Read the Docs build information Build id: 328856 Project: icb-scanpy-tutorials Version: latest Commit: f371b77b383c637012e71df119ff1f6ec87e9f0c Date: 2020-05-10T19:55:29.784956Z State: finished Success: True [rtd-command-info] start-time: 2020-05-10T19:55:31.929289Z, end-time: 2020-05-10T19:55:35.727585Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2020-05-10T19:55:36.039508Z, end-time: 2020-05-10T19:55:36.445414Z, 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 f371b77 added note on draft [rtd-command-info] start-time: 2020-05-10T19:55:36.573619Z, end-time: 2020-05-10T19:55:36.764418Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-10T19:55:38.090087Z, end-time: 2020-05-10T19:55:42.157901Z, duration: 4, 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-tutorials/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-10T19:55:42.276954Z, end-time: 2020-05-10T19:55:43.078410Z, 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-tutorials/envs/latest/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-10T19:55:43.285766Z, end-time: 2020-05-10T19:55:52.989778Z, 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 imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 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 chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 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=e58ab4fce90ad2fbd2a89cff98d9d870a3c801e164a4fe92c06408a5be2ce70d Stored in directory: /tmp/pip-ephem-wheel-cache-wmw1e8sd/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=f625a43faae3cc43132d6e0622caf6a86ecdfc3f8cbd678ed96c769cc80bbfc8 Stored in directory: /tmp/pip-ephem-wheel-cache-wmw1e8sd/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, sphinxcontrib-websupport, MarkupSafe, Jinja2, certifi, idna, urllib3, chardet, requests, pytz, babel, six, pyparsing, packaging, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 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-20.3 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: 2020-05-10T19:55:53.140106Z, end-time: 2020-05-10T19:56:16.856850Z, duration: 23, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.8.5) Collecting ipykernel Downloading ipykernel-5.2.1-py3-none-any.whl (118 kB) Collecting nbsphinx>=0.4 Downloading nbsphinx-0.7.0-py3-none-any.whl (24 kB) Collecting nbclean Downloading nbclean-0.3.2-py2.py3-none-any.whl (21 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.0.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.3.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.7.12) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.8.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.14.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.2.2) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (41.0.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.2.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.23.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (20.3) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.11.2) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.14) Collecting traitlets>=4.1.0 Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) Collecting jupyter-client Downloading jupyter_client-6.1.3-py3-none-any.whl (106 kB) Collecting ipython>=5.0.0 Downloading ipython-7.14.0-py3-none-any.whl (782 kB) Collecting tornado>=4.2 Downloading tornado-6.0.4.tar.gz (496 kB) Collecting nbconvert!=5.4 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) Collecting nbformat Downloading nbformat-5.0.6-py3-none-any.whl (170 kB) Collecting nbgrader Downloading nbgrader-0.6.1.tar.gz (13.3 MB) Collecting tqdm Downloading tqdm-4.46.0-py2.py3-none-any.whl (63 kB) Collecting matplotlib Downloading matplotlib-3.2.1-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB) Collecting numpy Downloading numpy-1.18.4-cp36-cp36m-manylinux1_x86_64.whl (20.2 MB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx>=1.4->-r requirements.txt (line 1)) (2020.1) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2.9) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2020.4.5.1) 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-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (1.25.9) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (3.0.4) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=1.4->-r requirements.txt (line 1)) (2.4.7) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 1)) (1.1.1) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting pyzmq>=13 Downloading pyzmq-19.0.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Collecting jupyter-core>=4.6.0 Downloading jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB) Collecting python-dateutil>=2.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.5-py3-none-any.whl (351 kB) Collecting pexpect; sys_platform != "win32" Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting backcall Downloading backcall-0.1.0.tar.gz (9.7 kB) Collecting jedi>=0.10 Downloading jedi-0.17.0-py2.py3-none-any.whl (1.1 MB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting bleach Downloading bleach-3.1.5-py2.py3-none-any.whl (151 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting mistune<2,>=0.8.1 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.2.tar.gz (14 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting sqlalchemy Downloading SQLAlchemy-1.3.16-cp36-cp36m-manylinux2010_x86_64.whl (1.2 MB) Collecting jupyter Downloading jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB) Collecting notebook>=4.2 Downloading notebook-6.0.3-py3-none-any.whl (9.7 MB) Collecting alembic Downloading alembic-1.4.2.tar.gz (1.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting fuzzywuzzy Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB) 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 wcwidth Downloading wcwidth-0.1.9-py2.py3-none-any.whl (19 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting parso>=0.7.0 Downloading parso-0.7.0-py2.py3-none-any.whl (100 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting importlib-metadata; python_version < "3.8" Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.16.0.tar.gz (108 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting ipywidgets Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB) Collecting qtconsole Downloading qtconsole-4.7.3-py2.py3-none-any.whl (117 kB) Collecting jupyter-console Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting prometheus-client Downloading prometheus_client-0.7.1.tar.gz (38 kB) Collecting terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB) Collecting Send2Trash Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting Mako Downloading Mako-1.1.2-py2.py3-none-any.whl (75 kB) Collecting python-editor>=0.3 Downloading python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Collecting widgetsnbextension~=3.5.0 Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB) Collecting qtpy Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB) Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, alembic, pyrsistent, prometheus-client Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.0.4-cp36-cp36m-linux_x86_64.whl