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Fix for incorrect file path in tests/io/test_zeopp.py #3784

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merged 4 commits into from
Apr 25, 2024

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AntObi
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@AntObi AntObi commented Apr 25, 2024

Summary

I've been testing using Zeo++ with pymatgen using io/zeopp and found that some of the tests were failing. I've determined that the tests were failing due to incorrect file paths to the tests files.

Major changes: Fixed incorrect file path in zeopp test file

  • fix 1: f"{TEST_FILES_DIR}/cssr/EDI.cssr" -> f"{TEST_FILES_DIR}/io/cssr/EDI.cssr"
  • fix 2: f"{TEST_FILES_DIR}/cssr/EDI_oxistate_decorated.cssr" -> f"{TEST_FILES_DIR}/io/cssr/EDI_oxistate_decorated.cssr"

Checklist

  • Google format doc strings added. Check with ruff.
  • Type annotations included. Check with mypy.
  • Tests added for new features/fixes.
  • If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

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coderabbitai bot commented Apr 25, 2024

Walkthrough

The changes involve enhancing parameter descriptions, improving code readability, and updating file paths for better organization and accessibility within the codebase across multiple files in different directories.

Changes

File Path Change Summary
pymatgen/core/structure.py Clarified the distance parameter description in the perturb method of the structure class.
pymatgen/util/due.py Updated logging message format from using %s to f-string interpolation for better readability and efficiency.
tests/analysis/test_graphs.py Split the condition in the @pytest.mark.skipif decorator over multiple lines for readability.
tests/io/test_zeopp.py Updated file paths in test_from_file method to include io subdirectory for CSSR file loading.

Recent Review Details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits Files that changed from the base of the PR and between 2753f4c and e64809b.
Files selected for processing (1)
  • pymatgen/util/due.py (1 hunks)
Files skipped from review due to trivial changes (1)
  • pymatgen/util/due.py

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@janosh janosh added tests Issues with or changes to the pymatgen test suite io Input/output functionality fix Bug fix PRs labels Apr 25, 2024
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thanks for the fix @AntObi! 👍

@DanielYang59 if you have time, could you see if there might be any other skipped tests where the test file path was not updated during the file migrations in #3746

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Actionable comments posted: 1

@@ -4291,8 +4291,7 @@ def perturb(self, distance: float, min_distance: float | None = None) -> Self:
symmetries. Modifies the structure in place.

Args:
distance (float): Distance in angstroms by which to perturb each
site.
distance (float): Distance in angstroms by which to perturb each site.
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Clarify the parameter description for the distance argument in the perturb method.

@janosh janosh merged commit f8fd454 into materialsproject:master Apr 25, 2024
22 checks passed
@AntObi AntObi deleted the zeopp_tests branch April 25, 2024 18:37
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Ah, looks like a miss by me, thanks for fixing.

@janosh, yes sure. It might be better for me to push #3684 forward to avoid future issues.

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3 participants