Bump pymatgen from 2025.2.18 to 2025.4.24

[dependabot]

Bumps pymatgen from 2025.2.18 to 2025.4.24.

Release notes

Sourced from pymatgen's releases.

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
• PR #4343 Drop duplicate iupac_ordering entries in core.periodic_table.json by @​DanielYang59
• PR #4348 Remove deprecated grain boundary analysis by @​DanielYang59
• PR #4357 Fix circular import of SymmOp by @​DanielYang59

v2025.4.10

• Parity with MPRester.materials.summary.search in MPResterBasic.
• PR #4355 Fix round-trip constraints handling of AseAtomsAdaptor by @​yantar92
  • src/pymatgen/io/ase.py (AseAtomsAdaptor.get_structure): When no explicit constraint is given for a site in ASE Atoms object, use "T T T" selective dynamics (no constraint). The old code is plain wrong.
  • tests/io/test_ase.py (test_back_forth): Add new test case. Fixes #4354.

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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
• PR #4343 Drop duplicate iupac_ordering entries in core.periodic_table.json by @​DanielYang59
• PR #4348 Remove deprecated grain boundary analysis by @​DanielYang59
• PR #4357 Fix circular import of SymmOp by @​DanielYang59

v2025.4.10

... (truncated)

Commits

• 34f5171 Update docs
• 0b03a6c Updated changelog.
• 86bf5db Add elasticity.
• 9ff249e Skip calc_prop test if matcalc is not installed.
• f86d515 Add calc_property method for Structure that enables you to use matcalc
• 594633c Allow best of both worlds - property data and summary data.
• eb954e4 modernize MPRester tests.
• e3e1160 Add test for uncorrected_energy_per_atom verfiication.
• b54ac3e Use thermo endpoint for property_data. Fixes #4379.
• 59d04ad Skip AIMS set test on Windows. Weird bug and not critical to test on all
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot]

Superseded by #384.