ouhft / COPE

Project Repository for Work Package 4 of the COPE Transplant Trial
https://cope.nds.ox.ac.uk
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Documentation build failing on Sphinx v2 #344

Open marshalc opened 5 years ago

marshalc commented 5 years ago

# Sphinx version: 2.0.1
# Python version: 3.7.3 (CPython)
# Docutils version: 0.14 
# Jinja2 version: 2.10.1
# Last messages:
#   reading sources... [ 37%] index
#   reading sources... [ 43%] models/adverse_event
#   reading sources... [ 50%] models/compare
#   reading sources... [ 56%] models/generated/wp4.followups.models
#   reading sources... [ 62%] models/generated/wp4.health_economics.models
#   reading sources... [ 68%] models/generated/wp4.locations.models
#   reading sources... [ 75%] models/generated/wp4.perfusion_machine.models
#   reading sources... [ 81%] models/generated/wp4.samples.models
#   reading sources... [ 87%] models/generated/wp4.staff.models
#   reading sources... [ 93%] models/index
# Loaded extensions:
#   sphinx.ext.mathjax (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/mathjax.py
#   sphinxcontrib.applehelp (1.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/applehelp/__init__.py
#   sphinxcontrib.devhelp (1.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/devhelp/__init__.py
#   sphinxcontrib.htmlhelp (1.0.2) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/htmlhelp/__init__.py
#   sphinxcontrib.serializinghtml (1.1.3) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/serializinghtml/__init__.py
#   sphinxcontrib.qthelp (1.0.2) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/qthelp/__init__.py
#   alabaster (0.7.12) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/alabaster/__init__.py
#   sphinx.ext.autodoc (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/autodoc/__init__.py
#   sphinx.ext.autosummary (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/autosummary/__init__.py
#   sphinx.ext.graphviz (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/graphviz.py
#   sphinx.ext.napoleon (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/napoleon/__init__.py
#   sphinx.ext.inheritance_diagram (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/inheritance_diagram.py
#   sphinx.ext.doctest (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/doctest.py
#   sphinx.ext.todo (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/todo.py
#   sphinx.ext.coverage (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/coverage.py
#   sphinx.ext.imgmath (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/imgmath.py
#   sphinx.ext.ifconfig (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/ifconfig.py
#   sphinx.ext.viewcode (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/viewcode.py
#   sphinx.ext.intersphinx (2.0.1) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/intersphinx.py
#   sphinxcontrib.spelling (unknown version) from /Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinxcontrib/spelling/__init__.py
Traceback (most recent call last):
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/cmd/build.py", line 284, in build_main
    app.build(args.force_all, filenames)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/application.py", line 337, in build
    self.builder.build_update()
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 326, in build_update
    len(to_build))
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 339, in build
    updated_docnames = set(self.read())
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 445, in read
    self._read_serial(docnames)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 467, in _read_serial
    self.read_doc(docname)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 511, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/io.py", line 323, in read_doc
    pub.publish()
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/io.py", line 116, in read
    self.parse()
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/parsers.py", line 94, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 171, in run
    input_source=document['source'])
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2753, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 327, in section
    self.new_subsection(title, lineno, messages)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 395, in new_subsection
    node=section_node, match_titles=True)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2753, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 327, in section
    self.new_subsection(title, lineno, messages)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 395, in new_subsection
    node=section_node, match_titles=True)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2326, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2338, in explicit_construct
    return method(self, expmatch)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2081, in directive
    directive_class, match, type_name, option_presets)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/parsers/rst/states.py", line 2130, in run_directive
    result = directive_instance.run()
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/autosummary/__init__.py", line 242, in run
    items = self.get_items(names)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/autosummary/__init__.py", line 341, in get_items
    summary = extract_summary(self.bridge.result.data[:], self.state.document)
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/sphinx/ext/autosummary/__init__.py", line 502, in extract_summary
    if not isinstance(node[0], nodes.paragraph):
  File "/Users/carl/.virtualenvs/cope/lib/python3.7/site-packages/docutils/nodes.py", line 569, in __getitem__
    return self.children[key]
IndexError: list index out of range

NB: Sphinx needs updating version from 2 to 2.1 (or latest)