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Avoid and fix Deprecation Warnings#4617

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kavanase wants to merge 17 commits intomaterialsproject:masterfrom
kavanase:patch-3
Open

Avoid and fix Deprecation Warnings#4617
kavanase wants to merge 17 commits intomaterialsproject:masterfrom
kavanase:patch-3

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@kavanase
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Summary

This PR:

  • Fixes some incorrectly swapped deprecation warnings (for entry_tools and correction_calculator).
  • Updates usages to match the new sub-package structure, avoiding deprecation warnings (caused by the internal code structure).

I would note that this PR update is likely not exhaustive; there are likely other usages of deprecated code in the pymatgen codebase following the big restructuring with pymatgen-core. It would be helpful to search through the DeprecationWarnings added in #4595 and check that the rest of the codebase has been updated accordingly. @DanielYang59 perhaps you could check this as you have a good understanding of the current code structure?
I imagine some code in pymatgen-core likely needs to be updated too, in a similar fashion.

There is also some issues with MPRester related to the code structure changes and deprecations, I will raise an issue for that now.

kavanase and others added 10 commits March 24, 2026 14:12
Update import paths to avoid deprecation warnings

Signed-off-by: Seán Kavanagh <51478689+kavanase@users.noreply.github.com>
Signed-off-by: Seán Kavanagh <51478689+kavanase@users.noreply.github.com>
…ompatibility`` to avoid deprecation warnings from ``pymatgen`` code
…tries`` to avoid deprecation warnings from ``pymatgen`` code
…patibility.entry_tools`` to avoid deprecation warnings from ``pymatgen`` code
…matgen.core.molecule_structure_comparator`` to avoid deprecation warnings from ``pymatgen`` code
…patibility.exp_entries`` to avoid deprecation warnings from ``pymatgen`` code
…alysis.compatibility.correction_calculator``
@kavanase
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These warnings were flagged by our warnings tests in doped and ShakeNBreak.

@kavanase
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Fyi, the issue with MPRester that I mentioned is raised here: materialsproject/api#1071

kavanase and others added 6 commits March 24, 2026 15:43
…structure_matcher`` to avoid internal deprecation warnings with ``pymatgen``
…gen.analysis.compatibility.computed_entries``
….structure_analyzer`` to avoid internal deprecation warnings with ``pymatgen``
… avoid internal deprecation warnings with ``pymatgen``
…v`` to avoid internal deprecation warnings with ``pymatgen``
@shyuep
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shyuep commented Apr 7, 2026

Thanks. Do you mind resolving the conflicts? I believe you just need to delete the entire docs directory.

@kavanase
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kavanase commented Apr 7, 2026

Yep certainly can do, though I think @DanielYang59 and I were going to try digging in a bit more to avoid any other instances of this first, and seemed like there was still some discussion about the repo structure (#4595 – I will add my thoughts there now).

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2 participants