Bump pymatgen from 2025.2.18 to 2025.5.28

[dependabot]

Bumps pymatgen from 2025.2.18 to 2025.5.28.

Release notes

Sourced from pymatgen's releases.

v2025.5.28

• PR #4411 Add orjson as required dependency as default JSON handler when custom encoder/decoder is not needed by @​DanielYang59
• PR #4417 adding radd dunder method to Volumetric data + test_outputs by @​wladerer
• PR #4418 JDFTXOutfileSlice Durability Improvement by @​benrich37 Major changes:
  • feature 1: Improved durability of JDFTXOutfileSlice._from_out_slice method (less likely to error out on unexpected termination) -- So long as one step of electronic minimization has started on an out file slice, parsing shouldn't error out
  • fix 1: Allow partially dumped eigstats
  • fix 2: Added missing optical band gap dumped by eigstats
  • fix 3: Protect the final JOutStructure in initializing a JOutStructures with a try/except block
  • fix 4: Detect if positions were only partially dumped and revert to data from init_structure in JOutStructure
  • fix 5: Prevent partially dumped matrices from being used in initializing a JOutStructure

  Todos

  • feature 1: Ensure parse-ability as long as a JDFTXOutfileSlice.infile can be initialized
• PR #4419 Fix Molecule.get_boxed_structure when reorder=False by @​gpetretto
• PR #4416 JDFTXInfile Comparison Methods by @​benrich37 Major changes:
  • feature 1: Convenience methods for comparing JDFTXInfile objects -- JDFTXInfile.is_comparable_to --- Returns True if at least one tag is found different --- Optional arguments exclude_tags, exclude_tag_categories, ensure_include_tags to ignore certain tags in the comparison ---- exclude_tag_categories defaults to ["export", "restart", "structure"] as "export" and "restart" are very rarely pertinent to comparability, "structure" as subtags of this category are generally the one thing being intentionally changed in comparisons (ie different local minima or a slab with/without an adsorbate) -- JDFTXInfile.get_filtered_differing_tags --- What is used in JDFTXInfile.is_comparable_to to get filtered differing tags between JDFTXInfile objects --- Convenient as a "verbose" alternative to JDFTXInfile.is_comparable_to -- AbstractTag.is_equal_to and AbstractTag._is_equal_to --- Used in tag comparison for finding differing tags --- AbstractTag._is_equal_to is an abstract method that must be implemented for each AbstractTag inheritor
  • feature 2: Default JDFTXInfile object pymatgen.io.jdftx.inputs.ref_infile -- Initialized from reading default JDFTx settings from pymatgen.io.jdftx.jdftxinfile_default_inputs.default_inputs: dict -- Used in JDFTXInfile.get_differing_tags_from for tags in self missing from other that are identical to the default setting
  • fix 1: Re-ordered contents of JDFTXInfile to follow the order: magic methods -> class methods / transformation methods -> validation methods -> properties -> private methods
  • fix 2: Checking for 'selective_dynamics' in site_properties for a Structure passed in JDFTXInfile.from_structure (used if selective_dynamics argument left as None)

  Todos

  • feature 1: Add examples to documentation on how to properly use new comparison methods
  • feature 2: Improve the mapping of TagContainers to their default values -- The current implementation of comparison for tags to default values only works if the tag as written exactly matches the full default value - at the very least the missing subtags of a partially filled TagContainer needs to be filled with the default values before comparing to the full default value -- Some subtags also change depending on the other subtags present for a particular tag (ie convergence threshold depending on algorithm specified for 'fluid-minimize', so an improved mapping for dynamic default values needs to be implemented
• PR #4413 JDFTXOutputs.bandstructure: BandStructure by @​benrich37 Major changes:
  • feature 1: Added 'kpts' storable variable to JDFTXOutputs -- Currently only able to obtain from the 'bandProjections' file
  • feature 2: Added bandstructure attribute to JDFTXOutputs -- Standard pymatgen BandStrucure object -- Request-able as a store_var, but functions slightly differently --- Ensures 'eigenvals' and 'kpts' are in store_vars and then is deleted -- Initialized if JDFTXOutputs has successfully stored at least 'kpts' and 'eigenvals' -- Fills projections field if also has stored 'bandProjections'
  • feature 3: Added wk_list to JDFTXOutputs -- List of weights for each k-point

