Read the Docs build information Build id: 303087 Project: icb-scanpy-tutorials Version: latest Commit: 28fb92aa66bc863a9713fda35398df0eaf3c793b Date: 2020-03-17T12:22:30.684487Z State: finished Success: True [rtd-command-info] start-time: 2020-03-17T12:22:33.557166Z, end-time: 2020-03-17T12:22:37.168400Z, 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: 2020-03-17T12:22:37.588237Z, end-time: 2020-03-17T12:22:38.071426Z, 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 28fb92a remove spatial branch path from pip (#12) [rtd-command-info] start-time: 2020-03-17T12:22:38.205770Z, end-time: 2020-03-17T12:22:38.526763Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-03-17T12:22:39.938984Z, end-time: 2020-03-17T12:22:44.533624Z, 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: 2020-03-17T12:22:44.693571Z, end-time: 2020-03-17T12:22:45.745236Z, duration: 1, 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 (20.0.2) [rtd-command-info] start-time: 2020-03-17T12:22:45.875249Z, end-time: 2020-03-17T12:22:58.073472Z, duration: 12, 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-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.0-py2.py3-none-any.whl (39 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.6-py2.py3-none-any.whl (67 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting certifi>=2017.4.17 Downloading certifi-2019.11.28-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 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=e6bca0ea28379c6a16da8f2abafaa1c4e8641d22a71eef1d22059bfca589aa49 Stored in directory: /tmp/pip-ephem-wheel-cache-joambp10/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=a32d586e5728213958133a142b9289dafb5a069e050b277953dfee7cc2e81b41 Stored in directory: /tmp/pip-ephem-wheel-cache-joambp10/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, pyparsing, six, packaging, urllib3, certifi, idna, chardet, requests, MarkupSafe, Jinja2, sphinxcontrib-websupport, snowballstemmer, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.0.0 Uninstalling setuptools-46.0.0: Successfully uninstalled setuptools-46.0.0 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 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-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 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-1.2.0 urllib3-1.25.8 [rtd-command-info] start-time: 2020-03-17T12:22:58.234810Z, end-time: 2020-03-17T12:23:33.600018Z, duration: 35, 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-5.1.4-py3-none-any.whl (116 kB) Collecting nbsphinx>=0.4 Downloading nbsphinx-0.5.1-py2.py3-none-any.whl (21 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: 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)) (1.2.0) 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: 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: 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: 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: 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: 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) 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: 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: 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: 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)) (2.11.1) Collecting jupyter-client Downloading jupyter_client-6.0.0-py3-none-any.whl (104 kB) Collecting tornado>=4.2 Downloading tornado-6.0.4.tar.gz (496 kB) Collecting ipython>=5.0.0 Downloading ipython-7.13.0-py3-none-any.whl (780 kB) Collecting traitlets>=4.1.0 Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) Collecting nbformat Downloading nbformat-5.0.4-py3-none-any.whl (169 kB) Collecting nbconvert!=5.4 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) Collecting matplotlib Downloading matplotlib-3.2.0-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB) Collecting tqdm Downloading tqdm-4.43.0-py2.py3-none-any.whl (59 kB) Collecting numpy Downloading numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl (20.1 MB) Collecting nbgrader Downloading nbgrader-0.6.1.tar.gz (13.3 MB) 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: 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)) (1.25.8) 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)) (2019.11.28) 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: 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)) (2.4.6) 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)) (2019.3) 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 python-dateutil>=2.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting pyzmq>=13 Downloading pyzmq-19.0.0-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 pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.4-py3-none-any.whl (351 kB) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting jedi>=0.10 Downloading jedi-0.16.0-py2.py3-none-any.whl (1.1 MB) Collecting pexpect; sys_platform != "win32" Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting backcall Downloading backcall-0.1.0.tar.gz (9.7 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 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 testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting bleach Downloading bleach-3.1.1-py2.py3-none-any.whl (150 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90 kB) Collecting sqlalchemy Downloading SQLAlchemy-1.3.15.tar.gz (6.1 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 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-1.4.1.tar.gz (1.1 MB) Collecting fuzzywuzzy Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB) Collecting wcwidth Downloading wcwidth-0.1.8-py2.py3-none-any.whl (17 kB) Collecting parso>=0.5.2 Downloading parso-0.6.2-py2.py3-none-any.whl (97 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting importlib-metadata; python_version < "3.8" Downloading importlib_metadata-1.5.0-py2.py3-none-any.whl (30 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.15.7.tar.gz (107 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting ipywidgets Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB) Collecting jupyter-console Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting qtconsole Downloading qtconsole-4.7.1-py2.py3-none-any.whl (117 kB) Collecting Send2Trash Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB) Collecting prometheus-client Downloading prometheus_client-0.7.1.tar.gz (38 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, sqlalchemy, 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=427640 sha256=6af32b252960d7f7c906cc4a0212acfa95e88f5b44db107a85e3da9cdf7bb188 Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/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=0c9b0e524904071b4fbc126fb51b6ea792eabf2a40d436c613c811608261f3fb Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/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=80aa309fc784641b67222d2a1e8b05eb24d9fb2b54141c0609af9b25fe9232f7 Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/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=ea46befbb2a0b04b1511829fc7c4e39d0a96b065a7ef23deb133047ae7e80b6d Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38 Building wheel for sqlalchemy (PEP 