size=427643 sha256=5228cfc7d21e05e6aa61c712d3083930c261c1928a2f364e2cf650936ee766e8 Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505 Building wheel for nbgrader (setup.py): started Building wheel for nbgrader (setup.py): finished with status 'done' Created wheel for nbgrader: filename=nbgrader-0.6.1-py3-none-any.whl size=13507856 sha256=6e2bec64551d13cb3105331873b574b9d72ab991ea096f89b8bf88c78947ce1c Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/13/3a/de/ac4f96b6bc643b13fb358e0b05f463e8843fef478e2086ebe0 Building wheel for backcall (setup.py): started Building wheel for backcall (setup.py): finished with status 'done' Created wheel for backcall: filename=backcall-0.1.0-py3-none-any.whl size=10413 sha256=772256d7da0d1addb43ecb2e4afe35f5c86415b0144d201ec692be9c9f21ee6b Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/b4/cb/f1/d142b3bb45d488612cf3943d8a1db090eb95e6687045ba61d1 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=e5e93d396c6d7f26727fe6be779a87a0a46ecb1b48db20cda96150e80075a11c Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38 Building wheel for alembic (PEP 517): started Building wheel for alembic (PEP 517): finished with status 'done' Created wheel for alembic: filename=alembic-1.4.2-py2.py3-none-any.whl size=159543 sha256=5b347fd9891a4e380c1ab8c9de4239d15edc6a0ac80a862e175886bb1d24a35c Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/f2/50/61/5cc491b0ca39be60dfb4dce940b389ff91b847d62e0eb2d680 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp36-cp36m-linux_x86_64.whl size=115064 sha256=cccdfb0503f3a6360d6f625722802fab7cd0470c47f2cb9d57f6be739ad43eb2 Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464 Building wheel for prometheus-client (setup.py): started Building wheel for prometheus-client (setup.py): finished with status 'done' Created wheel for prometheus-client: filename=prometheus_client-0.7.1-py3-none-any.whl size=41404 sha256=477c4f5567bb07a1c08cde7e1db2a60d5cc9a733d33a1f75ea92e4962bc8d595 Stored in directory: /tmp/pip-ephem-wheel-cache-rby_22ef/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Successfully built tornado nbgrader backcall pandocfilters alembic pyrsistent prometheus-client Installing collected packages: decorator, ipython-genutils, traitlets, pyzmq, tornado, jupyter-core, python-dateutil, jupyter-client, wcwidth, prompt-toolkit, ptyprocess, pexpect, pickleshare, backcall, parso, jedi, ipython, ipykernel, entrypoints, webencodings, bleach, testpath, defusedxml, zipp, importlib-metadata, pyrsistent, attrs, jsonschema, nbformat, mistune, pandocfilters, nbconvert, nbsphinx, sqlalchemy, prometheus-client, terminado, Send2Trash, notebook, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, tqdm, kiwisolver, numpy, cycler, matplotlib, nbclean Successfully installed Mako-1.1.2 Send2Trash-1.5.0 alembic-1.4.2 attrs-19.3.0 backcall-0.1.0 bleach-3.1.5 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.18.0 importlib-metadata-1.6.0 ipykernel-5.2.1 ipython-7.14.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.3 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.2.0 matplotlib-3.2.1 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.6 nbgrader-0.6.1 nbsphinx-0.7.0 notebook-6.0.3 numpy-1.18.4 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.5 ptyprocess-0.6.0 pyrsistent-0.16.0 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.1 qtconsole-4.7.3 qtpy-1.9.0 sqlalchemy-1.3.16 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.46.0 traitlets-4.3.3 wcwidth-0.1.9 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-10T19:56:17.859865Z, end-time: 2020-05-10T19:56:18.054838Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime project = 'Scanpy' author = 'Alex Wolf, Fidel Ramirez, Sergei Rybakov' copyright = f'{datetime.now():%Y}, {author}' version = '' release = version extensions = [ 'nbsphinx', ] templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' language = None exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] pygments_style = 'sphinx' # -- 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-tutorials', # Repo name github_version='master', # Version conf_py_path='/', # 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.add_stylesheet('css/custom.css') # -- Strip output ---------------------------------------------- import nbclean, glob for filename in glob.glob('**/*.ipynb', recursive=True): ntbk = nbclean.NotebookCleaner(filename) ntbk.clear('stderr') ntbk.save(filename) ########################################################################### # 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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ("html", "//scanpy-tutorials.readthedocs.io/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy-tutorials.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy-tutorials', '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': 'f371b77b', } 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: 2020-05-10T19:56:18.175691Z, end-time: 2020-05-10T19:56:31.878721Z, duration: 13, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] README reading sources... [ 18%] cite-seq/index reading sources... [ 27%] cite-seq/pbmc5k reading sources... [ 36%] cite-seq/pbmc5k_alex reading sources... [ 45%] index reading sources... [ 54%] integrating-data-using-ingest reading sources... [ 63%] paga-paul15 reading sources... [ 72%] pbmc3k reading sources... [ 81%] spatial/basic-analysis reading sources... [ 90%] spatial/integration-scanoroma reading sources... [100%] visualizing-marker-genes looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/cite-seq/index.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 9%] README writing output... [ 18%] cite-seq/index writing output... [ 27%] cite-seq/pbmc5k writing output... [ 36%] cite-seq/pbmc5k_alex writing output... [ 45%] index writing output... [ 54%] integrating-data-using-ingest writing output... [ 63%] paga-paul15 writing output... [ 72%] pbmc3k writing output... [ 81%] spatial/basic-analysis writing output... [ 90%] spatial/integration-scanoroma writing output... [100%] visualizing-marker-genes generating indices... genindex copying notebooks ... [ 12%] cite-seq/pbmc5k.ipynb copying notebooks ... [ 25%] cite-seq/pbmc5k_alex.ipynb copying notebooks ... [ 37%] integrating-data-using-ingest.ipynb copying notebooks ... [ 50%] paga-paul15.ipynb copying notebooks ... [ 62%] pbmc3k.ipynb copying notebooks ... [ 75%] spatial/basic-analysis.ipynb copying notebooks ... [ 87%] spatial/integration-scanoroma.ipynb copying notebooks ... [100%] visualizing-marker-genes.ipynb writing additional pages... search copying images... [ 0%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_19_1.png copying images... [ 1%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_19_2.png copying images... [ 2%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_24_0.png copying images... [ 3%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_37_0.png copying images... [ 3%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_37_1.png copying images... [ 