03-29T08:54:19.214069Z, end-time: 2019-03-29T08:54:19.236776Z, duration: 0, exit-code: 0 git checkout --force bc87c15a5482dcec5380965b990b6c6126ba8e8d Note: checking out 'bc87c15a5482dcec5380965b990b6c6126ba8e8d'. 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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at bc87c15 v1.4 [rtd-command-info] start-time: 2019-03-29T08:54:19.298239Z, end-time: 2019-03-29T08:54:19.306275Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-03-29T08:54:19.922328Z, end-time: 2019-03-29T08:54:22.776011Z, duration: 2, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.4' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python Installing setuptools, pip, wheel... done. 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.8) Collecting pbr>=0.11 (from mock>=2.0->tables->-r docs/requirements.txt (line 14)) Using cached https://files.pythonhosted.org/packages/14/09/12fe9a14237a6b7e0ba3a8d6fcf254bf4b10ec56a0185f73d651145e9222/pbr-5.1.3-py2.py3-none-any.whl Installing collected packages: sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, natsort, numpy, scipy, h5py, python-dateutil, pandas, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, pbr, mock, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba Found existing installation: mock 1.0.1 Uninstalling mock-1.0.1: Successfully uninstalled mock-1.0.1 Successfully installed anndata-0.6.19 cycler-0.10.0 decorator-4.4.0 future-fstrings-1.0.0 get-version-2.0.6 h5py-2.9.0 joblib-0.13.2 kiwisolver-1.0.1 llvmlite-0.28.0 matplotlib-3.0.3 mock-2.0.0 natsort-6.0.0 networkx-2.2 numba-0.43.1 numexpr-2.6.9 numpy-1.16.2 pandas-0.24.2 pbr-5.1.3 python-dateutil-2.8.0 scanpydoc-0.3.3 scikit-learn-0.20.3 scipy-1.2.1 seaborn-0.9.0 sphinx-autodoc-typehints-1.6.0 tables-3.5.1 [rtd-command-info] start-time: 2019-03-29T08:55:03.347767Z, end-time: 2019-03-29T08:55:03.415211Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime from jinja2.defaults import DEFAULT_FILTERS import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import scanpy # noqa logger = logging.getLogger(__name__) # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # 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 intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/latest/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), sklearn=('https://scikit-learn.org/stable/', None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=4, ) 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'] def setup(app): app.add_stylesheet('css/custom.css') # -- 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'), ] # -- Images for plot functions ------------------------------------------------- def api_image(qualname: str) -> str: # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path, # so no chance to not hardcode “api/” here. path = Path(__file__).parent / 'api' / f'{qualname}.png' print(path, path.is_file()) return f'.. image:: {path.name}\n :width: 200\n :align: right' if path.is_file() else '' # html_context doesn’t apply to autosummary templates ☹ # and there’s no way to insert filters into those templates # so we have to modify the default filters DEFAULT_FILTERS['api_image'] = api_image ########################################################################### # 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types 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 mulitple 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://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "stable", 'version_slug': "stable", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/stable/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', 'github_version': 'bc87c15a5482dcec5380965b990b6c6126ba8e8d', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'bc87c15a5482dcec5380965b990b6c6126ba8e8d', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'bc87c15a5482dcec5380965b990b6c6126ba8e8d', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'bc87c15a', } 