517): started Building wheel for sqlalchemy (PEP 517): finished with status 'done' Created wheel for sqlalchemy: filename=SQLAlchemy-1.3.15-cp36-cp36m-linux_x86_64.whl size=1230238 sha256=074d885941eaf7a81518494522e44f0bcbe7bc09d4b74655d2ab9881be9fd709 Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/wheels/4a/1b/3a/c73044d7be48baeb47cbee343334f7803726ca1e9ba7b29095 Building wheel for alembic (setup.py): started Building wheel for alembic (setup.py): finished with status 'done' Created wheel for alembic: filename=alembic-1.4.1-py2.py3-none-any.whl size=158154 sha256=094dcaa98c842a3468b27a507baa08a67c3488030a6d37e39eb115c00eae3cf3 Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/wheels/e9/7b/aa/e18c983d8236b141f85838ba0f8e4e4ae9bcf7f1e00ff726ec Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.15.7-cp36-cp36m-linux_x86_64.whl size=115013 sha256=79caba8d7135c55e6e53591d6be6006b19456ab2114c4b6a71e3419de6e8b002 Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/wheels/43/9a/e4/7f687f2bb934e9a26a6e1158778ed7c5436b9ea15db48c888a 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=bc67351e4a741caf9d8b774a82c0ae88f44e6c90844b4e192125a45658aaeedd Stored in directory: /tmp/pip-ephem-wheel-cache-6f0nq23q/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic pyrsistent prometheus-client Installing collected packages: decorator, ipython-genutils, traitlets, tornado, python-dateutil, pyzmq, jupyter-core, jupyter-client, pickleshare, wcwidth, prompt-toolkit, parso, jedi, ptyprocess, pexpect, backcall, ipython, ipykernel, zipp, importlib-metadata, attrs, pyrsistent, jsonschema, nbformat, entrypoints, mistune, pandocfilters, testpath, webencodings, bleach, defusedxml, nbconvert, nbsphinx, numpy, cycler, kiwisolver, matplotlib, tqdm, sqlalchemy, Send2Trash, terminado, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter-console, qtpy, qtconsole, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, nbclean Successfully installed Mako-1.1.2 Send2Trash-1.5.0 alembic-1.4.1 attrs-19.3.0 backcall-0.1.0 bleach-3.1.1 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.18.0 importlib-metadata-1.5.0 ipykernel-5.1.4 ipython-7.13.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.16.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.0.0 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.1.0 matplotlib-3.2.0 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.4 nbgrader-0.6.1 nbsphinx-0.5.1 notebook-6.0.3 numpy-1.18.1 pandocfilters-1.4.2 parso-0.6.2 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.4 ptyprocess-0.6.0 pyrsistent-0.15.7 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.0 qtconsole-4.7.1 qtpy-1.9.0 sqlalchemy-1.3.15 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.43.0 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-03-17T12:23:34.983282Z, end-time: 2020-03-17T12:23:35.297033Z, 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://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ("html", "//icb-scanpy-tutorials.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': '/_', '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': '28fb92aa', } 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: 2020-03-17T12:23:35.502240Z, end-time: 2020-03-17T12:23:47.247477Z, duration: 11, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... [ 14%] README reading sources... [ 28%] analysis-visualization-spatial reading sources... [ 42%] index reading sources... [ 57%] integrating-data-using-ingest reading sources... [ 71%] paga-paul15 reading sources... [ 85%] pbmc3k reading sources... [100%] visualizing-marker-genes looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 14%] README writing output... [ 28%] analysis-visualization-spatial writing output... [ 42%] index writing output... [ 57%] integrating-data-using-ingest writing output... [ 71%] paga-paul15 writing output... [ 85%] pbmc3k writing output... [100%] visualizing-marker-genes generating indices... genindex copying notebooks ... [ 20%] analysis-visualization-spatial.ipynb copying notebooks ... [ 40%] integrating-data-using-ingest.ipynb copying notebooks ... [ 60%] paga-paul15.ipynb copying notebooks ... [ 80%] pbmc3k.ipynb copying notebooks ... [100%] visualizing-marker-genes.ipynb writing additional pages... search copying images... [ 1%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_7_1.png copying images... [ 2%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_13_0.png copying images... [ 3%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_13_1.png copying images... [ 4%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_15_0.png copying images... [ 5%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_17_0.png copying images... [ 6%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_19_0.png copying images... [ 7%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_21_1.png copying images... [ 8%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_23_0.png copying images... [ 9%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_30_0.png copying images... [ 10%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_39_0.png copying images... [ 11%] _build/doctrees-readthedocs/nbsphinx/analysis-visualization-spatial_41_0.png copying images... [ 12%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_12_0.png copying images... [ 13%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_17_0.png copying images... [ 14%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_21_0.png copying images... [ 15%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_27_0.png copying images... [ 16%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_40_0.png copying images... [ 17%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_45_0.png copying images... [ 18%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_53_0.png copying images... [ 19%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_60_0.png copying images... [ 20%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_66_0.png copying images... [ 21%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_80_0.png copying images... [ 22%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_0.png copying images... [ 23%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_1.png copying images... [ 25%] _build/doctrees-readthedocs/nbsphinx/integrating-data-using-ingest_82_2.png copying images... [ 26%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_13_0.png copying images... [ 27%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_19_0.png copying images... [ 28%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_27_1.png copying images... [ 29%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_28_1.png copying images... [ 30%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_35_2.png copying images... [ 31%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_40_0.png copying images... [ 32%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_42_0.png copying images... [ 33%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_47_1.png copying images... [ 34%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_56_0.png copying images... [ 35%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_62_0.png