Bump pymatgen from 2024.11.13 to 2025.10.7

[dependabot]

Bumps pymatgen from 2024.11.13 to 2025.10.7.

Release notes

Sourced from pymatgen's releases.

v2025.10.7

• PR #4502 Fix: indexing error in Procar._read() by @​finnrk Major changes:
  • Fixes a bug related to indices when skipping repeated k-points while reading PROCAR (for example, the double-counting of symmetry points when using a k-path for plotting bandstructure). Previously, projections, eigenvalues, occupations and weights would be attributed to the wrong k-points. Also, the k-point following the skipped k-point would have complex projections of NaN, as well as an occupation, weight, eigenvalue and squared projections of 0.
• PR #4503 Replace print with logging by @​DanielYang59
  • replace print with logging, I assume pymatgen as a lib code shouldn't use print...
  • remove some print from tests
• PR #4510 suppress runtime warning from boltztrap2 by @​DanielYang59 close #2317
• PR #4512 Fix missing sdist from PyPI by @​DanielYang59 fix #4509 tested in my fork: https://github.com/DanielYang59/pymatgen/actions/runs/18279908313/job/52040659228
• PR #4491 Deprecate projected_magnetisation with projected_magnetization (US spelling) by @​DanielYang59 fix #4382
• PR #4493 Composition.get_wt_fraction return float instead of FloatWithUnit by @​DanielYang59 fix #4492
• PR #4496 Overwrite __rtruediv__ for FloatWithUnit, fix ArrayWithUnit loses unit_type when unpickled by @​DanielYang59
  • fix #4495
  • Check ArrayWithUnit behaviour
  • Fix unpickle ArrayWithUnit loses unit_type
  • Add some tests for core.units, https://app.codecov.io/gh/materialsproject/pymatgen/blob/master/pymatgen%2Fcore%2Funits.py
• PR #4490 Replace linear_assignment with scipy linear_sum_assignment by @​DanielYang59
  • Replace linear_assignment with scipy linear_sum_assignment
  • Speed benchmark

  Benchmark

  WSL2 Ubuntu 24.04 (AMD64) Master branch:

  n | avg_time (s) |  std_dev (s)
  ------------------------------------
  100 |     0.000104 |     0.000018
  500 |     0.004302 |     0.002333
  1000 |     0.018374 |     0.006702
  5000 |     1.049615 |     0.327349
  

  Current branch:

  n | avg_time (s) |  std_dev (s)
  ------------------------------------
  100 |     0.000121 |     0.000030
  500 |     0.005082 |     0.002957
  1000 |     0.018487 |     0.006484
  5000 |     1.062805 |     0.332552
  

• PR #4440 JDFTXOutfileSlice.vibrational_modes and JDFTXOutfileSlice.vibrational_energy_components by @​benrich37 Major changes:
  • feature 1: Parsing and storage of vibrational modes within a JDFTXOutfileSlice -- Stored as a list[dict], where each dict contains --- "Type": str