4%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_43_0.png copying images... [ 5%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_53_0.png copying images... [ 6%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_54_1.png copying images... [ 7%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_55_1.png copying images... [ 7%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_63_0.png copying images... [ 8%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_66_0.png copying images... [ 9%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_67_0.png copying images... [ 10%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_69_0.png copying images... [ 11%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_24_1.png copying images... [ 11%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_24_2.png copying images... [ 12%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_43_0.png copying images... [ 13%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_50_1.png copying images... [ 14%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_50_3.png copying images... [ 15%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_50_5.png copying images... [ 15%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_57_0.png copying images... [ 16%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_57_1.png copying images... [ 17%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_63_0.png copying images... [ 18%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_73_0.png copying images... [ 19%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_74_1.png copying images... [ 19%] cite-seq/../_build/doctrees-readthedocs/nbsphinx/cite-seq_pbmc5k_alex_75_1.png copying images... [ 20%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_12_0.png copying images... [ 21%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_17_0.png copying images... [ 22%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_21_0.png copying images... [ 23%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_27_0.png copying images... [ 23%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_40_0.png copying images... [ 24%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_45_0.png copying images... [ 25%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_53_0.png copying images... [ 26%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_60_0.png copying images... [ 26%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_66_0.png copying images... [ 27%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_80_0.png copying images... [ 28%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_0.png copying images... [ 29%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_1.png copying images... [ 30%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_2.png copying images... [ 30%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_13_0.png copying images... [ 31%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_19_0.png copying images... [ 32%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_27_1.png copying images... [ 33%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_28_1.png copying images... [ 34%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_35_2.png copying images... [ 34%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_40_0.png copying images... [ 35%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_42_0.png copying images... [ 36%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_47_1.png copying images... [ 37%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_56_0.png copying images... [ 38%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_62_0.png copying images... [ 38%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_14_1.png copying images... [ 39%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_21_0.png copying images... [ 40%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_23_0.png copying images... [ 41%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_23_1.png copying images... [ 42%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_36_0.png copying images... [ 42%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_47_0.png copying images... [ 43%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_49_0.png copying images... [ 44%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_59_0.png copying images... [ 45%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_61_0.png copying images... [ 46%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_66_0.png copying images... [ 46%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_71_1.png copying images... [ 47%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_74_1.png copying images... [ 48%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_78_1.png copying images... [ 49%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_89_1.png copying images... [ 50%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_91_0.png copying images... [ 50%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_94_0.png copying images... [ 51%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_96_0.png copying images... [ 52%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_99_1.png copying images... [ 53%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_101_0.png copying images... [ 53%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_103_0.png copying images... [ 54%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_9_0.png copying images... [ 55%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_17_0.png copying images... [ 56%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_20_0.png copying images... [ 57%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_22_0.png copying images... [ 57%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_25_0.png copying images... [ 58%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_28_1.png copying images... [ 59%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_30_0.png copying images... [ 60%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_basic-analysis_53_0.png copying images... [ 61%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_9_0.png copying images... [ 61%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_9_1.png copying images... [ 62%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_17_0.png copying images... [ 63%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_20_0.png copying images... [ 64%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_42_0.png copying images... [ 65%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_42_1.png copying images... [ 65%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_44_0.png copying images... [ 66%] spatial/../_build/doctrees-readthedocs/nbsphinx/spatial_integration-scanoroma_44_1.png copying images... [ 67%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_9_0.png copying images... [ 68%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_14_0.png copying images... [ 69%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_16_1.png copying images... [ 69%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_20_0.png