Read the Docs build information Build id: 332916 Project: icb-scanpy Version: stable Commit: 78c6a438c2ce2fdf1be03ffb36ee88db800daa4d Date: 2020-05-19T07:21:31.855770Z State: finished Success: True [rtd-command-info] start-time: 2020-05-19T07:21:34.083794Z, end-time: 2020-05-19T07:21:37.158486Z, 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: 2020-05-19T07:21:37.803987Z, end-time: 2020-05-19T07:21:38.090959Z, duration: 0, exit-code: 0 git checkout --force 78c6a438c2ce2fdf1be03ffb36ee88db800daa4d Note: checking out '78c6a438c2ce2fdf1be03ffb36ee88db800daa4d'. 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 78c6a43 add proper image (#1231) [rtd-command-info] start-time: 2020-05-19T07:21:38.208589Z, end-time: 2020-05-19T07:21:38.409065Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-19T07:21:39.901563Z, end-time: 2020-05-19T07:21:43.833907Z, duration: 3, exit-code: 0 python3.6 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.6.8' 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. [rtd-command-info] start-time: 2020-05-19T07:21:44.107302Z, end-time: 2020-05-19T07:21:44.938421Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-19T07:21:45.175123Z, end-time: 2020-05-19T07:21:54.805970Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=08780bdb9654ad1553b41b903c8ee0ae2ede296cb75cb5117d7a8b6fd2254642 Stored in directory: /tmp/pip-ephem-wheel-cache-j1_5gxd8/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=5c3a60611957d2ae5ba8ec8bf4f9786e0d859566b6d35a57a66f6a1d290c0dd6 Stored in directory: /tmp/pip-ephem-wheel-cache-j1_5gxd8/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, six, pyparsing, packaging, sphinxcontrib-websupport, imagesize, snowballstemmer, pytz, babel, chardet, urllib3, idna, certifi, requests, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.4.0 Uninstalling setuptools-46.4.0: Successfully uninstalled setuptools-46.4.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-19T07:21:54.944647Z, end-time: 2020-05-19T07:22:28.443492Z, duration: 33, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting anndata>=0.7 Downloading anndata-0.7.1-py3-none-any.whl (97 kB) Collecting matplotlib>=3.1.2 Downloading matplotlib-3.2.1-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB) Collecting pandas>=0.21 Downloading pandas-1.0.3-cp36-cp36m-manylinux1_x86_64.whl (10.0 MB) Collecting scipy>=1.3 Downloading scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB) Collecting seaborn Downloading seaborn-0.10.1-py3-none-any.whl (215 kB) Collecting h5py>=2.10.0 Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB) Collecting tables Downloading tables-3.6.1-cp36-cp36m-manylinux1_x86_64.whl (4.3 MB) Collecting tqdm Downloading tqdm-4.46.0-py2.py3-none-any.whl (63 kB) Collecting importlib_metadata>=0.7 Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB) Collecting scikit-learn>=0.21.2 Downloading scikit_learn-0.23.0-cp36-cp36m-manylinux1_x86_64.whl (7.3 MB) Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.11.1-cp36-cp36m-manylinux1_x86_64.whl (8.7 MB) Collecting patsy Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting networkx Downloading networkx-2.4-py3-none-any.whl (1.6 MB) Collecting natsort Downloading natsort-7.0.1-py3-none-any.whl (33 kB) Collecting joblib Downloading joblib-0.15.1-py3-none-any.whl (298 kB) Collecting numba>=0.41.0 Downloading numba-0.49.1-cp36-cp36m-manylinux2014_x86_64.whl (3.6 MB) Collecting umap-learn>=0.3.10 Downloading umap-learn-0.4.3.tar.gz (68 kB) Collecting legacy-api-wrap Downloading legacy_api_wrap-1.2-py3-none-any.whl (37 kB) Collecting setuptools_scm Downloading setuptools_scm-3.5.0-py2.py3-none-any.whl (26 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 22)) (20.4) Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3) Collecting sphinx>=2.0.1 Downloading Sphinx-3.0.3-py3-none-any.whl (2.8 MB) Collecting sphinx-autodoc-typehints Downloading sphinx_autodoc_typehints-1.10.3-py3-none-any.whl (8.4 kB) Collecting scanpydoc>=0.4.5 Downloading scanpydoc-0.4.5-py3-none-any.whl (23 kB) Collecting typing_extensions Downloading typing_extensions-3.7.4.2-py3-none-any.whl (22 kB) Collecting numpy~=1.14 Downloading numpy-1.18.4-cp36-cp36m-manylinux1_x86_64.whl (20.2 MB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.2.0-cp36-cp36m-manylinux1_x86_64.whl (88 kB) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting python-dateutil>=2.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from matplotlib>=3.1.2->-r docs/../requirements.txt (line 4)) (2.4.7) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from pandas>=0.21->-r docs/../requirements.txt (line 5)) (2020.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from h5py>=2.10.0->-r docs/../requirements.txt (line 8)) (1.14.0) Collecting numexpr>=2.6.2 Downloading numexpr-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (162 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-2.0.0-py3-none-any.whl (34 kB) Collecting decorator>=4.3.0 Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting llvmlite<=0.33.0.dev0,>=0.31.0.dev0 Downloading llvmlite-0.32.1-cp36-cp36m-manylinux1_x86_64.whl (20.2 MB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from numba>=0.41.0->-r docs/../requirements.txt (line 18)) (41.0.1) Collecting tbb Downloading tbb-2020.0.133-py2.py3-none-manylinux1_x86_64.whl (933 kB) Collecting get-version>=2.0.4 Downloading get_version-2.1-py3-none-any.whl (43 kB) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (0.14) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (2.11.2) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (1.2.0) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (2.3.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (2.8.0) Requirement already satisfied: alabaster<0.8,>=0.7 in 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Jinja2>=2.3->sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (1.1.1) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (2.9) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (2020.4.5.1) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (3.0.4) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 3)) (1.25.9) Building wheels for collected packages: umap-learn 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-0.4.3-py3-none-any.whl size=66577 sha256=c58e56e0f97f24dd1f94c30e3c5b077a5f4a2a9354d3c9694693141a77246ef2 Stored in directory: /tmp/pip-ephem-wheel-cache-e_1126of/wheels/68/91/c1/26b99fb497515f6df73a39b644595f4023dff150230c90dc87 Successfully built umap-learn Installing collected packages: natsort, zipp, importlib-metadata, numpy, scipy, h5py, python-dateutil, pandas, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, tables, tqdm, joblib, threadpoolctl, scikit-learn, patsy, statsmodels, decorator, networkx, llvmlite, numba, tbb, umap-learn, get-version, legacy-api-wrap, setuptools-scm, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinx, sphinx-autodoc-typehints, scanpydoc, typing-extensions Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed anndata-0.7.1 cycler-0.10.0 decorator-4.4.2 get-version-2.1 h5py-2.10.0 importlib-metadata-1.6.0 joblib-0.15.1 kiwisolver-1.2.0 legacy-api-wrap-1.2 llvmlite-0.32.1 matplotlib-3.2.1 natsort-7.0.1 networkx-2.4 numba-0.49.1 numexpr-2.7.1 numpy-1.18.4 pandas-1.0.3 patsy-0.5.1 python-dateutil-2.8.1 scanpydoc-0.4.5 scikit-learn-0.23.0 scipy-1.4.1 seaborn-0.10.1 setuptools-scm-3.5.0 sphinx-3.0.3 sphinx-autodoc-typehints-1.10.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 statsmodels-0.11.1 tables-3.6.1 tbb-2020.0.133 threadpoolctl-2.0.0 tqdm-4.46.0 typing-extensions-3.7.4.2 umap-learn-0.4.3 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-19T07:22:29.969963Z, end-time: 2020-05-19T07:22:30.183733Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys import warnings from pathlib import Path from datetime import datetime import matplotlib # noqa # 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'] # 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', *[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 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=('http://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/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), scvelo=('https://scvelo.readthedocs.io/', 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 = 'sphinx_rtd_theme' html_theme_options = dict(navigation_depth=4, logo_only=True) # Only show the logo 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 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', ) ] # -- 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", } 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'), ] ########################################################################### # 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 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': "stable", 'version_slug': "stable", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("1.4.4.post1", "/en/1.4.4.post1/"), ("1.1", "/en/1.1/"), ], 'downloads': [ ("html", "//scanpy.readthedocs.io/_/downloads/en/stable/htmlzip/"), ], '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': 'theislab', 'github_repo': 'scanpy', 'github_version': '78c6a438c2ce2fdf1be03ffb36ee88db800daa4d', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '78c6a438c2ce2fdf1be03ffb36ee88db800daa4d', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '78c6a438c2ce2fdf1be03ffb36ee88db800daa4d', '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': '78c6a438', } 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") 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' [rtd-command-info] start-time: 2020-05-19T07:22:30.347520Z, end-time: 2020-05-19T07:24:21.159431Z, duration: 110, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.0.3 loading translations [en]... done making output directory... done 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 http://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/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 https://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://scvelo.readthedocs.io/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, _links.rst, api/index.rst, api/plotting.