copying images... [ 36%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_13_1.png copying images... [ 37%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_20_0.png copying images... [ 38%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_22_0.png copying images... [ 39%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_22_1.png copying images... [ 40%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_35_0.png copying images... [ 41%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_46_0.png copying images... [ 42%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_48_0.png copying images... [ 43%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_58_0.png copying images... [ 44%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_60_0.png copying images... [ 45%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_65_0.png copying images... [ 46%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_70_1.png copying images... [ 47%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_73_1.png copying images... [ 48%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_77_1.png copying images... [ 50%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_88_1.png copying images... [ 51%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_90_0.png copying images... [ 52%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_93_0.png copying images... [ 53%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_95_0.png copying images... [ 54%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_98_1.png copying images... [ 55%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_100_0.png copying images... [ 56%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_102_0.png copying images... [ 57%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_8_0.png copying images... [ 58%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_13_0.png copying images... [ 59%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_15_1.png copying images... [ 60%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_19_0.png copying images... [ 61%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_21_0.png copying images... [ 62%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_23_1.png copying images... [ 63%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_25_1.png copying images... [ 64%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_28_0.png copying images... [ 65%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_30_1.png copying images... [ 66%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_33_0.png copying images... [ 67%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_36_0.png copying images... [ 68%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_38_1.png copying images... [ 69%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_42_0.png copying images... [ 70%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_47_0.png copying images... [ 71%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_49_0.png copying images... [ 72%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_51_1.png copying images... [ 73%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_53_1.png copying images... [ 75%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_55_0.png copying images... [ 76%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_57_0.png copying images... [ 77%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_59_0.png copying images... [ 78%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_60_0.png copying images... [ 79%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_62_0.png copying images... [ 80%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_64_0.png copying images... [ 81%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_65_0.png copying images... [ 82%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_67_0.png copying images... [ 83%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_69_0.png copying images... [ 84%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_75_0.png copying images... [ 85%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_77_1.png copying images... [ 86%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_82_0.png copying images... [ 87%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_84_0.png copying images... [ 88%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_85_0.png copying images... [ 89%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_87_0.png copying images... [ 90%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_88_0.png copying images... [ 91%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_0.png copying images... [ 92%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_1.png copying images... [ 93%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_2.png copying images... [ 94%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_3.png copying images... [ 95%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_4.png copying images... [ 96%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_5.png copying images... [ 97%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_93_0.png copying images... [ 98%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_96_0.png copying images... [100%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_100_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. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-03-17T12:23:47.476277Z, end-time: 2020-03-17T12:24:01.942760Z, duration: 14, 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: 7 added, 0 changed, 0 removed reading sources... [ 14%] README reading sources... [ 28%] analysis-visualization-spatial reading sources... [ 42%] index reading sources... [ 57%] integrating-data-using-ingest reading sources... [ 71%] paga-paul15 reading sources... [ 85%] pbmc3k reading sources... [100%] visualizing-marker-genes looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... pbmc3k paga-paul15 visualizing-marker-genes integrating-data-using-ingest analysis-visualization-spatial writing... done writing additional files... copying images... [ 1%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_13_1.png copying images... [ 2%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_20_0.png copying images... [ 3%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_22_0.png copying images... [ 4%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_22_1.png copying images... [ 5%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_35_0.png copying images... [ 6%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_46_0.png copying images... [ 7%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_48_0.png copying images... [ 8%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_58_0.png copying images... [ 9%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_60_0.png copying images... [ 10%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_65_0.png copying images... [ 11%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_70_1.png copying images... [ 12%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_73_1.png copying images... [ 13%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_77_1.png copying images... [ 