fix: fix deprecation warning - #153
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sbillinge merged 1 commit intoFeb 17, 2026
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Codecov Report✅ All modified and coverable lines are covered by tests. @@ Coverage Diff @@
## main #153 +/- ##
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Coverage 98.93% 98.93%
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Files 13 13
Lines 1878 1878
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Hits 1858 1858
Misses 20 20
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@sbillinge ready to review. As followed by running pytest on the skpkg version, there is one deprecation warning as shown below:
(diffpy.structure) ~/dbs/diffpy.structure git:[main] pytest ============================================================================================================== test session starts ============================================================================================================== platform darwin -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0 rootdir: /Users/huarundong/dbs/diffpy.structure configfile: pyproject.toml collected 137 items tests/test_atom.py .. [ 1%] tests/test_lattice.py ............ [ 10%] tests/test_loadstructure.py ...... [ 14%] tests/test_p_cif.py ..................... [ 29%] tests/test_p_discus.py ..... [ 33%] tests/test_p_pdffit.py ......... [ 40%] tests/test_parsers.py ............. [ 49%] tests/test_spacegroups.py ..... [ 53%] tests/test_structure.py ....................................... [ 81%] tests/test_supercell.py ... [ 83%] tests/test_symmetryutilities.py ..................... [ 99%] tests/test_version.py . [100%] =============================================================================================================== warnings summary ================================================================================================================ tests/test_parsers.py::TestP_xyz::test_write_xyz /opt/miniconda3/envs/diffpy.structure/lib/python3.14/site-packages/diffpy/structure/structure.py:350: DeprecationWarning: codecs.open() is deprecated. Use open() instead. with codecs.open(filename, "w", encoding="UTF-8") as fp: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================================================================================================== 137 passed, 1 warning in 0.63s =========================================================================================================After the fix done by this PR, I run the pip install -e . and then the pytest passed all tests without warnings as shown below: