Bump pymatgen from 2025.6.14 to 2025.10.7

[dependabot]

Bumps pymatgen from 2025.6.14 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)

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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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.78%. Comparing base (1d8136f) to head (fb0537f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #415   +/-   ##
=======================================
  Coverage   82.78%   82.78%           
=======================================
  Files          24       24           
  Lines        1807     1807           
=======================================
  Hits         1496     1496           
  Misses        311      311           

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