Use node.findall if available (docutils 18.x) #403

drammock · 2022-05-28T19:34:43Z

closes #399

jarrodmillman · 2022-05-28T20:02:57Z

You can fix the linter warnings via:

pip install pre-commit
pre-commit run --all-files --show-diff-on-failure --color always

Or do

 pip install pre-commit
 pre-commit install

and it will automatically run when you try to commit.

jarrodmillman · 2022-05-28T20:05:27Z

We will want to make sure we still support docutils < 0.18 and sphinx==4, I think.

drammock · 2022-05-28T20:06:38Z

pre-commit is failing, looks like it mistakes python 3.10 for python 3.1 (!!) here's the log

version information

pre-commit version: 2.19.0
git --version: git version 2.25.1
sys.version:
    3.10.4 | packaged by conda-forge | (main, Mar 24 2022, 17:39:04) [GCC 10.3.0]
sys.executable: /opt/miniforge3/envs/numpydoc-dev/bin/python3.1
os.name: posix
sys.platform: linux

error information

An unexpected error has occurred: CalledProcessError: command: ('/opt/miniforge3/envs/numpydoc-dev/bin/python3.1', '-mvirtualenv', '/home/drmccloy/.cache/pre-commit/repowbc6hl47/py_env-python3.1', '-p', 'python3.1')
return code: 1
expected return code: 0
stdout:
    RuntimeError: failed to find interpreter for Builtin discover of python_spec='python3.1'
    
stderr: (none)

Traceback (most recent call last):
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/error_handler.py", line 73, in error_handler
    yield
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/main.py", line 361, in main
    return hook_impl(
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/commands/hook_impl.py", line 238, in hook_impl
    return retv | run(config, store, ns)
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/commands/run.py", line 414, in run
    install_hook_envs(to_install, store)
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/repository.py", line 223, in install_hook_envs
    _hook_install(hook)
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/repository.py", line 79, in _hook_install
    lang.install_environment(
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/languages/python.py", line 219, in install_environment
    cmd_output_b(*venv_cmd, cwd='/')
  File "/opt/miniforge3/envs/numpydoc-dev/lib/python3.10/site-packages/pre_commit/util.py", line 146, in cmd_output_b
    raise CalledProcessError(returncode, cmd, retcode, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('/opt/miniforge3/envs/numpydoc-dev/bin/python3.1', '-mvirtualenv', '/home/drmccloy/.cache/pre-commit/repowbc6hl47/py_env-python3.1', '-p', 'python3.1')
return code: 1
expected return code: 0
stdout:
    RuntimeError: failed to find interpreter for Builtin discover of python_spec='python3.1'
    
stderr: (none)

EDIT fixed by manually typing the zero into .git/hooks/pre-commit 🤦🏻

drammock · 2022-05-28T20:16:07Z

We will want to make sure we still support docutils < 0.18 and sphinx==4, I think.

my change to test_reference will break that, I think. Stand by.

numpydoc/numpydoc.py

numpydoc/tests/test_full.py

Co-authored-by: Jarrod Millman <[email protected]>

rossbar · 2022-05-31T23:16:02Z

numpydoc/numpydoc.py

+    """Triage node.traverse (docutils <0.18) vs node.findall.
+
+    TODO: This check can be removed when the minimum supported docutils version
+    for numpydoc is docutils>=0.18


Just to be clear, the findall method was only added in docutils 0.18, correct?

I double-checked, and in fact it wasn't introduced until 0.18.1:

Release 0.18.1 ============== * docutils/nodes.py - `Node.traverse()` returns a list again to restore backwards compatibility. Fixes bug #431. - New method `Node.findall()`: like `Node.traverse()` but returns an iterator. Obsoletes `Node.traverse()`.