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2025.10.7

• PR #4503 Replace print statements with logging across library code and tests (by @​DanielYang59)
• PR #4510 Suppress noisy RuntimeWarning messages from BoltzTraP2 during transport analysis (by @​DanielYang59)
• PR #4512 Ensure source distribution (sdist) is published to PyPI alongside wheels (by @​DanielYang59)
• PR #4494 Re-enable mypy “misc” rule and perform minor documentation, typing, and test cleanups (by @​DanielYang59)
• PR #4491 Deprecate projected_magnetisation in favor of projected_magnetization (US spelling) (by @​DanielYang59)
• PR #4493 Composition.get_wt_fraction now returns a float instead of FloatWithUnit (by @​DanielYang59)
• PR #4496 Implement rtruediv for FloatWithUnit and fix ArrayWithUnit losing unit_type on unpickling; add unit tests (by @​DanielYang59)
• PR #4497 Improve pmg CLI tests; fix pmg diff header ordering and resolve pmg view color handling error (by @​DanielYang59)
• PR #4490 Replace internal linear_assignment with scipy.optimize.linear_sum_assignment (by @​DanielYang59)
• PR #4440 Add parsing/storage of vibrational modes and vibrational energy components to JDFTXOutfileSlice with tests (by @​benrich37)
• PR #4487 Fix variable name collision in TranslateSitesTransformation.apply_transformation; strengthen test to catch issue (by @​Rastow)
• PR #4463 Remove dev-only “ci” optional dependency group, migrate CI to uv, and update markdown docs (by @​DanielYang59)
• PR #4447 Correct has_cobicar detection when NcICOBILIST is present in LOBSTER outputs (by @​tomdemeyere)
• PR #4469 Loosen requests version pin and fix deprecations/new ruff issues (by @​DanielYang59)
• PR #4479 Introduce JdftxInputSet (moved from atomate2), add base YAML preset and basic tests (by @​cote3804)
• PR #4484 Make jdftx.outputs compatible with Python versions prior to 3.11 by removing starred-subscript usage (by @​DanielYang59)
• PR #4473 Fix labels and values in NEBAnalysis plots, prefer exact glob matches, and deprecate spline_options in favor of zero_slope_saddle flag (by @​DanielYang59)
• PR #4260 Move FHI-aims IO to external package (pyfhiaims) to reduce duplication and ease maintenance (by @​tpurcell90)
• PR #4476 Patch ReDOS vulnerability in GaussianInput.from_string (by @​lbluque)
• PR #4449 Address ruff PERF401 (manual list comprehension) for minor performance/cleanliness improvements (by @​DanielYang59)
• PR #4448 Remove sensitivity to trailing newline in LOBSTER output parsers; improves robustness (by @​DanielYang59)
• PR #4454 Correct documentation for Element density_of_solid and molar volume units (by @​DanielYang59)
• PR #4455 Cache optional dependency installs in CI for macOS/Ubuntu; enable mcsqs and pyzeo tests; convert some skips to xfail (by @​DanielYang59)
• PR #4461 Allow numpy arrays for selective dynamics in Structure and add tests; ensure JSON roundtrips (by @​DanielYang59)
• PR #4464 Fix typo referencing site.species in SpacegroupAnalyzer.get_primitive_standard_structure (by @​boyoungzheng)
• PR #4446 Improve performance of Species.str by reducing redundant attribute lookups (by @​kavanase)
• PR #4438 Add basic S3 object retrieval support to the pymatgen user agent for large MP datasets (by @​esoteric-ephemera)

v2025.6.14

• Treat LATTICE_CONSTRAINTS as is for INCARs.
• PR #4425 JDFTXOutfileSlice.trajectory revision by @​benrich37 Major changes:
  • feature 1: JDFTXOutfileSlice.trajectory is now initialized with frame_properties set -- JOutStructure.properties filled with relevant data for frame_properties -- More properties added to JOutStructure.site_properties

  Todos

  • Remove class attributes in JOutStructure now redundant to data stored in JOutStructure.properties and JOutStructure.site_properties
• PR #4431 Single source of truth for POTCAR directory structure by @​esoteric-ephemera Modifies the pymatgen CLI to use the same POTCAR library directory structure as in pymatgen.io.vasp.inputs to close #4430. Possibly breaking from the CLI side (the directory structure will change) Pinging @​mkhorton since #4424 was probably motivated by similar concerns?
• PR #4433 Speed up symmetry functions with faster is_periodic_image algorithm by @​kavanase I noticed that in some of our doped testing workflows, SpacegroupAnalyzer.get_primitive_standard_structure() is one of the main bottlenecks (as to be expected). One of the dominant cost factors here is the usage of is_periodic_image, which can be expensive for large structures due to many np.allclose() calls. This PR implements a small change to instead use an equivalent (but faster) pure Python loop, which also breaks early if the tolerance is exceeded. In my test case, this reduced the time spent on is_periodic_image (and thus SpacegroupAnalyzer.get_primitive_standard_structure()) from 35s to 10s.
• PR #4432 Fingerprint sources by @​JaGeo Add correct papers to tanimoto fingerprints
• PR #4061 Fix branch directory check in io.vasp.outputs.get_band_structure_from_vasp_multiple_branches by @​DanielYang59

... (truncated)

Commits

• 770791a Update docs
• 18cc17b Update changelog,
• fb6ba71 Remove defunct PDM.lock.
• a2096b1 Ignore Pattern passed to match= contains metacharacters.
• 7270ff5 Fix mypy errors.
• b5480c7 Fix tests.
• afb2867 Fix lint.
• 4adb224 Fix: indexing error in Procar._read() (#4502)
• 19ede6d Replace print with logging (#4503)
• b2e5f1a suppress runtime warning from boltztrap2 (#4510)
• Additional commits viewable in compare view

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