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Commit d16d9a6 is a breaking change #9832

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Yoshanuikabundi opened this issue Nov 9, 2021 · 2 comments · Fixed by #9833
Closed

Commit d16d9a6 is a breaking change #9832

Yoshanuikabundi opened this issue Nov 9, 2021 · 2 comments · Fixed by #9833
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type:bug

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@Yoshanuikabundi
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Describe the bug

When testing #9831 on a work project, I found that it could not build on the current state of the 4.x branch. I've bisected it down to commit d16d9a6 and confirmed that reverting this commit fixes the error. I haven't dug any further than that.

Traceback/log
# Sphinx version: 4.3.0+/d16d9a666
# Python version: 3.9.7 (CPython)
# Docutils version: 0.17.1 release
# Jinja2 version: 3.0.2
# Last messages:
#   reading sources... [  7%] _autosummary/openff.bespokefit.executor.services.coordinator
#   reading sources... [  7%] _autosummary/openff.bespokefit.executor.services.coordinator.app
#   reading sources... [  7%] _autosummary/openff.bespokefit.executor.services.coordinator.app.get_molecule_image
#   reading sources... [  8%] _autosummary/openff.bespokefit.executor.services.coordinator.app.get_optimization
#   reading sources... [  8%] _autosummary/openff.bespokefit.executor.services.coordinator.app.get_optimizations
#   reading sources... [  8%] _autosummary/openff.bespokefit.executor.services.coordinator.app.post_optimization
#   reading sources... [  8%] _autosummary/openff.bespokefit.executor.services.coordinator.app.shutdown
#   reading sources... [  8%] _autosummary/openff.bespokefit.executor.services.coordinator.app.startup
#   reading sources... [  9%] _autosummary/openff.bespokefit.executor.services.coordinator.models
#   reading sources... [  9%] _autosummary/openff.bespokefit.executor.services.coordinator.models.CoordinatorGETPageResponse
# Loaded extensions:
#   sphinx.ext.mathjax (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/mathjax.py
#   sphinxcontrib.applehelp (1.0.2) from /home/joshmitchell/.local/lib/python3.9/site-packages/sphinxcontrib/applehelp/__init__.py
#   sphinxcontrib.devhelp (1.0.2) from /home/joshmitchell/.local/lib/python3.9/site-packages/sphinxcontrib/devhelp/__init__.py
#   sphinxcontrib.htmlhelp (2.0.0) from /home/joshmitchell/.local/lib/python3.9/site-packages/sphinxcontrib/htmlhelp/__init__.py
#   sphinxcontrib.serializinghtml (1.1.5) from /home/joshmitchell/.local/lib/python3.9/site-packages/sphinxcontrib/serializinghtml/__init__.py
#   sphinxcontrib.qthelp (1.0.3) from /home/joshmitchell/.local/lib/python3.9/site-packages/sphinxcontrib/qthelp/__init__.py
#   alabaster (0.7.12) from /home/joshmitchell/.local/lib/python3.9/site-packages/alabaster/__init__.py
#   sphinx.ext.autodoc.preserve_defaults (1.0) from /home/joshmitchell/Documents/sphinx/sphinx/ext/autodoc/preserve_defaults.py
#   sphinx.ext.autodoc.type_comment (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/autodoc/type_comment.py
#   sphinx.ext.autodoc (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/autodoc/__init__.py
#   sphinx.ext.autosummary (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/autosummary/__init__.py
#   sphinx.ext.viewcode (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/viewcode.py
#   sphinx.ext.napoleon (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/napoleon/__init__.py
#   sphinx.ext.intersphinx (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/intersphinx.py
#   sphinx.ext.extlinks (4.3.0+/d16d9a666) from /home/joshmitchell/Documents/sphinx/sphinx/ext/extlinks.py
#   myst_parser (0.15.2) from /home/joshmitchell/conda/envs/bespokefitdev/lib/python3.9/site-packages/myst_parser/__init__.py
#   sphinxcontrib.autodoc_pydantic (1.5.0) from /home/joshmitchell/conda/envs/bespokefitdev/lib/python3.9/site-packages/sphinxcontrib/autodoc_pydantic/__init__.py
#   openff_sphinx_theme (0.0.32+104.g47ffca4) from /home/joshmitchell/Documents/openff/openff-sphinx-theme/openff_sphinx_theme/__init__.py
Traceback (most recent call last):
  File "/home/joshmitchell/Documents/sphinx/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/joshmitchell/Documents/sphinx/sphinx/application.py", line 343, in build
    self.builder.build_update()
  File "/home/joshmitchell/Documents/sphinx/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/home/joshmitchell/Documents/sphinx/sphinx/builders/__init__.py", line 307, in build
    updated_docnames = set(self.read())
  File "/home/joshmitchell/Documents/sphinx/sphinx/builders/__init__.py", line 414, in read
    self._read_serial(docnames)
  File "/home/joshmitchell/Documents/sphinx/sphinx/builders/__init__.py", line 435, in _read_serial
    self.read_doc(docname)
  File "/home/joshmitchell/Documents/sphinx/sphinx/builders/__init__.py", line 475, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/joshmitchell/Documents/sphinx/sphinx/io.py", line 189, in read_doc
    pub.publish()
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/joshmitchell/Documents/sphinx/sphinx/io.py", line 109, in read
    self.parse()
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/home/joshmitchell/Documents/sphinx/sphinx/parsers.py", line 101, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 170, in run
    results = StateMachineWS.run(self, input_lines, input_offset,
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 239, in run
    context, next_state, result = self.check_line(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 451, in check_line
    return method(match, context, next_state)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2769, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 327, in section
    self.new_subsection(title, lineno, messages)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 393, in new_subsection
    newabsoffset = self.nested_parse(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 281, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 239, in run
    context, next_state, result = self.check_line(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 451, in check_line
    return method(match, context, next_state)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2344, in explicit_markup
    self.explicit_list(blank_finish)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2369, in explicit_list
    newline_offset, blank_finish = self.nested_list_parse(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 318, in nested_list_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 239, in run
    context, next_state, result = self.check_line(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 451, in check_line
    return method(match, context, next_state)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2647, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2354, in explicit_construct
    return method(self, expmatch)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2096, in directive
    return self.run_directive(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2146, in run_directive
    result = directive_instance.run()
  File "/home/joshmitchell/Documents/sphinx/sphinx/ext/autodoc/directive.py", line 173, in run
    result = parse_generated_content(self.state, params.result, documenter)
  File "/home/joshmitchell/Documents/sphinx/sphinx/ext/autodoc/directive.py", line 120, in parse_generated_content
    state.nested_parse(content, 0, node)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 281, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 239, in run
    context, next_state, result = self.check_line(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/statemachine.py", line 451, in check_line
    return method(match, context, next_state)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2342, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2354, in explicit_construct
    return method(self, expmatch)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2096, in directive
    return self.run_directive(
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/parsers/rst/states.py", line 2146, in run_directive
    result = directive_instance.run()
  File "/home/joshmitchell/Documents/sphinx/sphinx/domains/__init__.py", line 286, in run
    return super().run()
  File "/home/joshmitchell/Documents/sphinx/sphinx/directives/__init__.py", line 189, in run
    name = self.handle_signature(sig, signode)
  File "/home/joshmitchell/Documents/sphinx/sphinx/domains/python.py", line 485, in handle_signature
    signode += addnodes.desc_annotation(str(sig_prefix), '', *sig_prefix)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 1170, in __init__
    TextElement.__init__(self, rawsource, text, *children, **attributes)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 1162, in __init__
    Element.__init__(self, rawsource, *children, **attributes)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 554, in __init__
    self.extend(children)           # maintain parent info
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 754, in extend
    self.append(node)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 749, in append
    self.setup_child(item)
  File "/home/joshmitchell/.local/lib/python3.9/site-packages/docutils/nodes.py", line 146, in setup_child
    child.parent = self
AttributeError: 'str' object has no attribute 'parent'

