Read the Docs build information Build id: 177325 Project: icb-scanpy-tutorials Version: latest Commit: 6fa8251182605a36807acc4d1aa7ae7fbf5bc009 Date: 2019-01-24T20:47:48.563828Z State: finished Success: False [rtd-command-info] start-time: 2019-01-24T20:47:49.548236Z, end-time: 2019-01-24T20:47:49.553329Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy-tutorials.git [rtd-command-info] start-time: 2019-01-24T20:47:49.612936Z, end-time: 2019-01-24T20:47:49.833798Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy-tutorials 9c35d80..6fa8251 master -> origin/master [rtd-command-info] start-time: 2019-01-24T20:47:50.004964Z, end-time: 2019-01-24T20:47:50.012337Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 9c35d80 linked notebook HEAD is now at 6fa8251 amended requirements [rtd-command-info] start-time: 2019-01-24T20:47:50.095376Z, end-time: 2019-01-24T20:47:50.102107Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-24T20:47:50.746007Z, end-time: 2019-01-24T20:47:52.986799Z, duration: 2, exit-code: 0 python3.5 -mvirtualenv --no-site-packages --no-download Using base prefix '/usr' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.5 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.5) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-01-24T20:47:53.066317Z, end-time: 2019-01-24T20:47:53.606005Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages [rtd-command-info] start-time: 2019-01-24T20:47:53.672912Z, end-time: 2019-01-24T20:47:55.536423Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Requirement already up-to-date: Pygments==2.2.0 in 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https://files.pythonhosted.org/packages/50/7a/17bc17b3f5b01ebd3af38d71a15baa33beb241ab280b6ad0977ae24ec208/alembic-1.0.6.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 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/7e/31/d6fedd4fb2c94755cd101191e581af30e1650ccce7a35bddb7930fed6574/kiwisolver-1.0.1-cp35-cp35m-manylinux1_x86_64.whl (949kB) Requirement already satisfied: parso>=0.3.0 in 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(line 4)) Downloading https://files.pythonhosted.org/packages/e0/7a/8aefbc0ed078dec7951ac9a06dcd1869243ecd7bcbce26fa47bf5e469a8f/qtconsole-4.4.3-py2.py3-none-any.whl (113kB) 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/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/bc/e1/3cddac03c8992815519c5f50493097f6508fa153d067b494db8ab5e9c4ce/prometheus_client-0.5.0.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/65/1e/adf6e000ea5dc909aa420352d6ba37f16434c8a3c2fa030445411a1ed545/python-editor-1.0.3.tar.gz 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: nbgrader, sqlalchemy, alembic, prometheus-client, Mako, python-editor Running setup.py bdist_wheel for nbgrader: started Running setup.py bdist_wheel for nbgrader: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/85/0c/c6/1acdac76caa164ba58e4f0103a90c3bb6082ff177ae6bc3628 Running setup.py bdist_wheel for sqlalchemy: started Running setup.py bdist_wheel for sqlalchemy: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/71/b5/67/1b1ae0279de6e79ee0d0a4061cdfa0604908e6052046671480 Running setup.py bdist_wheel for alembic: started Running setup.py bdist_wheel for alembic: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/b5/d9/40/70735a053fb156f7f359917a6bc80df6afe0b28b328f6004d9 Running setup.py bdist_wheel for prometheus-client: started Running setup.py bdist_wheel for prometheus-client: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/1a/74/d7/dc59e0bf44fdfd6395c0076129453abf563e4aeca5d72c8574 Running setup.py bdist_wheel for Mako: started Running setup.py bdist_wheel for Mako: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/15/35/25/dbcb848832ccb1a4b4ad23f529badfd3bce9bf88017f7ca510 Running setup.py bdist_wheel for python-editor: started Running setup.py bdist_wheel for python-editor: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/36/e0/98/ba386b125a00ea9dd52e2c16aa2ec0adbbd639b84bfe2e001d Successfully built nbgrader sqlalchemy alembic prometheus-client Mako python-editor Installing collected packages: sqlalchemy, qtconsole, jupyter-console, terminado, Send2Trash, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter, Mako, python-editor, alembic, nbgrader, cycler, kiwisolver, numpy, matplotlib, tqdm, nbclean Successfully installed Mako-1.0.7 Send2Trash-1.5.0 alembic-1.0.6 cycler-0.10.0 ipywidgets-7.4.2 jupyter-1.0.0 jupyter-console-5.2.0 kiwisolver-1.0.1 matplotlib-3.0.2 nbclean-0.3.2 nbgrader-0.5.5 notebook-5.7.4 numpy-1.16.0 prometheus-client-0.5.0 python-editor-1.0.3 qtconsole-4.4.3 sqlalchemy-1.2.16 terminado-0.8.1 tqdm-4.29.1 widgetsnbextension-3.4.2 [rtd-command-info] start-time: 2019-01-24T20:48:23.131546Z, end-time: 2019-01-24T20:48:23.192595Z, 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 else: SUFFIX = source_suffix[0] 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': '6fa82511', } 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: 2019-01-24T20:48:23.251328Z, end-time: 2019-01-24T20:48:24.022121Z, duration: 0, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/util/pycompat.py", line 141, in execfile_ code = compile(source, filepath_enc, 'exec') File "conf.py", line 4 copyright = f'{datetime.now():%Y}, {author}.' ^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/util/pycompat.py", line 73, in convert_with_2to3 tree = refactoring_tool.refactor_string(source, 'conf.py') File "/usr/lib/python3.5/lib2to3/refactor.py", line 380, in refactor_string name, err.__class__.__name__, err) File "/usr/lib/python3.5/lib2to3/refactor.py", line 377, in refactor_string tree = self.driver.parse_string(data) File "/usr/lib/python3.5/lib2to3/pgen2/driver.py", line 106, in parse_string return self.parse_tokens(tokens, debug) File "/usr/lib/python3.5/lib2to3/pgen2/driver.py", line 71, in parse_tokens if p.addtoken(type, value, (prefix, start)): File "/usr/lib/python3.5/lib2to3/pgen2/parse.py", line 159, in addtoken raise ParseError("bad input", type, value, context) lib2to3.pgen2.parse.ParseError: bad input: type=3, value="'{datetime.now():%Y}, {author}.'", context=('', (4, 13)) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/config.py", line 161, in __init__ execfile_(filename, config) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/util/pycompat.py", line 146, in execfile_ source = convert_with_2to3(filepath) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/util/pycompat.py", line 78, in convert_with_2to3 raise SyntaxError(err.msg, (filepath, lineno, offset, err.value)) File "conf.py", line 4 '{datetime.now():%Y}, {author}.' ^ SyntaxError: bad input During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/cmdline.py", line 303, in main args.warningiserror, args.tags, args.verbosity, args.jobs) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/application.py", line 163, in __init__ confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages/sphinx/config.py", line 163, in __init__ raise ConfigError(CONFIG_SYNTAX_ERROR % err) sphinx.errors.ConfigError: There is a syntax error in your configuration file: bad input (conf.py, line 4) Did you change the syntax from 2.x to 3.x? Configuration error: There is a syntax error in your configuration file: bad input (conf.py, line 4) Did you change the syntax from 2.x to 3.x?