14%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_88_1.png copying images... [ 15%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_90_0.png copying images... [ 16%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_93_0.png copying images... [ 17%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_95_0.png copying images... [ 18%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_98_1.png copying images... [ 19%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_100_0.png copying images... [ 20%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_102_0.png copying images... [ 21%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_13_0.png copying images... [ 22%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_19_0.png copying images... [ 23%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_27_1.png copying images... [ 25%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_28_1.png copying images... [ 26%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_35_2.png copying images... [ 27%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_40_0.png copying images... [ 28%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_42_0.png copying images... [ 29%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_47_1.png copying images... [ 30%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_56_0.png copying images... [ 31%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_62_0.png copying images... [ 32%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_8_0.png copying images... [ 33%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_13_0.png copying images... [ 34%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_15_1.png copying images... [ 35%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_19_0.png copying images... [ 36%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_21_0.png copying images... [ 37%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_23_1.png copying images... [ 38%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_25_1.png copying images... [ 39%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_28_0.png copying images... [ 40%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_30_1.png copying images... [ 41%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_33_0.png copying images... [ 42%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_36_0.png copying images... [ 43%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_38_1.png copying images... [ 44%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_42_0.png copying images... [ 45%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_47_0.png copying images... [ 46%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_49_0.png copying images... [ 47%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_51_1.png copying images... [ 48%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_53_1.png copying images... [ 50%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_55_0.png copying images... [ 51%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_57_0.png copying images... [ 52%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_59_0.png copying images... [ 53%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_60_0.png copying images... [ 54%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_62_0.png copying images... [ 55%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_64_0.png copying images... [ 56%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_65_0.png copying images... [ 57%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_67_0.png copying images... [ 58%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_69_0.png copying images... [ 59%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_75_0.png copying images... [ 60%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_77_1.png copying images... [ 61%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_82_0.png copying images... [ 62%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_84_0.png copying images... [ 63%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_85_0.png copying images... [ 64%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_87_0.png copying images... [ 65%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_88_0.png copying images... [ 66%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_0.png copying images... [ 67%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_1.png copying images... [ 68%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_2.png copying images... [ 69%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_3.png copying images... [ 70%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_4.png copying images... [ 71%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_5.png copying images... [ 72%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_93_0.png copying images... [ 73%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_96_0.png copying images... [ 75%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_100_1.png copying images... [ 76%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_12_0.png copying images... [ 77%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_17_0.png copying images... [ 78%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_21_0.png copying images... [ 79%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_27_0.png copying images... [ 80%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_40_0.png copying images... [ 81%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_45_0.png copying images... [ 82%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_53_0.png copying images... [ 83%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_60_0.png copying images... [ 84%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_66_0.png copying images... [ 85%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_80_0.png copying images... [ 86%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_0.png copying images... [ 87%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_1.png copying images... [ 88%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/integrating-data-using-ingest_82_2.png copying images... [ 89%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_7_1.png copying images... [ 90%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_13_0.png copying images... [ 91%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_13_1.png copying images... [ 92%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_15_0.png copying images... [ 93%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_17_0.png copying images... [ 94%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_19_0.png copying images... [ 95%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_21_1.png copying images... [ 96%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_23_0.png copying images... [ 97%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_30_0.png copying images... [ 98%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_39_0.png copying images... [100%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/analysis-visualization-spatial_41_0.png copying static files... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia.