Read the Docs build information Build id: 185732 Project: icb-scanpy-tutorials Version: latest Commit: 7bc67bd66b05d87d38211765e1b4399452390442 Date: 2019-02-22T08:18:35.157511Z State: finished Success: True [rtd-command-info] start-time: 2019-02-22T08:18:35.647448Z, end-time: 2019-02-22T08:18:38.026517Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2019-02-22T08:18:38.191692Z, end-time: 2019-02-22T08:18:38.239853Z, 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 7bc67bd amended paga notebook [rtd-command-info] start-time: 2019-02-22T08:18:38.302538Z, end-time: 2019-02-22T08:18:38.308750Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-02-22T08:18:38.933918Z, end-time: 2019-02-22T08:18:41.798611Z, duration: 2, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.4' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-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. 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ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl Collecting jedi>=0.10 (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/c2/bc/54d53f5bc4658380d0eca9055d72be4df45e5bfd91a4bac97da224a92553/jedi-0.13.2-py2.py3-none-any.whl (177kB) Collecting prompt-toolkit<2.1.0,>=2.0.0 (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/f7/a7/9b1dd14ef45345f186ef69d175bdd2491c40ab1dfa4b2b3e4352df719ed7/prompt_toolkit-2.0.9-py3-none-any.whl (337kB) Collecting backcall (from ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/84/71/c8ca4f5bb1e08401b916c68003acf0a0655df935d74d93bf3f3364b310e0/backcall-0.1.0.tar.gz Collecting entrypoints>=0.2.2 (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/4c/ea/236e2584af67bb6df960832731a6e5325fd4441de001767da328c33368ce/pandocfilters-1.4.2.tar.gz Collecting defusedxml (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/87/1c/17f3e3935a913dfe2a5ca85fa5ccbef366bfd82eb318b1f75dadbf0affca/defusedxml-0.5.0-py2.py3-none-any.whl Collecting mistune>=0.8.1 (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl Collecting testpath (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl (163kB) Collecting bleach (from nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl (157kB) Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/77/de/47e35a97b2b05c2fadbec67d44cfcdcd09b8086951b331d82de90d2912da/jsonschema-2.6.0-py2.py3-none-any.whl Collecting cycler>=0.10 (from matplotlib->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Collecting kiwisolver>=1.0.1 (from matplotlib->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl (949kB) Collecting sqlalchemy (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/21/ed/7eb53305b43ca51774a458d7c292f3bc7664d7a9bbb5bac4149fa34756b9/SQLAlchemy-1.2.18.tar.gz (5.7MB) Collecting jupyter (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl Collecting notebook>=4.2 (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/f8/a6/dbdf0954d073ab2cf5421cad20334d1e4c780da37205c04522c045298f67/notebook-5.7.4-py2.py3-none-any.whl (9.0MB) Collecting alembic (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/a4/06/f1ae8393463c26f3dafa21eebac611088da02a26e1f1e23bd75fee2dbffe/alembic-1.0.7.tar.gz (1.0MB) Collecting jupyter-console<=5.2.0 (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/77/82/6469cd7fccf7958cbe5dce2e623f1e3c5e27f1bb1ad36d90519bc2d5d370/jupyter_console-5.2.0-py2.py3-none-any.whl Collecting ptyprocess>=0.5 (from pexpect; sys_platform != "win32"->ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl Collecting parso>=0.3.0 (from jedi>=0.10->ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/19/b1/522b2671cc6d134c9d3f5dfc0d02fee07cab848e908d03d2bffea78cca8f/parso-0.3.4-py2.py3-none-any.whl (93kB) Collecting wcwidth (from prompt-toolkit<2.1.0,>=2.0.0->ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Downloading https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl Collecting webencodings (from bleach->nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl Collecting ipywidgets (from jupyter->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/30/9a/a008c7b1183fac9e52066d80a379b3c64eab535bd9d86cdc29a0b766fd82/ipywidgets-7.4.2-py2.py3-none-any.whl (111kB) Collecting qtconsole (from jupyter->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/e0/7a/8aefbc0ed078dec7951ac9a06dcd1869243ecd7bcbce26fa47bf5e469a8f/qtconsole-4.4.3-py2.py3-none-any.whl (113kB) Collecting terminado>=0.8.1 (from notebook>=4.2->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/2e/20/a26211a24425923d46e1213b376a6ee60dc30bcdf1b0c345e2c3769deb1c/terminado-0.8.1-py2.py3-none-any.whl Collecting Send2Trash (from notebook>=4.2->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/49/46/c3dc27481d1cc57b9385aff41c474ceb7714f7935b1247194adae45db714/Send2Trash-1.5.0-py3-none-any.whl Collecting prometheus-client (from notebook>=4.2->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/4c/bd/b42db3ec90ffc6be805aad09c1cea4bb13a620d0cd4b21aaa44d13541d71/prometheus_client-0.6.0.tar.gz