Read the Docs build information Build id: 170879 Project: icb-scanpy Version: stable Commit: c017b2afa903c549ab2d5c221e4ea0e210d6b6fa Date: 2019-01-02T02:11:42.201490Z State: finished Success: True [rtd-command-info] start-time: 2019-01-02T02:12:39.047156Z, end-time: 2019-01-02T02:12:40.523065Z, duration: 1, exit-code: 0 git clone --depth 50 --no-single-branch https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2019-01-02T02:12:40.746370Z, end-time: 2019-01-02T02:12:40.839180Z, duration: 0, exit-code: 0 git checkout --force c017b2afa903c549ab2d5c221e4ea0e210d6b6fa Note: checking out 'c017b2afa903c549ab2d5c221e4ea0e210d6b6fa'. 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 c017b2a release 1.3.7 [rtd-command-info] start-time: 2019-01-02T02:12:40.933203Z, end-time: 2019-01-02T02:12:40.941215Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-02T02:12:41.634916Z, end-time: 2019-01-02T02:12:44.354666Z, duration: 2, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.2' 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) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.1.0) Installing collected packages: sphinx, sphinx-autodoc-typehints, numpy, scipy, h5py, python-dateutil, pandas, natsort, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba Found existing installation: Sphinx 1.7.9 Uninstalling Sphinx-1.7.9: Successfully uninstalled Sphinx-1.7.9 Successfully installed anndata-0.6.16 cycler-0.10.0 decorator-4.3.0 h5py-2.9.0 joblib-0.13.0 kiwisolver-1.0.1 llvmlite-0.27.0 matplotlib-3.0.2 natsort-5.5.0 networkx-2.2 numba-0.42.0 numexpr-2.6.9 numpy-1.15.4 pandas-0.23.4 python-dateutil-2.7.5 scikit-learn-0.20.2 scipy-1.2.0 seaborn-0.9.0 sphinx-1.8.3 sphinx-autodoc-typehints-1.6.0 tables-3.4.4 [rtd-command-info] start-time: 2019-01-02T02:13:19.640704Z, end-time: 2019-01-02T02:13:19.711504Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import inspect import logging from pathlib import Path from datetime import datetime from typing import Optional, Union, Mapping from sphinx.application import Sphinx from sphinx.ext import autosummary # remove PyCharm’s old six module if 'six' in sys.modules: print(*sys.path, sep='\n') for pypath in list(sys.path): if any(p in pypath for p in ['PyCharm', 'pycharm']) and 'helpers' in pypath: sys.path.remove(pypath) del sys.modules['six'] 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.api # noqa logger = logging.getLogger(__name__) # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx.ext.napoleon', 'sphinx_autodoc_typehints', 'sphinx.ext.intersphinx', # 'ipython_directive', # 'ipython_console_highlighting', ] # Generate the API documentation when building autosummary_generate = True # both of the following two lines don't work # see falexwolf's issue for numpydoc # 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')] intersphinx_mapping = dict( python=('https://docs.python.org/3', None), numpy=('https://docs.scipy.org/doc/numpy/', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), sklearn=('https://scikit-learn.org/stable/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), matplotlib=('https://matplotlib.org/', None), 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), ) templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' project = 'Scanpy' author = 'Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup, Sergei Rybakov, Davide Cittaro, Gokcen Eraslan, Tom White, Tobias Callies, Andrés R. Muñoz-Rojas' copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' todo_include_todos = False # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=2, ) 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 = 'Scanpydoc' latex_documents = [ (master_doc, 'Scanpy.tex', 'Scanpy Documentation', 'Alex Wolf, Philipp Angerer', 'manual'), ] man_pages = [ (master_doc, 'scanpy', 'Scanpy Documentation', [author], 1) ] texinfo_documents = [ (master_doc, 'Scanpy', 'Scanpy Documentation', author, 'Scanpy', 'One line description of project.', 'Miscellaneous'), ] # -- generate_options override ------------------------------------------ # The only thing changed here is that we specify imported_members=True # in the generate_autosummary_docs call. def process_generate_options(app: Sphinx): genfiles = app.config.autosummary_generate if genfiles and not hasattr(genfiles, '__len__'): env = app.builder.env genfiles = [ env.doc2path(x, base=None) for x in env.found_docs if Path(env.doc2path(x)).is_file() ] if not genfiles: return ext = app.config.source_suffix genfiles = [ genfile + ('' if genfile.endswith(tuple(ext)) else ext[0]) for genfile in genfiles ] suffix = autosummary.get_rst_suffix(app) if suffix is None: return from sphinx.ext.autosummary.generate import generate_autosummary_docs generate_autosummary_docs( genfiles, builder=app.builder, warn=logger.warning, info=logger.info, suffix=suffix, base_path=app.srcdir, imported_members=True, app=app, ) autosummary.process_generate_options = process_generate_options # -- GitHub URLs for class and method pages ------------------------------------------ def get_obj_module(qualname): """Get a module/class/attribute and its original module by qualname""" modname = qualname classname = None attrname = None while modname not in sys.modules: attrname = classname modname, classname = modname.rsplit('.', 1) # retrieve object and find original module name if classname: cls = getattr(sys.modules[modname], classname) try: modname = cls.__module__ except AttributeError as e: print(e) obj = getattr(cls, attrname) if attrname else cls else: obj = None return obj, sys.modules[modname] def get_linenos(obj): """Get an object’s line numbers""" try: lines, start = inspect.getsourcelines(obj) except TypeError: return None, None else: return start, start + len(lines) - 1 project_dir = Path(__file__).parent.parent # project/docs/conf.py/../.. → project/ github_url1 = 'https://github.com/{github_user}/{github_repo}/tree/{github_version}'.format_map(html_context) github_url2 = 'https://github.com/theislab/anndata/tree/master' def modurl(qualname: str) -> str: """Get the full GitHub URL for some object’s qualname.""" obj, module = get_obj_module(qualname) github_url = github_url1 try: path = Path(module.