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Refactor analyze, add quality module and deprecate cohp module (replaced by coxx)#428

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naik-aakash merged 45 commits intoJaGeo:mainfrom
naik-aakash:refactor_analyze
May 6, 2026
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Refactor analyze, add quality module and deprecate cohp module (replaced by coxx)#428
naik-aakash merged 45 commits intoJaGeo:mainfrom
naik-aakash:refactor_analyze

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@naik-aakash naik-aakash commented Jan 31, 2026

Changes

  • Add Devcontainer config
  • Add deprecation warning of path_to_* in Analyze.__init__ class
  • Deprecate cohp submodule and move to coxx module
  • Added from_files , from_directory, as_dict and from_dict method to Analyze.__init__ class
  • Created separate class for CalcQualityAnalysis in quality module
  • Added tests to ensure CalcQualityAnalysis has same behaviour as existing methods that will be deprecated in sometime
  • Add utils.py module and move some functions from featurize.utils in this new module
  • Replaced the manually defined dictionary mapping CE symbol to name with AllCoordinationGeometries from pymatgen instead
  • Removed the custom defined LSE class and set on_error variable instead when getting LSE (It is taken care of in pymatgen LobsterNeighbors via this PR Simplify and clean up LobsterNeighbors materialsproject/pymatgen#4482 )
  • Add tests for MSONable and class methods

@naik-aakash naik-aakash marked this pull request as draft January 31, 2026 16:20
@naik-aakash naik-aakash self-assigned this Jan 31, 2026
@naik-aakash naik-aakash added enhancement New feature or request housekeeping labels Jan 31, 2026
@naik-aakash naik-aakash changed the title [WIP] Refactor analyze Refactor analyze, add quality module and deprecate cohp module (replaced by coxx) May 6, 2026
@naik-aakash naik-aakash requested a review from JaGeo May 6, 2026 17:16
@naik-aakash naik-aakash marked this pull request as ready for review May 6, 2026 17:16
@naik-aakash naik-aakash enabled auto-merge May 6, 2026 17:17
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@JaGeo JaGeo left a comment

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With the moved files, I cannot make a thorough review. However, I assume everything is still working as the tests run and pass

@naik-aakash naik-aakash merged commit ba982e6 into JaGeo:main May 6, 2026
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