Some warnings contain non-existing paths

[astrojuanlu]

Describe the bug

While investigating sktime/sktime#1181, I noticed that the warnings (turned into errors) contained some weird paths:

$ python -m sphinx -v -W -T -E -b html -d _build/doctrees -D language=en source/ _build/html
...                                                                                                                                                                                                          
  File "/usr/lib/python3.7/logging/__init__.py", line 751, in filter                                                                                                                                                                          
    result = f.filter(record)                                                                                          
  File "/home/juanlu/Projects/RTD/tmp/sktime/.venv/lib/python3.7/site-packages/sphinx/util/logging.py", line 421, in filter
    raise exc                                              
sphinx.errors.SphinxWarning: /home/juanlu/Projects/RTD/tmp/sktime/docs/source/source/api_reference/classification.rst.rst:16:autosummary: stub file not found 'sktime.classification.compose.ColumnEnsembleClassifier'. Check your autosummary_generate setting. 

Rather than /home/juanlu/Projects/RTD/tmp/sktime/docs/source/source/api_reference/classification.rst.rst, it should say /home/juanlu/Projects/RTD/tmp/sktime/docs/source/api_reference/classification.rst (notice the extra source/ segment and extra .rst extension).

After some debugging, I traced it to this function call:

(Pdb) p self.app.env.doc2path("source/api_reference/classification.rst")
'/home/juanlu/Projects/RTD/tmp/sktime/docs/source/source/api_reference/classification.rst.rst'

happening in these lines:

sphinx/sphinx/util/logging.py

Lines 487 to 490 in f9941b9

	if isinstance(location, tuple):
	docname, lineno = location
	if docname and lineno:
	record.location = '%s:%s' % (self.app.env.doc2path(docname), lineno)

How to Reproduce

$ git clone https://github.com/alan-turing-institute/sktime
$ cd sktime
$ pip install -r docs/requirements.txt  # Installation instructions taken from https://www.sktime.org/en/latest/contributing.html#id18
$ cd docs
$ python -m sphinx -v -W -T -E -b html -d _build/doctrees -D language=en source/ _build/html
# See error

Expected behavior

The error should contain an actual path, in this case /home/juanlu/Projects/RTD/tmp/sktime/docs/source/api_reference/classification.rst.

Your project

https://github.com/alan-turing-institute/sktime

Screenshots

No response

OS

Linux

Python version

3.7

Sphinx version

3.2.1

Sphinx extensions

sphinx.ext.autodoc, sphinx.ext.autosummary, others

Extra tools

No response

Additional context

sktime/sktime#1181

[tk0miya]

Hmm... it's strange. source/api_reference/classification.rst is not a name of document. So we need to investigate what code passes it to the doc2path.

(Pdb) p self.app.env.doc2path("source/api_reference/classification.rst")
'/home/juanlu/Projects/RTD/tmp/sktime/docs/source/source/api_reference/classification.rst.rst'

Unfortunately, I can't reproduce the error with the reported procedure.

FROM python:3.7-slim

RUN apt update; apt install -y build-essential curl git unzip vim
RUN git clone https://github.com/alan-turing-institute/sktime
WORKDIR /sktime
RUN pip3 install -r docs/requirements.txt
WORKDIR /sktime/docs
RUN python -m sphinx -v -W -T -E -b html -d _build/doctrees -D language=en source/ _build/html

Could you check the procedure please? It would be nice if you create a minimal reproducible example :-)

[astrojuanlu]

Right, I'm finding other problems with sktime now, and in any case the project is too big. I'll try to send a smaller reproducer.

[astrojuanlu]

Hah, the problem I'm having is #7989 again :) I think I'll focus on that one first.

[astrojuanlu]

Here is a simple reproducer: https://github.com/astrojuanlu/sphinx-autosummary-tracebacks/tree/weird-paths

(.venv) $ pip install -r requirements.txt
(.venv) $ python -c "from test_pkg import A; print(A)"
<class 'test_pkg.A'>
(.venv) $ make html
Running Sphinx v4.1.1
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 1 source files that are out of date
updating environment: [config changed ('autosummary_generate')] 2 added, 0 changed, 0 removed
reading sources... [100%] index
/home/juanlu/Projects/RTD/tmp/sphinx-autosummary-tracebacks/source/index.rst.rst:13: WARNING: autosummary: stub file not found 'test_pkg.A'. Check your autosummary_generate setting.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/juanlu/Projects/RTD/tmp/sphinx-autosummary-tracebacks/source/autogen/test_pkg.A.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] index
generating indices... genindex done
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.

The HTML pages are in build/html.
(.venv) $ python -m sphinx -W -b html source/ build/html
Running Sphinx v4.1.1
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 2 source files that are out of date
updating environment: [new config] 2 added, 0 changed, 0 removed
reading sources... [100%] index

Warning, treated as error:
/home/juanlu/Projects/RTD/tmp/sphinx-autosummary-tracebacks/source/index.rst.rst:13:autosummary: stub file not found 'test_pkg.A'. Check your autosummary_generate setting.