Collecting Mako (from alembic->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/eb/f3/67579bb486517c0d49547f9697e36582cd19dafb5df9e687ed8e22de57fa/Mako-1.0.7.tar.gz (564kB) Collecting python-editor>=0.3 (from alembic->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/c6/d3/201fc3abe391bbae6606e6f1d598c15d367033332bd54352b12f35513717/python_editor-1.0.4-py3-none-any.whl Collecting widgetsnbextension~=3.4.0 (from ipywidgets->jupyter->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/8a/81/35789a3952afb48238289171728072d26d6e76649ddc8b3588657a2d78c1/widgetsnbextension-3.4.2-py2.py3-none-any.whl (2.2MB) Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, sqlalchemy, alembic, prometheus-client, Mako Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6d/e1/ce/f4ee2fa420cc6b940123c64992b81047816d0a9fad6b879325 Building wheel for nbgrader (setup.py): started Building wheel for nbgrader (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/85/0c/c6/1acdac76caa164ba58e4f0103a90c3bb6082ff177ae6bc3628 Building wheel for backcall (setup.py): started Building wheel for backcall (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20 Building wheel for sqlalchemy (setup.py): started Building wheel for sqlalchemy (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/46/56/55/bf9346b13dfdf010316b16d554d4ae7362f7f6b5de0032d587 Building wheel for alembic (setup.py): started Building wheel for alembic (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/f9/71/46/604b8a4f0a04b513f5799c974b556c1de19a70fde41d25672b Building wheel for prometheus-client (setup.py): started Building wheel for prometheus-client (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/4b/04/b8/3709c73e7453f311ebd46ad581b89642543213f995e2659b9e Building wheel for Mako (setup.py): started Building wheel for Mako (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/15/35/25/dbcb848832ccb1a4b4ad23f529badfd3bce9bf88017f7ca510 Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic prometheus-client Mako jupyter-console 5.2.0 has requirement prompt-toolkit<2.0.0,>=1.0.0, but you'll have prompt-toolkit 2.0.9 which is incompatible. nbgrader 0.5.5 has requirement ipython<=6.2.1, but you'll have ipython 7.3.0 which is incompatible. Installing collected packages: decorator, ipython-genutils, traitlets, tornado, pyzmq, python-dateutil, jupyter-core, jupyter-client, ptyprocess, pexpect, pickleshare, parso, jedi, wcwidth, prompt-toolkit, backcall, ipython, ipykernel, entrypoints, pandocfilters, defusedxml, jsonschema, nbformat, mistune, testpath, webencodings, bleach, nbconvert, nbsphinx, cycler, kiwisolver, numpy, matplotlib, sqlalchemy, terminado, Send2Trash, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter-console, qtconsole, jupyter, Mako, python-editor, alembic, nbgrader, tqdm, nbclean Successfully installed Mako-1.0.7 Send2Trash-1.5.0 alembic-1.0.7 backcall-0.1.0 bleach-3.1.0 cycler-0.10.0 decorator-4.3.2 defusedxml-0.5.0 entrypoints-0.3 ipykernel-5.1.0 ipython-7.3.0 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.2 jsonschema-2.6.0 jupyter-1.0.0 jupyter-client-5.2.4 jupyter-console-5.2.0 jupyter-core-4.4.0 kiwisolver-1.0.1 matplotlib-3.0.2 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.4.1 nbformat-4.4.0 nbgrader-0.5.5 nbsphinx-0.3.5 notebook-5.7.4 numpy-1.16.1 pandocfilters-1.4.2 parso-0.3.4 pexpect-4.6.0 pickleshare-0.7.5 prometheus-client-0.6.0 prompt-toolkit-2.0.9 ptyprocess-0.6.0 python-dateutil-2.8.0 python-editor-1.0.4 pyzmq-18.0.0 qtconsole-4.4.3 sqlalchemy-1.2.18 terminado-0.8.1 testpath-0.4.2 tornado-5.1.1 tqdm-4.31.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.4.2 [rtd-command-info] start-time: 2019-02-22T08:19:35.102403Z, end-time: 2019-02-22T08:19:35.172047Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime project = 'Scanpy' author = 'Scanpy authors' 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=2, ) 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'] 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 mulitple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"), ], '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', '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': '7bc67bd6', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2019-02-22T08:19:35.236730Z, end-time: 2019-02-22T08:19:44.717716Z, duration: 9, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2019-02-22T08:19:44.829379Z, end-time: 2019-02-22T08:19:50.963050Z, duration: 6, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.7.9 loading translations [en]... done making output directory... loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 5 added, 0 changed, 0 removed reading sources... [ 20%] README reading sources... [ 40%] index reading sources... [ 60%] paga-paul15 reading sources... [ 80%] pbmc3k reading sources... 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