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Merged
merged 15 commits into from
Jul 9, 2025

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@dependabot dependabot bot commented on behalf of github Jul 8, 2025

Bumps sphinx-parser from 0.0.1 to 0.0.2.

Release notes

Sourced from sphinx-parser's releases.

sphinx_parser-0.0.2

What's Changed

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Full Changelog: https://github.com/pyiron/sphinx_parser/commits/sphinx_parser-0.0.2

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Bumps [sphinx-parser](https://github.com/pyiron/sphinx_parser) from 0.0.1 to 0.0.2.
- [Release notes](https://github.com/pyiron/sphinx_parser/releases)
- [Commits](pyiron/sphinx_parser@0.0.1...sphinx_parser-0.0.2)

---
updated-dependencies:
- dependency-name: sphinx-parser
  dependency-version: 0.0.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file patch backward compatible bug fixes python Pull requests that update python code labels Jul 8, 2025
@jan-janssen
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@samwaseda it seems the Sphinx parser changed

======================================================================
ERROR: setUpClass (sphinx.test_base.TestSphinx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/sphinx/test_base.py", line 78, in setUpClass
    cls.sphinx_2_5.collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/interactive.py", line 215, in collect_output
    super(SphinxInteractive, self).collect_output(
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 1474, in collect_output
    self.output.collect(directory=self.working_directory)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 2111, in collect
    self.collect_energy_struct(file_name="energy-structOpt.dat", cwd=directory)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 1990, in collect_energy_struct
    results = collect_energy_struct(file_name=file_name, cwd=cwd)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: collect_energy_struct() got an unexpected keyword argument 'cwd'

======================================================================
ERROR: sphinx.test_parsers (unittest.loader._FailedTest.sphinx.test_parsers)
----------------------------------------------------------------------
ImportError: Failed to import test module: sphinx.test_parsers
Traceback (most recent call last):
  File "/home/runner/miniconda3/envs/test/lib/python3.12/unittest/loader.py", line 382, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/miniconda3/envs/test/lib/python3.12/unittest/loader.py", line 325, in _get_module_from_name
    __import__(name)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/sphinx/test_parsers.py", line 9, in <module>
    from sphinx_parser.output import (
ImportError: cannot import name 'SphinxWavesReader' from 'sphinx_parser.output' (/home/runner/miniconda3/envs/test/lib/python3.12/site-packages/sphinx_parser/output.py)


----------------------------------------------------------------------

@jan-janssen
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======================================================================
ERROR: setUpClass (sphinx.test_base.TestSphinx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/sphinx/test_base.py", line 78, in setUpClass
    cls.sphinx_2_5.collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/interactive.py", line 215, in collect_output
    super(SphinxInteractive, self).collect_output(
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 1474, in collect_output
    self.output.collect(directory=self.working_directory)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 2120, in collect
    self.collect_eps_dat(file_name=None, cwd=directory)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/sphinx/base.py", line 1971, in collect_eps_dat
    results = collect_eps_dat(
              ^^^^^^^^^^^^^^^^
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/sphinx_parser/output.py", line 73, in collect_eps_dat
    raise ValueError("cwd or file_name must be defined")
ValueError: cwd or file_name must be defined

----------------------------------------------------------------------

@jan-janssen
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@samwaseda I am not exactly sure how to fix this, as the working directory variable was removed from the sphinx parser - https://github.com/pyiron/sphinx_parser/pull/38/files#r2193389518

@jan-janssen jan-janssen marked this pull request as draft July 8, 2025 20:33
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codecov bot commented Jul 9, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 66.92%. Comparing base (8f8c6d2) to head (1e885bd).
Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1762      +/-   ##
==========================================
- Coverage   67.01%   66.92%   -0.09%     
==========================================
  Files          75       75              
  Lines       12101    12101              
==========================================
- Hits         8109     8099      -10     
- Misses       3992     4002      +10     

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@samwaseda samwaseda marked this pull request as ready for review July 9, 2025 05:19
@github-actions github-actions bot merged commit b5f5c84 into main Jul 9, 2025
26 of 27 checks passed
@github-actions github-actions bot deleted the dependabot/pip/sphinx-parser-0.0.2 branch July 9, 2025 05:23
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3 participants