copying images... [ 70%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_22_0.png copying images... [ 71%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_24_1.png copying images... [ 72%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_26_1.png copying images... [ 73%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_29_0.png copying images... [ 73%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_31_1.png copying images... [ 74%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_34_0.png copying images... [ 75%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_37_0.png copying images... [ 76%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_39_1.png copying images... [ 76%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_43_0.png copying images... [ 77%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_48_0.png copying images... [ 78%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_50_0.png copying images... [ 79%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_52_1.png copying images... [ 80%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_54_1.png copying images... [ 80%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_56_0.png copying images... [ 81%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_58_0.png copying images... [ 82%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_60_0.png copying images... [ 83%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_61_0.png copying images... [ 84%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_63_0.png copying images... [ 84%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_65_0.png copying images... [ 85%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_66_0.png copying images... [ 86%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_68_0.png copying images... [ 87%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_70_0.png copying images... [ 88%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_76_0.png copying images... [ 88%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_78_1.png copying images... [ 89%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_83_0.png copying images... [ 90%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_85_0.png copying images... [ 91%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_86_0.png copying images... [ 92%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_88_0.png copying images... [ 92%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_89_0.png copying images... [ 93%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_0.png copying images... [ 94%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_1.png copying images... [ 95%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_2.png copying images... [ 96%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_3.png copying images... [ 96%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_4.png copying images... [ 97%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_92_5.png copying images... [ 98%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_94_0.png copying images... [ 99%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_97_0.png copying images... [100%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_101_1.png copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-05-10T19:56:32.142668Z, end-time: 2020-05-10T19:56:48.747013Z, duration: 16, 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... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] README reading sources... [ 18%] cite-seq/index reading sources... [ 27%] cite-seq/pbmc5k reading sources... [ 36%] cite-seq/pbmc5k_alex reading sources... [ 45%] index reading sources... [ 54%] integrating-data-using-ingest reading sources... [ 63%] paga-paul15 reading sources... [ 72%] pbmc3k reading sources... [ 81%] spatial/basic-analysis reading sources... [ 90%] spatial/integration-scanoroma reading sources... [100%] visualizing-marker-genes looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/cite-seq/index.rst: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... pbmc3k paga-paul15 visualizing-marker-genes integrating-data-using-ingest spatial/basic-analysis spatial/integration-scanoroma cite-seq/pbmc5k writing... done writing additional files... copying images... [ 0%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_14_1.png copying images... [ 1%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_21_0.png copying images... [ 2%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_23_0.png copying images... [ 3%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_23_1.png copying images... [ 4%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_36_0.png copying images... [ 5%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_47_0.png copying images... [ 6%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_49_0.png copying images... [ 7%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_59_0.png copying images... [ 7%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_61_0.png copying images... [ 8%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_66_0.png copying images... [ 9%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_71_1.png copying images... [ 10%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_74_1.png copying images... [ 11%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_78_1.png copying images... [ 12%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_89_1.png copying images... [ 13%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_91_0.png copying images... [ 14%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_94_0.png copying images... [ 14%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_96_0.png copying images... [ 15%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_99_1.png copying images... [ 16%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_101_0.png copying images... [ 17%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_103_0.png copying images... [ 18%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_13_0.png copying images... [ 19%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_19_0.png copying images... [ 20%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_27_1.png copying images... [ 21%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_28_1.png copying images... [ 21%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_35_2.png copying images... [ 22%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_40_0.png copying images... [ 23%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_42_0.png copying images... [ 24%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_47_1.png copying images... [ 25%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_56_0.png copying images... [ 26%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_62_0.png copying images... [ 27%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_9_0.png copying images... [ 28%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_14_0.png copying images... [ 28%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_16_1.png copying images... [ 29%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_20_0.png copying images... [ 30%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_22_0.png copying images... [ 31%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_24_1.png copying images... [ 32%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_26_1.png copying images... [ 33%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_29_0.png copying images... [ 34%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_31_1.png copying images... [ 35%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_34_0.png copying images... [ 35%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_37_0.png copying images... [ 36%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_39_1.png copying images... [ 37%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_43_0.png copying images... [ 38%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_48_0.png copying images... [ 39%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_50_0.png copying images... [ 40%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_52_1.png copying images... [ 41%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_54_1.png copying images... [ 42%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_56_0.png copying images... [ 42%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_58_0.png copying images... [ 43%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_60_0.png copying images... [ 44%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_61_0.png copying images... [ 45%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_63_0.png copying images... [ 46%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_65_0.png copying images... [ 47%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_66_0.png copying images... [ 48%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_68_0.png copying images... [ 49%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_70_0.png copying images... [ 50%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_76_0.png copying images... [ 50%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_78_1.png copying images... [ 51%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_83_0.png copying images... [ 52%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_85_0.png copying images... [ 53%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_86_0.png copying images... [ 54%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_88_0.png copying images... [ 55%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_89_0.png copying images... [ 56%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_0.png copying images... [ 57%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_1.png copying images... [ 57%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_2.png copying images... [ 58%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_3.png copying images... [ 59%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_4.png copying images... [ 60%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_92_5.png copying images... [ 61%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_94_0.png copying images... [ 62%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_97_0.png copying images... [ 63%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_101_1.png copying images... [ 64%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_12_0.png copying images... [ 64%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_17_0.png copying images... [ 65%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_21_0.png copying images... [ 66%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_27_0.png copying images... [ 67%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_40_0.png copying images... [ 68%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_45_0.png copying images... [ 69%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_53_0.png copying images... [ 70%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_60_0.png copying images... [ 71%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_66_0.png copying images... [ 71%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_80_0.png copying images... [ 72%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_0.png copying images... [ 73%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_1.png copying images... [ 74%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_2.png copying images... [ 75%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_9_0.png copying images... [ 76%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_17_0.png copying images... [ 77%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_20_0.png copying images... [ 78%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_22_0.png copying images... [ 78%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_25_0.png copying images... [ 79%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_28_1.png copying images... [ 80%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_30_0.png copying images... [ 81%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_basic-analysis_53_0.png copying images... [ 82%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_9_0.png copying images... [ 83%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_9_1.png copying images... [ 84%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_17_0.png copying images... [ 85%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_20_0.png copying images... [ 85%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_42_0.png copying images... [ 86%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_42_1.png copying images... [ 87%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_44_0.png copying images... [ 88%] spatial/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/spatial_integration-scanoroma_44_1.png copying images... [ 89%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_19_1.png copying images... [ 90%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_19_2.png copying images... [ 91%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_24_0.png copying images... [ 92%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_37_0.png copying images... [ 92%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_37_1.png copying images... [ 93%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_43_0.png copying images... [ 94%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_53_0.png copying images... [ 95%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_54_1.png copying images... [ 96%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_55_1.png copying images... [ 97%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_63_0.png copying images... [ 98%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_66_0.png copying images... [ 99%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_67_0.png copying images... [100%] cite-seq/../_build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/cite-seq_pbmc5k_69_0.png copying static files... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 1 warning. The HTML page is in _build/localmedia.