(from https://sourceforge.net/p/docutils/code/HEAD/tree/trunk/docutils/HISTORY.txt)

I'll push a commit to be more specific about the version.

numpydoc/tests/test_full.py

drammock · 2022-06-01T14:47:14Z

Just a note that although the CIs were coming back green before the last commit, I don't think they're actually testing against sphinx 5.0beta / docutils 0.18 ? Locally I still see this:

=================================== short test summary info ===================================
XFAIL numpydoc/tests/test_validate.py::TestValidator::test_bad_docstrings[BadParameters-blank_lines-msgs30]
XFAIL numpydoc/tests/test_validate.py::TestValidator::test_bad_docstrings[BadReturns-no_type-msgs33]
=============================== 237 passed, 2 xfailed in 1.73s ================================

and I'm not sure how to fix it... that pytest.parametrize is over 200 lines long and I haven't had the time to wrap my head around it. Maybe @datapythonista or @larsoner have time to look?

drammock · 2022-06-01T15:00:53Z

Just a note that although the CIs were coming back green before the last commit, I don't think they're actually testing against sphinx 5.0beta / docutils 0.18 ?

Never mind, I'm wrong, I just spotted the prerelease jobs. And I also just realized that I was mis-reading the pytest output. Those are successfully failing XFAILs not unexpectedly passing XFAILs. So I think this is ready for review/merge @jarrodmillman

larsoner

Code changes LGTM, +1 for merge. Feel free to merge if you're happy @jarrodmillman !

I can also confirm that on docutils 0.18.1 I have failures building MNE-Python's doc, and with this PR things build fine.

jarrodmillman · 2022-06-02T00:31:40Z

See #404. That should fix the test failures.

drammock · 2022-06-02T11:07:13Z

See #404. That should fix the test failures.

Ok great! Can you manually re-trigger the failing runs? I can't just push an empty commit; as a first time contrib here, the CIs will wait for maintainer approval anyway.

larsoner · 2022-06-02T11:10:35Z

Since it's a change to the CI yaml you'll need to merge or rebase I think

drammock · 2022-06-02T11:15:09Z

Since it's a change to the CI yaml you'll need to merge or rebase I think

Ah right, of course. Will do when I'm not on a phone

larsoner · 2022-06-02T15:55:20Z

All green!

jarrodmillman · 2022-06-02T16:03:11Z

Thanks!!

drammock mentioned this pull request May 28, 2022

sphinx 5 compatibility #399

Closed

drammock added 2 commits May 28, 2022 15:13

use node.findall if available (docutils 18.x)

76c033b

fix test_reference

29caa49

drammock force-pushed the node-traverse branch from 84d8512 to 29caa49 Compare May 28, 2022 20:14

keep test_reference backwards-compatible

61becba

jarrodmillman changed the title ~~use node.findall if available (docutils 18.x)~~ Use node.findall if available (docutils 18.x) May 31, 2022

jarrodmillman added this to the 1.4.0 milestone May 31, 2022

jarrodmillman requested changes May 31, 2022

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jarrodmillman marked this pull request as ready for review May 31, 2022 17:47

drammock and others added 2 commits May 31, 2022 13:24

Add comments about when triage becomes unnecessary/obsolete

99d0961

Co-authored-by: Jarrod Millman <[email protected]>

whitespace

0df45f0

rossbar reviewed May 31, 2022

View reviewed changes

drammock commented Jun 1, 2022

View reviewed changes

numpydoc/tests/test_full.py Show resolved Hide resolved

fix docutils version as noted in docstring

296bbde

larsoner approved these changes Jun 1, 2022

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Merge remote-tracking branch 'upstream/main' into node-traverse

04c812d

jarrodmillman approved these changes Jun 2, 2022

View reviewed changes

jarrodmillman merged commit 601642b into numpy:main Jun 2, 2022

jarrodmillman mentioned this pull request Jun 2, 2022

Test docutils 0.18.1 #402

Merged

This was referenced Jun 2, 2022

Future: _traverse_or_findall -> findall when docutils 0.18 is the minimum version #405

Open

1.4.0 release plan #408

Closed

drammock mentioned this pull request Jun 24, 2022

[MAINT, MRG] Fix nilearn intersphinx mne-tools/mne-python#10825

Merged

drammock deleted the node-traverse branch June 24, 2022 21:01

jarrodmillman mentioned this pull request Feb 19, 2025

Require Sphinx 7 #607

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Use node.findall if available (docutils 18.x) #403

Use node.findall if available (docutils 18.x) #403

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Use node.findall if available (docutils 18.x) #403

Use node.findall if available (docutils 18.x) #403

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