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"] [rtd-command-info] start-time: 2019-03-29T08:55:03.483748Z, end-time: 2019-03-29T08:55:39.392011Z, duration: 35, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/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/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.tl.score_genes.png False /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.tl.score_genes_cell_cycle.png False /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.tl.sim.png False /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.tl.tsne.png False /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.tl.umap.png False [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.blobs.rst, 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[rtd-command-info] start-time: 2019-03-29T08:55:39.555137Z, end-time: 2019-03-29T08:56:00.772310Z, duration: 21, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/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/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... [autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., api/scanpy.tl.sim.rst, api/scanpy.tl.tsne.rst, api/scanpy.tl.umap.rst, basic_usage.rst, examples.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 190 added, 0 changed, 0 removed reading sources... [ 0%] api/index reading sources... [ 1%] api/plotting reading sources... [ 1%] api/scanpy.Neighbors reading sources... [ 2%] api/scanpy.Neighbors.compute_eigen reading sources... 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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:docstring of scanpy.api:208: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:45: WARNING: Citation [Fruchterman91] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:49: WARNING: Citation [Hagberg08] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:53: WARNING: Citation [Hastie09] is not referenced. 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api/index api/scanpy.pp.calculate_qc_metrics api/scanpy.pp.filter_cells api/scanpy.pp.filter_genes api/scanpy.pp.highly_variable_genes api/scanpy.pp.filter_genes_dispersion api/scanpy.pp.log1p api/scanpy.pp.pca api/scanpy.pp.normalize_per_cell api/scanpy.pp.regress_out api/scanpy.pp.scale api/scanpy.pp.subsample api/scanpy.pp.downsample_counts api/scanpy.pp.recipe_zheng17 api/scanpy.pp.recipe_weinreb17 api/scanpy.pp.recipe_seurat api/scanpy.pp.neighbors api/scanpy.tl.pca api/scanpy.tl.tsne api/scanpy.tl.umap api/scanpy.tl.draw_graph api/scanpy.tl.diffmap api/scanpy.tl.leiden api/scanpy.tl.louvain api/scanpy.tl.dpt api/scanpy.tl.paga api/scanpy.tl.rank_genes_groups api/scanpy.tl.score_genes api/scanpy.tl.score_genes_cell_cycle api/scanpy.tl.sim api/plotting api/scanpy.read api/scanpy.read_10x_h5 api/scanpy.read_10x_mtx api/scanpy.read_h5ad api/scanpy.read_csv api/scanpy.read_excel api/scanpy.read_hdf api/scanpy.read_loom api/scanpy.read_mtx api/scanpy.read_text api/scanpy.read_umi_tools api/scanpy.queries.mitochondrial_genes api/scanpy.Neighbors api/scanpy.Neighbors.connectivities api/scanpy.Neighbors.distances api/scanpy.Neighbors.distances_dpt api/scanpy.Neighbors.eigen_basis api/scanpy.Neighbors.eigen_values api/scanpy.Neighbors.getdoc api/scanpy.Neighbors.laplacian api/scanpy.Neighbors.transitions api/scanpy.Neighbors.transitions_sym api/scanpy.Neighbors.compute_eigen api/scanpy.Neighbors.compute_neighbors api/scanpy.Neighbors.compute_transitions api/scanpy.Neighbors.to_igraph api/scanpy.set_figure_params api/scanpy.logging.print_versions api/scanpy.datasets.blobs api/scanpy.datasets.krumsiek11 api/scanpy.datasets.moignard15 api/scanpy.datasets.pbmc3k api/scanpy.datasets.pbmc68k_reduced api/scanpy.datasets.paul15 api/scanpy.datasets.toggleswitch