Read the Docs build information Build id: 177322 Project: icb-scanpy-tutorials Version: latest Commit: 9c35d80a478c4fb8b79d4f190af20a5a870500eb Date: 2019-01-24T20:45:00.890660Z State: finished Success: False [rtd-command-info] start-time: 2019-01-24T20:45:01.308643Z, end-time: 2019-01-24T20:45:01.316100Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy-tutorials.git [rtd-command-info] start-time: 2019-01-24T20:45:01.387122Z, end-time: 2019-01-24T20:45:01.646864Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy-tutorials 3a0bc24..9c35d80 master -> origin/master [rtd-command-info] start-time: 2019-01-24T20:45:01.932713Z, end-time: 2019-01-24T20:45:01.940212Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 3a0bc24 added paga notebook HEAD is now at 9c35d80 linked notebook [rtd-command-info] start-time: 2019-01-24T20:45:02.066611Z, end-time: 2019-01-24T20:45:02.073320Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-24T20:45:02.848892Z, end-time: 2019-01-24T20:45:06.196894Z, duration: 3, 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: 2019-01-24T20:45:06.265309Z, end-time: 2019-01-24T20:45:07.012295Z, 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 Cache entry deserialization failed, entry ignored 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: 2019-01-24T20:45:07.070454Z, end-time: 2019-01-24T20:45:10.791812Z, duration: 3, 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 Cache entry deserialization failed, entry ignored Requirement already up-to-date: Pygments==2.2.0 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages (from jedi>=0.10->ipython>=5.0.0->ipykernel->-r requirements.txt (line 2)) Requirement already satisfied: webencodings in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.5/site-packages (from bleach->nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) [rtd-command-info] start-time: 2019-01-24T20:45:12.102329Z, end-time: 2019-01-24T20:45:12.156565Z, 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': '9c35d80a', } 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: 2019-01-24T20:45:12.224026Z, end-time: 2019-01-24T20:45:13.025428Z, 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?