Read the Docs build information Build id: 195011 Project: icb-scanpy Version: latest Commit: 4b1504c52250cdc3d40db781eaf807fe59fd8856 Date: 2019-03-26T11:03:00.835526Z State: finished Success: True [rtd-command-info] start-time: 2019-03-26T11:03:01.299458Z, end-time: 2019-03-26T11:03:05.029728Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2019-03-26T11:03:05.347842Z, end-time: 2019-03-26T11:03:05.382784Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out '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 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 4b1504c added scanpy logo [rtd-command-info] start-time: 2019-03-26T11:03:05.443142Z, end-time: 2019-03-26T11:03:05.450783Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-03-26T11:03:06.081795Z, end-time: 2019-03-26T11:03:09.373179Z, duration: 3, 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/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-03-26T11:03:09.439554Z, end-time: 2019-03-26T11:03:11.845244Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip Collecting pip Downloading https://files.pythonhosted.org/packages/d8/f3/413bab4ff08e1fc4828dfc59996d721917df8e8583ea85385d51125dceff/pip-19.0.3-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 18.1 Uninstalling pip-18.1: Successfully uninstalled pip-18.1 Successfully installed pip-19.0.3 [rtd-command-info] start-time: 2019-03-26T11:03:11.903605Z, end-time: 2019-03-26T11:03:35.562983Z, duration: 23, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (3.0.4) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.1.1) Collecting pbr>=0.11 (from mock>=2.0->tables->-r docs/requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/14/09/12fe9a14237a6b7e0ba3a8d6fcf254bf4b10ec56a0185f73d651145e9222/pbr-5.1.3-py2.py3-none-any.whl (107kB) Building wheels for collected packages: anndata, networkx Building wheel for anndata (setup.py): started Building wheel for anndata (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7f/e5/74/a94b1e21a75fbdff29343aeb9970279fbc9ab8a2a8cfaa87dc Building wheel for 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natsort-6.0.0 networkx-2.2 numba-0.43.0 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-1.8.5 sphinx-autodoc-typehints-1.6.0 tables-3.5.1 [rtd-command-info] start-time: 2019-03-26T11:04:09.398870Z, end-time: 2019-03-26T11:04:09.461833Z, 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), networkx=('https://networkx.github.io/documentation/networkx-1.10/', 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 logo_only=True, # Only show the logo ) html_static_path = ['_static'] html_logo = '_static/img/Scanpy_Logo_RGB.png' 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': "latest", 'version_slug': "latest", '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/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', '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, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '4b1504c5', } 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: 2019-03-26T11:04:09.523420Z, end-time: 2019-03-26T11:04:49.388096Z, duration: 39, exit-code: 0 python sphinx-build -T -E -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://networkx.github.io/documentation/networkx-1.10/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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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: failed to import tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: toctree references unknown document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: failed to import tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: toctree references unknown document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:212: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:103: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:10: WARNING: Unexpected section title. 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[ 35%] api/scanpy.api.read_mtx writing output... [ 36%] api/scanpy.api.read_text writing output... [ 36%] api/scanpy.api.read_umi_tools writing output... [ 37%] api/scanpy.api.set_figure_params writing output... [ 37%] api/scanpy.api.tl.cyclone writing output... [ 38%] api/scanpy.api.tl.diffmap writing output... [ 38%] api/scanpy.api.tl.dpt writing output... [ 39%] api/scanpy.api.tl.draw_graph writing output... [ 40%] api/scanpy.api.tl.leiden writing output... [ 40%] api/scanpy.api.tl.louvain writing output... [ 41%] api/scanpy.api.tl.paga writing output... [ 41%] api/scanpy.api.tl.pca writing output... [ 42%] api/scanpy.api.tl.phate writing output... [ 42%] api/scanpy.api.tl.rank_genes_groups writing output... [ 43%] api/scanpy.api.tl.sandbag writing output... [ 43%] api/scanpy.api.tl.score_genes writing output... [ 44%] api/scanpy.api.tl.score_genes_cell_cycle writing output... [ 44%] api/scanpy.api.tl.sim writing output... [ 45%] api/scanpy.api.tl.tsne writing output... [ 45%] api/scanpy.api.tl.umap writing output... [ 46%] api/scanpy.datasets.blobs writing output... [ 46%] api/scanpy.datasets.krumsiek11 writing output... [ 47%] api/scanpy.datasets.moignard15 writing output... [ 47%] api/scanpy.datasets.paul15 writing output... [ 48%] api/scanpy.datasets.pbmc3k writing output... [ 48%] api/scanpy.datasets.pbmc68k_reduced writing output... [ 49%] api/scanpy.datasets.toggleswitch writing output... [ 49%] api/scanpy.external writing output... [ 50%] api/scanpy.external.exporting.cellbrowser writing output... [ 50%] api/scanpy.external.exporting.spring_project writing output... [ 51%] api/scanpy.external.pl.phate writing output... [ 51%] api/scanpy.external.pp.bbknn writing output... [ 52%] api/scanpy.external.pp.dca writing output... [ 52%] api/scanpy.external.pp.magic writing output... [ 53%] api/scanpy.external.pp.mnn_correct writing output... [ 53%] api/scanpy.external.tl.cyclone writing output... [ 54%] api/scanpy.external.tl.palantir writing output... [ 54%] api/scanpy.external.tl.phate writing output... [ 55%] api/scanpy.external.tl.phenograph writing output... [ 55%] api/scanpy.external.tl.sandbag writing output... [ 56%] api/scanpy.logging.print_versions writing output... [ 56%] api/scanpy.pl.clustermap writing output... [ 57%] api/scanpy.pl.diffmap writing output... [ 57%] api/scanpy.pl.dotplot writing output... [ 58%] api/scanpy.pl.dpt_groups_pseudotime writing output... [ 58%] api/scanpy.pl.dpt_timeseries writing output... [ 59%] api/scanpy.pl.draw_graph writing output... [ 60%] api/scanpy.pl.embedding_density writing output... [ 60%] api/scanpy.pl.filter_genes_dispersion writing output... [ 61%] api/scanpy.pl.heatmap writing output... [ 61%] api/scanpy.pl.highest_expr_genes writing output... [ 62%] api/scanpy.pl.highly_variable_genes writing output... [ 62%] api/scanpy.pl.matrixplot writing output... [ 63%] api/scanpy.pl.paga writing output... [ 63%] api/scanpy.pl.paga_compare writing output... [ 64%] api/scanpy.pl.paga_path writing output... [ 64%] api/scanpy.pl.pca writing output... [ 65%] api/scanpy.pl.pca_loadings writing output... [ 65%] api/scanpy.pl.pca_overview writing output... [ 66%] api/scanpy.pl.pca_variance_ratio writing output... [ 66%] api/scanpy.pl.rank_genes_groups writing output... [ 67%] api/scanpy.pl.rank_genes_groups_dotplot writing output... [ 67%] api/scanpy.pl.rank_genes_groups_heatmap writing output... [ 68%] api/scanpy.pl.rank_genes_groups_matrixplot writing output... [ 68%] api/scanpy.pl.rank_genes_groups_stacked_violin writing output... [ 69%] api/scanpy.pl.rank_genes_groups_violin writing output... [ 69%] api/scanpy.pl.ranking writing output... [ 70%] api/scanpy.pl.scatter writing output... [ 70%] api/scanpy.pl.sim writing output... [ 71%] api/scanpy.pl.stacked_violin writing output... [ 71%] api/scanpy.pl.tsne writing output... [ 72%] api/scanpy.pl.umap writing output... [ 72%] api/scanpy.pl.violin writing output... [ 73%] api/scanpy.plotting writing output... [ 73%] api/scanpy.pp.calculate_qc_metrics writing output... [ 74%] api/scanpy.pp.combat writing output... [ 74%] api/scanpy.pp.downsample_counts writing output... [ 75%] api/scanpy.pp.filter_cells writing output... [ 75%] api/scanpy.pp.filter_genes writing output... [ 76%] api/scanpy.pp.filter_genes_dispersion writing output... [ 76%] api/scanpy.pp.highly_variable_genes writing output... [ 77%] api/scanpy.pp.log1p writing output... [ 77%] api/scanpy.pp.neighbors writing output... [ 78%] api/scanpy.pp.normalize_per_cell writing output... [ 78%] api/scanpy.pp.normalize_quantile writing output... [ 79%] api/scanpy.pp.normalize_total writing output... [ 80%] api/scanpy.pp.pca writing output... [ 80%] api/scanpy.pp.recipe_seurat writing output... [ 81%] api/scanpy.pp.recipe_weinreb17 writing output... [ 81%] api/scanpy.pp.recipe_zheng17 writing output... [ 82%] api/scanpy.pp.regress_out writing output... [ 82%] api/scanpy.pp.scale writing output... [ 83%] api/scanpy.pp.subsample writing output... [ 83%] api/scanpy.queries.mitochondrial_genes writing output... [ 84%] api/scanpy.read writing output... [ 84%] api/scanpy.read_10x_h5 writing output... [ 85%] api/scanpy.read_10x_mtx writing output... [ 85%] api/scanpy.read_csv writing output... [ 86%] api/scanpy.read_excel writing output... [ 86%] api/scanpy.read_h5ad writing output... [ 87%] api/scanpy.read_hdf writing output... [ 87%] api/scanpy.read_loom writing output... [ 88%] api/scanpy.read_mtx writing output... [ 88%] api/scanpy.read_text writing output... [ 89%] api/scanpy.read_umi_tools writing output... [ 89%] api/scanpy.set_figure_params writing output... [ 90%] api/scanpy.tl.diffmap writing output... [ 90%] api/scanpy.tl.dpt writing output... [ 91%] api/scanpy.tl.draw_graph writing output... [ 91%] api/scanpy.tl.leiden writing output... [ 92%] api/scanpy.tl.louvain writing output... [ 92%] api/scanpy.tl.paga writing output... [ 93%] api/scanpy.tl.pca writing output... [ 93%] api/scanpy.tl.rank_genes_groups writing output... [ 94%] api/scanpy.tl.score_genes writing output... [ 94%] api/scanpy.tl.score_genes_cell_cycle writing output... [ 95%] api/scanpy.tl.sim writing output... [ 95%] api/scanpy.tl.tsne writing output... [ 96%] api/scanpy.tl.umap writing output... [ 96%] basic_usage writing output... [ 97%] examples writing output... [ 97%] index writing output... [ 98%] installation writing output... [ 98%] references writing output... [ 99%] release_notes writing output... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:145: 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/latest/docs/api/index.rst:270::: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:270::: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:152: 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/latest/scanpy/api/__init__.py:docstring of scanpy.api:111::: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:120::: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: 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reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.dendrogram' b'':: WARNING: toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:32: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:22: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:25: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) generating indices... genindex py-modindex writing additional pages... search copying images... 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[rtd-command-info] start-time: 2019-03-26T11:04:49.571948Z, end-time: 2019-03-26T11:05:25.241134Z, duration: 35, 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://networkx.github.io/documentation/networkx-1.10/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 WARNING: [autosummary] failed to import 'scanpy.api.tl.dendrogram': no module named scanpy.api.tl.dendrogram WARNING: [autosummary] failed to import 'scanpy.api.tl.filter_rank_genes_groups': no module named scanpy.api.tl.filter_rank_genes_groups building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 195 added, 0 changed, 0 removed reading sources... 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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: failed to import tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: toctree references unknown document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: failed to import tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: toctree references unknown document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:212: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:103: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:10: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:33: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:40: WARNING: Unexpected section title. Examples -------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/__init__.py:docstring of scanpy.plotting:101: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_quantile:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:24: WARNING: Bullet list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.embedding_density.rst: WARNING: document isn't included in any toctree 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:138: 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.log1p api/scanpy.pp.pca api/scanpy.pp.normalize_total api/scanpy.pp.normalize_quantile 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.combat 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.palantir 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/tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.rst: WARNING: toctree contains ref to nonexisting file 'api/tl.dendrogram' api/scanpy.api.tl.rank_genes_groups api/tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.rst: WARNING: toctree contains ref to nonexisting file 'api/tl.filter_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 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api/scanpy.pl.rank_genes_groups_matrixplot api/scanpy.pl.sim api/scanpy.pp.filter_genes_dispersion api/scanpy.pp.normalize_per_cell references /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:145: 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/latest/scanpy/api/__init__.py:docstring of scanpy.api:152: 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/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:32: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:25: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:22: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) writing... 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