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, ecosystem.rst, external/index.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst [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._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc3k_processed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc68k_reduced.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pp.scvi.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.wishbone.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_eigen.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.rp_forest.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 16 source files that are out of date updating environment: [new config] 172 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 1%] _links reading sources... [ 1%] api/index /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable" is shallow and may cause errors warnings.warn('"{}" is shallow and may cause errors'.format(wd.path)) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/deprecation.py:52: RemovedInSphinx40Warning: sphinx.builders.html.DirectoryHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. return getattr(self._module, name) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/readthedocs_ext/readthedocs.py:14: RemovedInSphinx40Warning: sphinx.builders.html.SingleFileHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. from sphinx.builders.html import (DirectoryHTMLBuilder, SingleFileHTMLBuilder, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/conf.py:112: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('css/custom.css') /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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The HTML pages are in _build/html. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) [rtd-command-info] start-time: 2020-05-19T07:24:21.365111Z, end-time: 2020-05-19T07:25:18.838338Z, duration: 57, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.0.3 loading translations [en]... done making output directory... done 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 http://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/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 https://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://scvelo.readthedocs.io/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, _links.rst, 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, ..., external/scanpy.external.tl.sandbag.rst, external/scanpy.external.tl.trimap.rst, external/scanpy.external.tl.wishbone.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 172 added, 0 changed, 0 removed reading sources... [ 0%] _key_contributors reading sources... [ 1%] _links reading sources... [ 1%] api/index /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable" is shallow and may cause errors warnings.warn('"{}" is shallow and may cause errors'.format(wd.path)) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/deprecation.py:52: RemovedInSphinx40Warning: sphinx.builders.html.DirectoryHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. return getattr(self._module, name) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/readthedocs_ext/readthedocs.py:14: RemovedInSphinx40Warning: sphinx.builders.html.SingleFileHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. from sphinx.builders.html import (DirectoryHTMLBuilder, SingleFileHTMLBuilder, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/conf.py:112: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead. app.add_stylesheet('css/custom.css') /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/inspect.py:555: RemovedInSphinx40Warning: sphinx.util.inspect.Signature() is deprecated RemovedInSphinx40Warning) 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[100%] usage-principles looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... tutorials usage-principles 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.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.embedding_density api/scanpy.tl.leiden api/scanpy.tl.louvain api/scanpy.tl.dendrogram api/scanpy.tl.dpt api/scanpy.tl.paga api/scanpy.tl.ingest api/scanpy.tl.rank_genes_groups api/scanpy.tl.filter_rank_genes_groups 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