__file__).relative_to(project_dir) except ValueError: # trying to document something from another package github_url = github_url2 path = '/'.join(module.__file__.split('/')[-2:]) start, end = get_linenos(obj) fragment = f'#L{start}-L{end}' if start and end else '' return f'{github_url}/{path}{fragment}' def api_image(qualname: str) -> Optional[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 from jinja2.defaults import DEFAULT_FILTERS DEFAULT_FILTERS.update(modurl=modurl, api_image=api_image) # -- Override some classnames in autodoc -------------------------------------------- # This makes sure that automatically documented links actually # end up being links instead of pointing nowhere. import sphinx_autodoc_typehints qualname_overrides = { 'anndata.base.AnnData': 'anndata.AnnData', 'pandas.core.frame.DataFrame': 'pandas.DataFrame', 'scipy.sparse.base.spmatrix': 'scipy.sparse.spmatrix', 'scipy.sparse.csr.csr_matrix': 'scipy.sparse.csr_matrix', 'scipy.sparse.csc.csc_matrix': 'scipy.sparse.csc_matrix', } fa_orig = sphinx_autodoc_typehints.format_annotation def format_annotation(annotation): if getattr(annotation, '__origin__', None) is Union or hasattr(annotation, '__union_params__'): params = getattr(annotation, '__union_params__', None) or getattr(annotation, '__args__', None) return ', '.join(map(format_annotation, params)) if getattr(annotation, '__origin__', None) is Mapping: return ':class:`~typing.Mapping`' if inspect.isclass(annotation): full_name = '{}.{}'.format(annotation.__module__, annotation.__qualname__) override = qualname_overrides.get(full_name) if override is not None: return f':py:class:`~{qualname_overrides[full_name]}`' return fa_orig(annotation) sphinx_autodoc_typehints.format_annotation = format_annotation # -- Change default role -------------------------------------------- from docutils.parsers.rst import roles roles.DEFAULT_INTERPRETED_ROLE = 'literal' # -- Prettier Param docs -------------------------------------------- # Our PrettyTypedField is the same as the default PyTypedField, # except that the items (e.g. function parameters) get rendered as # definition list instead of paragraphs with some formatting. from typing import Dict, List, Tuple from docutils import nodes from sphinx import addnodes from sphinx.domains.python import PyTypedField, PyObject from sphinx.environment import BuildEnvironment class PrettyTypedField(PyTypedField): list_type = nodes.definition_list def make_field( self, types: Dict[str, List[nodes.Node]], domain: str, items: Tuple[str, List[nodes.inline]], env: BuildEnvironment = None ) -> nodes.field: def makerefs(rolename, name, node): return self.make_xrefs(rolename, domain, name, node, env=env) def handle_item(fieldarg: str, content: List[nodes.inline]) -> nodes.definition_list_item: head = nodes.term() head += makerefs(self.rolename, fieldarg, addnodes.literal_strong) fieldtype = types.pop(fieldarg, None) if fieldtype is not None: head += nodes.Text(' : ') if len(fieldtype) == 1 and isinstance(fieldtype[0], nodes.Text): text_node, = fieldtype # type: nodes.Text head += makerefs(self.typerolename, text_node.astext(), addnodes.literal_emphasis) else: head += fieldtype body_content = nodes.paragraph('', '', *content) body = nodes.definition('', body_content) return nodes.definition_list_item('', head, body) fieldname = nodes.field_name('', self.label) if len(items) == 1 and self.can_collapse: fieldarg, content = items[0] bodynode = handle_item(fieldarg, content) else: bodynode = self.list_type() for fieldarg, content in items: bodynode += handle_item(fieldarg, content) fieldbody = nodes.field_body('', bodynode) return nodes.field('', fieldname, fieldbody) # replace matching field types with ours PyObject.doc_field_types = [ PrettyTypedField( ft.name, names=ft.names, typenames=ft.typenames, label=ft.label, rolename=ft.rolename, typerolename=ft.typerolename, can_collapse=ft.can_collapse, ) if isinstance(ft, PyTypedField) else ft for ft in PyObject.doc_field_types ] ########################################################################### # 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. 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'bitbucket_repo': 'None', 'bitbucket_version': 'c017b2afa903c549ab2d5c221e4ea0e210d6b6fa', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'c017b2afa903c549ab2d5c221e4ea0e210d6b6fa', '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': 'c017b2af', } 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: 2019-01-02T02:13:19.774994Z, end-time: 2019-01-02T02:13:51.673296Z, duration: 31, 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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:217: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/_exporting.py:docstring of scanpy.external.exporting.cellbrowser:56: WARNING: Inline interpreted text or phrase reference start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/_exporting.py:docstring of scanpy.external.exporting.cellbrowser:57: WARNING: Inline interpreted text or phrase reference start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/_exporting.py:docstring of scanpy.external.exporting.cellbrowser:22: WARNING: Unknown target name: "x". 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/examples.rst: WARNING: document isn't included in any toctree /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. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:70: WARNING: Citation [Huber15] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:86: WARNING: Citation [Krumsiek10] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:130: WARNING: Citation [Murphy12] is not referenced. done preparing documents... done assembling single document... tutorials basic_usage installation 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.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.phate 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 writing... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst:129: WARNING: toctree contains reference to document 'api/plotting' that doesn't have a title: no link will be generated /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:docstring of 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