Bump pymatgen from 2024.11.13 to 2025.1.24

[dependabot]

Bumps pymatgen from 2024.11.13 to 2025.1.24.

Release notes

Sourced from pymatgen's releases.

v2025.1.24

PR #4159 by @​DanielYang59

• Objective: Enhance the reliability and efficiency of float comparison in the codebase.
• Improvements:
  • Avoid using == for float comparisons to fix issue #4158.
  • Replace assert_array_equal with suitable alternatives like assert_allclose for floating-point arrays to accommodate numerical imprecision.
  • Improve the _proj function implementation, resulting in approximately a threefold speed increase.
  • Substitute sequences of float comparisons using == in list/tuple/dict structures.
  • Conduct various type and comment enhancements.

PR #4190 by @​benrich37

• Objective: Introduce a structured and organized approach to represent data from JDFTx output files.
• Key Features:
  • Hierarchical Class Structure: Implemented a hierarchy of classes to represent JDFTx output file data, without inheriting from one another. Key classes include:
    • JDFTXOutputs, JDFTXOutfile, JDFTXOutfileSlice
    • Sub-structures like JOutStructures, JElSteps, etc.
  • Modules Introduced:
    • outputs.py: Provides a robust Pythonic representation of a JDFTx output file.
    • jdftxoutfileslice.py: Represents a “slice” of a JDFTx output file.
    • joutstructures.py: Represents a series of structures within an output file slice.
    • joutstructure.py: Represents a single structure within an output file.
    • jelstep.py: Manages SCF steps and convergence data.
    • jminsettings.py: Abstract class for managing input minimization settings, with subclasses for various settings types.

PR #4189 by @​benrich37

• Objective: Develop a Pythonic representation for inputs used in JDFTx calculations.
• Key Features:
  • inputs.py module introducing JDFTXInfile class.
  • Helper modules:
    • generic_tags.py: Includes "Tag" objects to define structures expected by JDFTx inputs.
    • jdftxinfile_master_format.py: Facilitates the creation of appropriate "Tag" objects.
    • jdftxinfile_ref_options.py: Contains lists of valid inputs for various tags, such as XC functionals for the "elec-ex-corr" tag.

v2025.1.23

1. PR #4255 by @​peikai: This PR resolves an inconsistency in the run_type for entries in a mixing scheme. The entry type was changed to 'r2SCAN', but the MaterialsProjectDFTMixingScheme() expected 'R2SCAN', causing errors and ignored entries in GGA(+U)/R2SCAN mixing scheme corrections.

2. PR #4160 by @​DanielYang59: Enhancements and clarifications were made to the io.vasp.outputs.Outcar docstring/comment. This includes more specific type annotations for parsers and updating the default value in getattr to False for condition checks.

3. PR #4257 by @​njzjz: This PR covers the intention to build Linux arm64 wheels, referencing the availability of free hosted runners for public repositories. However, specific features and fixes were not detailed.

4. PR #4240 by @​kavanase: A minor fix in FermiDos improves the robustness of the get_doping method, addressing issues with handling rare cases with minimal energy increments between VBM and CBM indices.

5. PR #4254 by @​tpurcell90: Adjustments regarding the use of libxc with FHI-aims to automatically add an override warning call, ensuring the process behaves as expected.

6. PR #4256 by @​kavanase: Addresses a behavior issue with Composition for mixed species and element compositions, providing a fix that ensures compositions are interpreted correctly, avoiding incorrect results in representations and calculations.

7. PR #4253 by @​esoteric-ephemera: This PR introduces the ability to convert between ASE and pymatgen trajectories, maintaining additional data such as energies, forces, and stresses, thus improving integration between the two programs and addressing related issues.

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2025.1.24

1. PR #4159 by @​DanielYang59

   • Avoid using full equality == to compare float values to address issue #4158.
   • Recommend using assert_allclose over assert_array_equal for float arrays due to numerical imprecision.
   • Implement a ~3x speedup tweak to the _proj implementation.
   • Partially replace sequence of float comparison using == for list/tuple/dict as referenced here.
   • Introduce other type and comment tweaks.

2. PR #4190 by @​benrich37

   • Feature 0: Hierarchical structure using class objects to represent data within a JDFTx out file.
     • Main hierarchy classes:
       • JDFTXOutputs
         • JDFTXOutputs.outfile
         • JDFTXOutfile
         • JDFTXOutfile.slices[i]
         • JDFTXOutfileSlice, etc.
   • Feature 1: outputs.py module with JDFTXOutfile for representing a JDFTx out file.
   • Feature 2: jdftxoutfileslice.py module with JDFTXOutfileSlice for file slices of a single JDFTx call.
   • Feature 3: joutstructures.py with JOutStructures for representing structures from an out file slice.
   • Feature 4: joutstructure.py with JOutStructure for each single structure within an out file.
   • Feature 5: jelstep.py with JElStep and JElSteps for SCF steps and convergences.
   • Feature 6: jminsettings.py with JMinSettings for minimization settings representations.

3. PR #4189 by @​benrich37

   • Feature 1: inputs.py module containing JDFTXInfile for Pythonic representation of JDFTx calculation inputs.
   • Feature 2: generic_tags.py module with "Tag" objects (AbstractTag and its inheritors) for JDFTx input structure representation.
   • Feature 3: jdftxinfile_master_format.py for creating proper "Tag" objects for inputs.
   • Feature 4: jdftxinfile_ref_options.py for holding lists of acceptable strings for input tags.

v2025.1.23

1. PR #4255 by @​peikai: This PR resolves an inconsistency in the run_type for entries in a mixing scheme. The entry type was changed to 'r2SCAN', but the MaterialsProjectDFTMixingScheme() expected 'R2SCAN', causing errors and ignored entries in GGA(+U)/R2SCAN mixing scheme corrections.

2. PR #4160 by @​DanielYang59: Enhancements and clarifications were made to the io.vasp.outputs.Outcar docstring/comment. This includes more specific type annotations for parsers and updating the default value in getattr to False for condition checks.

3. PR #4257 by @​njzjz: This PR covers the intention to build Linux arm64 wheels, referencing the availability of free hosted runners for public repositories. However, specific features and fixes were not detailed.

4. PR #4240 by @​kavanase: A minor fix in FermiDos improves the robustness of the get_doping method, addressing issues with handling rare cases with minimal energy increments between VBM and CBM indices.

5. PR #4254 by @​tpurcell90: Adjustments regarding the use of libxc with FHI-aims to automatically add an override warning call, ensuring the process behaves as expected.

6. PR #4256 by @​kavanase: Addresses a behavior issue with Composition for mixed species and element compositions, providing a fix that ensures compositions are interpreted correctly, avoiding incorrect results in representations and calculations.

7. PR #4253 by @​esoteric-ephemera: This PR introduces the ability to convert between ASE and pymatgen trajectories, maintaining additional data such as energies, forces, and stresses, thus improving integration between the two programs and addressing related issues.

These updates range from bug fixes and enhancements to new features aimed at improving the functionality and reliability of the codebase.

2025.1.9

• Iterating Element no longer contains isotopes (D and T). (@​DanielYang59)

... (truncated)

Commits

• 8599968 Update docs
• 2d1e5db Update changelog.
• c14ec67 Improve test.
• ef5321b Use md5 for unique hash.
• 7e7756e Avoid using full equality (==) to compare float, avoid assert_array_equal...
• 5f744f2 Outputs - JDFTx IO Module (#4190)
• eb66a63 Inputs - JDFTx IO Module (#4189)
• 3395429 Fix release workflow.
• 117729d Minor error in code.
• 4c8f451 invoke update-changelog now uses ChatGPT to summarize PRs.
• Additional commits viewable in compare view

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