Read the Docs build information Build id: 213627 Project: icb-scanpy-tutorials Version: latest Commit: f3e1e94bc4737ccfe02b2cdecbcd1014fcd2013f Date: 2019-06-05T20:52:11.594015Z State: finished Success: True [rtd-command-info] start-time: 2019-06-05T20:52:12.113303Z, end-time: 2019-06-05T20:52:15.558457Z, 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: 2019-06-05T20:52:15.733024Z, end-time: 2019-06-05T20:52:15.847272Z, 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 f3e1e94 Merge pull request #4 from fidelram/update_visualization [rtd-command-info] start-time: 2019-06-05T20:52:15.909003Z, end-time: 2019-06-05T20:52:15.916388Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-06-05T20:52:16.864021Z, end-time: 2019-06-05T20:52:19.978779Z, duration: 3, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.4' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-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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requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl 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 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 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 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 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/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB) Collecting sqlalchemy (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/ba/37/094ecf4b218f20572986dc90fe8c6aed32e2a711bcd02ce8ef251fde2011/SQLAlchemy-1.3.4.tar.gz (5.9MB) 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/f6/36/89ebfffc9dd8c8dbd81c1ffb53e3d4233ee666414c143959477cb07cc5f5/notebook-5.7.8-py2.py3-none-any.whl (9.0MB) Collecting alembic (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/6e/8b/fa3bd058cccd5e9177fea4efa26bfb769228fdd3178436ad5e05830ef6ef/alembic-1.0.10.tar.gz (1.0MB) Collecting jupyter-console<=5.2.0 (from nbgrader->nbclean->-r requirements.txt (line 4)) Downloading 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jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/68/0b/f514e76b4e074386b60cfc6c8c2d75ca615b81e415417ccf3fac80ae0bf6/pyrsistent-0.15.2.tar.gz (106kB) Collecting attrs>=17.4.0 (from jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-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 qtconsole (from jupyter->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/79/0b/efb5a694b6922bb85c35e4f1db6197daae23c764dd384023fc9517d79e26/qtconsole-4.5.1-py2.py3-none-any.whl (118kB) 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 terminado>=0.8.1 (from notebook>=4.2->nbgrader->nbclean->-r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/a7/56/80ea7fa66565fa75ae21ce0c16bc90067530e5d15e48854afcc86585a391/terminado-0.8.2-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/37/d7/2287b48aaeccdf2c75040fa5db69f6fad1877483aa6ce68316ab959ad1a0/Mako-1.0.11.tar.gz (461kB) 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, pyrsistent, 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/61/7e/7a/5e02e60dc329aef32ecf70e0425319ee7e2198c3a7cf98b4a2 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/cc/b2/b8/54b71f2c27738fc6f9d1b68b6cf653c28a5fa0a9846d02be32 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/de/cf/b3/0eb5c89ea6aa1b49cb41315f9ec139ada8cbffd575bf170d43 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6b/b9/15/c8c6a1e095a370e8c3273e65a5c982e5cf355dde16d77502f5 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/b4/cb/4b/b64eabdf5c11ecb491a37c72819148976f276d323ca12bcaf4 Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic pyrsistent prometheus-client Mako ERROR: 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. ERROR: nbgrader 0.5.5 has requirement ipython<=6.2.1, but you'll have ipython 7.5.0 which is incompatible. Installing collected packages: tornado, ipython-genutils, decorator, traitlets, jupyter-core, python-dateutil, pyzmq, jupyter-client, pickleshare, backcall, wcwidth, prompt-toolkit, ptyprocess, pexpect, parso, jedi, ipython, ipykernel, pyrsistent, attrs, jsonschema, nbformat, defusedxml, entrypoints, mistune, testpath, pandocfilters, webencodings, bleach, nbconvert, nbsphinx, cycler, kiwisolver, numpy, matplotlib, tqdm, sqlalchemy, qtconsole, terminado, Send2Trash, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter-console, jupyter, Mako, python-editor, alembic, nbgrader, nbclean Successfully installed Mako-1.0.11 Send2Trash-1.5.0 alembic-1.0.10 attrs-19.1.0 backcall-0.1.0 bleach-3.1.0 cycler-0.10.0 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 ipykernel-5.1.1 ipython-7.5.0 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.3 jsonschema-3.0.1 jupyter-1.0.0 jupyter-client-5.2.4 jupyter-console-5.2.0 jupyter-core-4.4.0 kiwisolver-1.1.0 matplotlib-3.1.0 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.5.0 nbformat-4.4.0 nbgrader-0.5.5 nbsphinx-0.3.5 notebook-5.7.8 numpy-1.16.4 pandocfilters-1.4.2 parso-0.4.0 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.6.0 prompt-toolkit-2.0.9 ptyprocess-0.6.0 pyrsistent-0.15.2 python-dateutil-2.8.0 python-editor-1.0.4 pyzmq-18.0.1 qtconsole-4.5.1 sqlalchemy-1.3.4 terminado-0.8.2 testpath-0.4.2 tornado-6.0.2 tqdm-4.32.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.4.2 [rtd-command-info] start-time: 2019-06-05T20:53:03.077171Z, end-time: 2019-06-05T20:53:03.383723Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime project = 'Scanpy' author = 'Alex Wolf, Fidel Ramirez' 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': [ ("pdf", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/pdf/latest/"), ("html", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/epub/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': 'f3e1e94b', } 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"] 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: 2019-06-05T20:53:03.446364Z, end-time: 2019-06-05T20:53:12.716577Z, duration: 9, 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 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... 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