Bump pymatgen from 2025.2.18 to 2025.5.2

[dependabot]

Bumps pymatgen from 2025.2.18 to 2025.5.2.

Release notes

Sourced from pymatgen's releases.

v2025.5.2

• Remove lxml since it is slower for many Vasprun parsing situations.

v2025.5.1

• lxml is now used for faster Vasprun parsing.
• Minor bug fix for MPRester.get_entries summary_data for larger queries.
• New JSON for ptable with better value/unit handling (also slightly faster) (@​DanielYang59)
• Handle missing trailing newline in ICOHPLIST.lobster (@​alibh95)
• Updated MVLSlabSet with MPSurfaceSet parameters from atomate1 (@​abhardwaj73)

v2025.4.24

• Structure now has a calc_property method that enables one to get a wide range of elasticity, EOS, and phonon properties using matcalc. Requires matcalc to be installed.
• Bug fix and expansion of pymatgen.ext.matproj.MPRester. Now property_data is always consistent with the returned entry in get_entries. Summary data, which is not always consistent but is more comprehensive, can be obtained via a summary_data kwarg.
• PR #4378 Avoid merging if a structure has only one site by @​kmu This PR fixes an error that occurs when calling merge_sites on a structure with only one site. For example:
• PR #4372 Reapply update to ptable vdw radii CSV source and JSON with CRC handbook by @​DanielYang59
  • Update ptable vdw radii CSV source, to fix #4370
  • Revert #4345 and apply changes to CSV vdw radii data source:

  John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL. If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.

v2025.4.20

• Updated perturb method to be in parity for Structure and Molecule.
• PR #4226 Fix file existence check in ChargemolAnalysis to verify directory instead. by @​lllangWV
• PR #4324 GibbsComputedStructureEntry update to handle float temperature values by @​slee-lab
• PR #4303 Fix mcl kpoints by @​dgaines2 Fixed errors in two of the k-points for the MCL reciprocal lattice (according to Table 16 in Setyawan-Curtarolo 2010) M2 and D1 aren't included in the recommended k-point path, but third-party software that plots k-point paths using pymatgen labelled M2 in the path instead of M1 due to it being the "same" k-point.
• PR #4344 Update "electron affinities" in periodic_table.json by @​DanielYang59
• PR #4365 Python 3.13 support by @​DanielYang59

v2025.4.19

• MPRester.get_entries and get_entries_in_chemsys now supports property_data. inc_structure, conventional_only and
• PR #4367 fix perturb bug that displaced all atoms equally by @​skasamatsu
• PR #4361 Replace pybtex with bibtexparser by @​DanielYang59
• PR #4362 fix(MVLSlabSet): convert DIPOL vector to pure Python list before writing INCAR by @​atulcthakur
• PR #4363 Ensure actual_kpoints_weights is list[float] and add test by @​kavanase
• PR #4345 Fix inconsistent "Van der waals radius" and "Metallic radius" in core.periodic_table.json by @​DanielYang59
• PR #4212 Deprecate PymatgenTest, migrate tests to pytest from unittest by @​DanielYang59

v2025.4.17

• Bug fix for list based searches in MPRester.

v2025.4.16

• Major new feature and breaking change: Legacy MP API is no longer supported. Pymatgen also no longer support mp-api in the backend. Instead, Pymatgen's MPRester now has nearly 100% feature parity with mp-api's document searches. One major difference is that pymatgen's MPRester will follow the documented REST API end points exactly, i.e., users just need to refer to https://api.materialsproject.org/docs for the exact field names.
• PR #4360 Speed up Vasprun parsing by @​kavanase

... (truncated)

Changelog

Sourced from pymatgen's changelog.

2025.5.2

• Remove lxml since it is slower for many Vasprun parsing situations.

v2025.5.1

• lxml is now used for faster Vasprun parsing.
• Minor bug fix for MPRester.get_entries summary_data for larger queries.
• New JSON for ptable with better value/unit handling (also slightly faster) (@​DanielYang59)
• Handle missing trailing newline in ICOHPLIST.lobster (@​alibh95)
• Updated MVLSlabSet with MPSurfaceSet parameters from atomate1 (@​abhardwaj73)

v2025.4.24

• Structure now has a calc_property method that enables one to get a wide range of elasticity, EOS, and phonon properties using matcalc. Requires matcalc to be installed.
• Bug fix and expansion of pymatgen.ext.matproj.MPRester. Now property_data is always consistent with the returned entry in get_entries. Summary data, which is not always consistent but is more comprehensive, can be obtained via a summary_data kwarg.
• PR #4378 Avoid merging if a structure has only one site by @​kmu This PR fixes an error that occurs when calling merge_sites on a structure with only one site. For example:
• PR #4372 Reapply update to ptable vdw radii CSV source and JSON with CRC handbook by @​DanielYang59
  • Update ptable vdw radii CSV source, to fix #4370
  • Revert #4345 and apply changes to CSV vdw radii data source:

  John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL. If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.

v2025.4.20

• Updated perturb method to be in parity for Structure and Molecule.
• PR #4226 Fix file existence check in ChargemolAnalysis to verify directory instead. by @​lllangWV
• PR #4324 GibbsComputedStructureEntry update to handle float temperature values by @​slee-lab
• PR #4303 Fix mcl kpoints by @​dgaines2 Fixed errors in two of the k-points for the MCL reciprocal lattice (according to Table 16 in Setyawan-Curtarolo 2010) M2 and D1 aren't included in the recommended k-point path, but third-party software that plots k-point paths using pymatgen labelled M2 in the path instead of M1 due to it being the "same" k-point.
• PR #4344 Update "electron affinities" in periodic_table.json by @​DanielYang59
• PR #4365 Python 3.13 support by @​DanielYang59

v2025.4.19

• MPRester.get_entries and get_entries_in_chemsys now supports property_data. inc_structure, conventional_only and
• PR #4367 fix perturb bug that displaced all atoms equally by @​skasamatsu
• PR #4361 Replace pybtex with bibtexparser by @​DanielYang59
• PR #4362 fix(MVLSlabSet): convert DIPOL vector to pure Python list before writing INCAR by @​atulcthakur
• PR #4363 Ensure actual_kpoints_weights is list[float] and add test by @​kavanase
• PR #4345 Fix inconsistent "Van der waals radius" and "Metallic radius" in core.periodic_table.json by @​DanielYang59
• PR #4212 Deprecate PymatgenTest, migrate tests to pytest from unittest by @​DanielYang59

v2025.4.17

... (truncated)

Commits

• 46258d1 Update docs
• 7eef04f Update changelog.
• 5b0d0e9 Revert lxml since for our use case, it is a bit slower.
• c5eda1c Set remove_blank_text=True.
• 0704037 Update docs
• ed69e59 Updated vasp input sets with MPSurfaceSet from atomate1 (#4287)
• 45e8bd4 fix(outputs.py): handle missing trailing newline in ICOHPLIST.lobster (#4350)
• 9dfe704 Use new JSON for ptable with better value/unit handling (also slightly faster...
• 160d699 Merge branch 'master' of github.com:materialsproject/pymatgen
• 191e6bb Add lxml for faster Vasprun parsing.
• Additional commits viewable in compare view

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