Read the Docs build information Build id: 190503 Project: icb-scanpy Version: latest Commit: b43bc1af2952f07d4e6574b0967448048a1532e4 Date: 2019-03-10T18:38:53.332562Z State: finished Success: False [rtd-command-info] start-time: 2019-03-10T18:38:53.841861Z, end-time: 2019-03-10T18:38:53.848064Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy.git [rtd-command-info] start-time: 2019-03-10T18:38:53.909124Z, end-time: 2019-03-10T18:38:54.501747Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy 3707b14..b43bc1a master -> origin/master [rtd-command-info] start-time: 2019-03-10T18:38:54.723517Z, end-time: 2019-03-10T18:38:54.736945Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 3707b14 added comment about plotting HEAD is now at b43bc1a Merge pull request #466 from theislab/pca_test [rtd-command-info] start-time: 2019-03-10T18:38:54.798693Z, end-time: 2019-03-10T18:38:54.808824Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-03-10T18:38:55.440696Z, end-time: 2019-03-10T18:38:58.770862Z, 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/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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(from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (2019.3.9) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (3.0.4) Requirement already satisfied: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.24.1) Installing collected packages: sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, scipy, h5py, python-dateutil, pandas, natsort, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba Found existing installation: Sphinx 1.7.9 Uninstalling Sphinx-1.7.9: Successfully uninstalled Sphinx-1.7.9 Successfully installed anndata-0.6.18 cycler-0.10.0 decorator-4.3.2 future-fstrings-1.0.0 get-version-2.0.6 h5py-2.9.0 joblib-0.13.2 kiwisolver-1.0.1 llvmlite-0.27.1 matplotlib-3.0.3 natsort-6.0.0 networkx-2.2 numba-0.42.1 numexpr-2.6.9 numpy-1.16.2 pandas-0.24.1 python-dateutil-2.8.0 scanpydoc-0.3.3 scikit-learn-0.20.3 scipy-1.2.1 seaborn-0.9.0 sphinx-1.8.5 sphinx-autodoc-typehints-1.6.0 tables-3.4.4 [rtd-command-info] start-time: 2019-03-10T18:39:38.163093Z, end-time: 2019-03-10T18:39:38.226913Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime from jinja2.defaults import DEFAULT_FILTERS import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import scanpy # noqa logger = logging.getLogger(__name__) # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/latest/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), sklearn=('https://scikit-learn.org/stable/', None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=4, ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] def setup(app): app.add_stylesheet('css/custom.css') # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [ (master_doc, f'{project}.tex', doc_title, author, 'manual'), ] man_pages = [ (master_doc, project, doc_title, [author], 1) ] texinfo_documents = [ (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'), ] # -- Images for plot functions ------------------------------------------------- def api_image(qualname: str) -> str: # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path, # so no chance to not hardcode “api/” here. path = Path(__file__).parent / 'api' / f'{qualname}.png' print(path, path.is_file()) return f'.. image:: {path.name}\n :width: 200\n :align: right' if path.is_file() else '' # html_context doesn’t apply to autosummary templates ☹ # and there’s no way to insert filters into those templates # so we have to modify the default filters DEFAULT_FILTERS['api_image'] = api_image ########################################################################### # 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/"), ("stable", "/en/stable/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', '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': 'b43bc1af', } 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: 2019-03-10T18:39:38.323815Z, end-time: 2019-03-10T18:39:46.020759Z, duration: 7, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 14, in import scanpy # noqa File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 34, in from . import datasets, logging, queries, settings, external File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/__init__.py", line 3, in from . import pp File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp.py", line 3, in from ..preprocessing._dca import dca File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_dca.py", line 154 return_model=return_model ^ SyntaxError: unexpected EOF while parsing During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 303, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 201, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 203, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 373, in eval_config_file raise ConfigError(msg % err) sphinx.errors.ConfigError: There is a syntax error in your configuration file: unexpected EOF while parsing (_dca.py, line 154) Did you change the syntax from 2.x to 3.x? Configuration error: There is a syntax error in your configuration file: unexpected EOF while parsing (_dca.py, line 154) Did you change the syntax from 2.x to 3.x?