api/scanpy.external api/scanpy.external.pp.bbknn api/scanpy.external.pp.mnn_correct api/scanpy.external.pp.dca api/scanpy.external.pp.magic api/scanpy.external.tl.phate api/scanpy.external.tl.phenograph api/scanpy.external.tl.sandbag api/scanpy.external.tl.cyclone api/scanpy.external.pl.phate api/scanpy.external.exporting.spring_project api/scanpy.external.exporting.cellbrowser api/scanpy.api api/scanpy.api.pp.calculate_qc_metrics api/scanpy.api.pp.filter_cells api/scanpy.api.pp.filter_genes api/scanpy.api.pp.highly_variable_genes api/scanpy.api.pp.filter_genes_dispersion api/scanpy.api.pp.log1p api/scanpy.api.pp.pca api/scanpy.api.pp.normalize_per_cell api/scanpy.api.pp.regress_out api/scanpy.api.pp.scale api/scanpy.api.pp.subsample api/scanpy.api.pp.downsample_counts api/scanpy.api.pp.recipe_zheng17 api/scanpy.api.pp.recipe_weinreb17 api/scanpy.api.pp.recipe_seurat api/scanpy.api.pp.bbknn api/scanpy.api.pp.mnn_correct api/scanpy.api.pp.dca api/scanpy.api.pp.magic api/scanpy.api.pp.neighbors api/scanpy.api.tl.pca api/scanpy.api.tl.tsne api/scanpy.api.tl.umap api/scanpy.api.tl.draw_graph api/scanpy.api.tl.diffmap api/scanpy.api.tl.phate api/scanpy.api.tl.leiden api/scanpy.api.tl.louvain api/scanpy.api.tl.dpt api/scanpy.api.tl.paga api/scanpy.api.tl.rank_genes_groups api/scanpy.api.tl.score_genes api/scanpy.api.tl.score_genes_cell_cycle api/scanpy.api.tl.sandbag api/scanpy.api.tl.cyclone api/scanpy.api.tl.sim api/scanpy.api.read api/scanpy.api.read_10x_h5 api/scanpy.api.read_10x_mtx api/scanpy.api.read_h5ad api/scanpy.api.read_csv api/scanpy.api.read_excel api/scanpy.api.read_hdf api/scanpy.api.read_loom api/scanpy.api.read_mtx api/scanpy.api.read_text api/scanpy.api.read_umi_tools api/scanpy.api.queries.mitochondrial_genes api/scanpy.api.Neighbors api/scanpy.api.Neighbors.connectivities api/scanpy.api.Neighbors.distances api/scanpy.api.Neighbors.distances_dpt api/scanpy.api.Neighbors.eigen_basis api/scanpy.api.Neighbors.eigen_values api/scanpy.api.Neighbors.getdoc api/scanpy.api.Neighbors.laplacian api/scanpy.api.Neighbors.transitions api/scanpy.api.Neighbors.transitions_sym api/scanpy.api.Neighbors.compute_eigen api/scanpy.api.Neighbors.compute_neighbors api/scanpy.api.Neighbors.compute_transitions api/scanpy.api.Neighbors.to_igraph api/scanpy.api.set_figure_params api/scanpy.api.logging.print_versions api/scanpy.api.datasets.blobs api/scanpy.api.datasets.krumsiek11 api/scanpy.api.datasets.moignard15 api/scanpy.api.datasets.pbmc3k api/scanpy.api.datasets.pbmc68k_reduced api/scanpy.api.datasets.paul15 api/scanpy.api.datasets.toggleswitch api/scanpy.api.export_to.spring_project api/scanpy.plotting api/scanpy.pl.scatter api/scanpy.pl.heatmap api/scanpy.pl.dotplot api/scanpy.pl.violin api/scanpy.pl.stacked_violin api/scanpy.pl.matrixplot api/scanpy.pl.clustermap api/scanpy.pl.ranking api/scanpy.pl.highest_expr_genes api/scanpy.pl.filter_genes_dispersion api/scanpy.pl.highly_variable_genes api/scanpy.pl.pca api/scanpy.pl.pca_loadings api/scanpy.pl.pca_variance_ratio api/scanpy.pl.pca_overview api/scanpy.pl.tsne api/scanpy.pl.umap api/scanpy.pl.diffmap api/scanpy.pl.draw_graph api/scanpy.pl.dpt_groups_pseudotime api/scanpy.pl.dpt_timeseries api/scanpy.pl.paga api/scanpy.pl.paga_path api/scanpy.pl.paga_compare api/scanpy.pl.rank_genes_groups api/scanpy.pl.rank_genes_groups_violin api/scanpy.pl.rank_genes_groups_stacked_violin api/scanpy.pl.rank_genes_groups_heatmap api/scanpy.pl.rank_genes_groups_dotplot api/scanpy.pl.rank_genes_groups_matrixplot api/scanpy.pl.sim references /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst:140: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:docstring of scanpy.api:148: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header) writing... done writing additional files... copying images... 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