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2025.5.28

• PR #4411 Add orjson as required dependency as default JSON handler when custom encoder/decoder is not needed by @​DanielYang59
• PR #4417 adding radd dunder method to Volumetric data + test_outputs by @​wladerer
• PR #4418 JDFTXOutfileSlice Durability Improvement by @​benrich37 Major changes:
  • feature 1: Improved durability of JDFTXOutfileSlice._from_out_slice method (less likely to error out on unexpected termination) -- So long as one step of electronic minimization has started on an out file slice, parsing shouldn't error out
  • fix 1: Allow partially dumped eigstats
  • fix 2: Added missing optical band gap dumped by eigstats
  • fix 3: Protect the final JOutStructure in initializing a JOutStructures with a try/except block
  • fix 4: Detect if positions were only partially dumped and revert to data from init_structure in JOutStructure
  • fix 5: Prevent partially dumped matrices from being used in initializing a JOutStructure

  Todos

  • feature 1: Ensure parse-ability as long as a JDFTXOutfileSlice.infile can be initialized
• PR #4419 Fix Molecule.get_boxed_structure when reorder=False by @​gpetretto
• PR #4416 JDFTXInfile Comparison Methods by @​benrich37 Major changes:
  • feature 1: Convenience methods for comparing JDFTXInfile objects -- JDFTXInfile.is_comparable_to --- Returns True if at least one tag is found different --- Optional arguments exclude_tags, exclude_tag_categories, ensure_include_tags to ignore certain tags in the comparison ---- exclude_tag_categories defaults to ["export", "restart", "structure"] as "export" and "restart" are very rarely pertinent to comparability, "structure" as subtags of this category are generally the one thing being intentionally changed in comparisons (ie different local minima or a slab with/without an adsorbate) -- JDFTXInfile.get_filtered_differing_tags --- What is used in JDFTXInfile.is_comparable_to to get filtered differing tags between JDFTXInfile objects --- Convenient as a "verbose" alternative to JDFTXInfile.is_comparable_to -- AbstractTag.is_equal_to and AbstractTag._is_equal_to --- Used in tag comparison for finding differing tags --- AbstractTag._is_equal_to is an abstract method that must be implemented for each AbstractTag inheritor
  • feature 2: Default JDFTXInfile object pymatgen.io.jdftx.inputs.ref_infile -- Initialized from reading default JDFTx settings from pymatgen.io.jdftx.jdftxinfile_default_inputs.default_inputs: dict -- Used in JDFTXInfile.get_differing_tags_from for tags in self missing from other that are identical to the default setting
  • fix 1: Re-ordered contents of JDFTXInfile to follow the order: magic methods -> class methods / transformation methods -> validation methods -> properties -> private methods
  • fix 2: Checking for 'selective_dynamics' in site_properties for a Structure passed in JDFTXInfile.from_structure (used if selective_dynamics argument left as None)

  Todos

  • feature 1: Add examples to documentation on how to properly use new comparison methods
  • feature 2: Improve the mapping of TagContainers to their default values -- The current implementation of comparison for tags to default values only works if the tag as written exactly matches the full default value - at the very least the missing subtags of a partially filled TagContainer needs to be filled with the default values before comparing to the full default value -- Some subtags also change depending on the other subtags present for a particular tag (ie convergence threshold depending on algorithm specified for 'fluid-minimize', so an improved mapping for dynamic default values needs to be implemented
• PR #4413 JDFTXOutputs.bandstructure: BandStructure by @​benrich37 Major changes:
  • feature 1: Added 'kpts' storable variable to JDFTXOutputs -- Currently only able to obtain from the 'bandProjections' file
  • feature 2: Added bandstructure attribute to JDFTXOutputs -- Standard pymatgen BandStrucure object -- Request-able as a store_var, but functions slightly differently --- Ensures 'eigenvals' and 'kpts' are in store_vars and then is deleted -- Initialized if JDFTXOutputs has successfully stored at least 'kpts' and 'eigenvals' -- Fills projections field if also has stored 'bandProjections'
  • feature 3: Added wk_list to JDFTXOutputs

... (truncated)

Commits

• 20afc86 Update docs
• 9051ced Update changelog.
• dd4da5f Add orjson as required dependency as default JSON handler when custom encod...
• 57d7f57 adding radd dunder method to Volumetric data + test_outputs (#4417)
• 9fea170 JDFTXOutfileSlice Durability Improvement (#4418)
• c6031ff fix Molecule.get_boxed_structure when reorder=False (#4419)
• 55f70b2 JDFTXInfile Comparison Methods (#4416)
• 12c573a bandstructure attribute for JDFTOutputs - initializes to BandStructure if...
• e82356d More test fixes.
• 378eea9 Write better tests.
• Additional commits viewable in compare view

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[dependabot]

Superseded by #401.