How to Reproduce

$ git clone https://github.com/openforcefield/bespoke-fit.git
$ cd bespoke-fit
$ git checkout docs-update
$ mamba env create --file devtools/conda-envs/test-env.yaml --name bespokefit
$ mamba activate bespokefit
$ cd docs
$ make html

Expected behavior

The docs build successfully.

Your project

https://github.com/openforcefield/bespoke-fit

Screenshots

No response

OS

Linux Arch

Python version

3.10

Sphinx version

Commits on 4.x after d16d9a6

Sphinx extensions

"sphinx.ext.autosummary",     "sphinx.ext.autodoc",     "sphinx.ext.mathjax",     "sphinx.ext.viewcode",     "sphinx.ext.napoleon",     "sphinx.ext.intersphinx",     "sphinx.ext.extlinks",     "myst_parser",     "sphinxcontrib.autodoc_pydantic",

Extra tools

No response

Additional context

No response
jakobandersen added a commit to jakobandersen/sphinx that referenced this issue Nov 9, 2021
@jakobandersen
Make fallback for changed get_signature_prefix()
3599f7d 
Fixes sphinx-doc#9832
@jakobandersen jakobandersen mentioned this issue Nov 9, 2021
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@jakobandersen
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I think the triggering rst line is .. autopydantic_model:: BaseOptimizerSchema in _autosummary/openff.bespokefit.schema.optimizers.BaseOptimizerSchema.rst. This directive seems to be implemented in sphinxcontrib.autodoc_pydantic.
It overwrites get_signature_prefix which has its signature changed for 4.3 to allow better styling of declarations (https://www.sphinx-doc.org/en/master/changes.html#id2).
I have made #9833 to mitigate this, and your project should compile, but warn and render the pydantic model as plain text.

@Yoshanuikabundi
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@jakobandersen Wow thanks! I'll report this to autodoc_pydantic too.

@Yoshanuikabundi Yoshanuikabundi mentioned this issue Nov 9, 2021
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Make fallback for changed get_signature_prefix() jakobandersen/sphinx
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@jakobandersen @Yoshanuikabundi