Bump pymatgen from 2025.4.24 to 2025.6.14

[dependabot]

Bumps pymatgen from 2025.4.24 to 2025.6.14.

Release notes

Sourced from pymatgen's releases.

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

  Summary

  • Fix branch directory check in io.vasp.outputs.get_band_structure_from_vasp_multiple_branches, to fix #4060
  • Improve unit test (waiting for data, I don't have experience with "VASP multi-branch bandstructure calculation")
• PR #4409 Packmol constraints by @​davidwaroquiers Added possibility to set individual constraints in packmol. Added some sanity checks. Added unit tests.
• PR #4428 Fixes a bug in NanoscaleStability.plot_one_stability_map and plot_all_stability_map. by @​kmu Major changes:
  • Replaced incorrect ax.xlabel() and ax.ylabel() calls with correct ax.set_xlabel() and ax.set_ylabel().
  • Added ax.legend() to plot_all_stability_map so that labels passed via ax.plot(..., label=...) are displayed.
  • Added test_plot() to test_surface_analysis.py.
• PR #4424 Add additional name mappings for new LDA v64 potcars by @​mkhorton As title.
• PR #4426 Fix uncertainty as int for EnergyAdjustment by @​DanielYang59
  • Avoid == or != for possible float comparison
  • Fix uncertainty as int for EnergyAdjustment cannot generate repr:

  from pymatgen.entries.computed_entries import EnergyAdjustment
  print(EnergyAdjustment(10, uncertainty=0))

  Gives:

  Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/test_json.py", line 25, in <module>
  print(EnergyAdjustment(10, uncertainty=0))
  File "/Users/yang/developer/pymatgen/src/pymatgen/entries/computed_entries.py", line 108, in __repr__
  return f"{type(self).__name__}({name=}, {value=:.3}, {uncertainty=:.3}, {description=}, {generated_by=})"
  ^^^^^^^^^^^^^^^^^
  ValueError: Precision not allowed in integer format specifier
  

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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

  Summary

  • Fix branch directory check in io.vasp.outputs.get_band_structure_from_vasp_multiple_branches, to fix #4060
  • Improve unit test (waiting for data, I don't have experience with "VASP multi-branch bandstructure calculation")
• PR #4409 Packmol constraints by @​davidwaroquiers Added possibility to set individual constraints in packmol. Added some sanity checks. Added unit tests.
• PR #4428 Fixes a bug in NanoscaleStability.plot_one_stability_map and plot_all_stability_map. by @​kmu Major changes:
  • Replaced incorrect ax.xlabel() and ax.ylabel() calls with correct ax.set_xlabel() and ax.set_ylabel().
  • Added ax.legend() to plot_all_stability_map so that labels passed via ax.plot(..., label=...) are displayed.
  • Added test_plot() to test_surface_analysis.py.
• PR #4424 Add additional name mappings for new LDA v64 potcars by @​mkhorton As title.
• PR #4426 Fix uncertainty as int for EnergyAdjustment by @​DanielYang59
  • Avoid == or != for possible float comparison
  • Fix uncertainty as int for EnergyAdjustment cannot generate repr:

  from pymatgen.entries.computed_entries import EnergyAdjustment
  print(EnergyAdjustment(10, uncertainty=0))

  Gives:

  Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/test_json.py", line 25, in <module>
  print(EnergyAdjustment(10, uncertainty=0))
  File "/Users/yang/developer/pymatgen/src/pymatgen/entries/computed_entries.py", line 108, in __repr__
  return f"{type(self).__name__}({name=}, {value=:.3}, {uncertainty=:.3}, {description=}, {generated_by=})"
  ^^^^^^^^^^^^^^^^^
  ValueError: Precision not allowed in integer format specifier
  

... (truncated)

Commits

• 682bfd8 Update docs
• da30857 Update changelog.
• 02bed16 Merge branch 'master' of github.com:materialsproject/pymatgen
• 3de47f3 Treat LATTICE_CONSTRAINTS as a as-is tag for now. Fixes #4325.
• 234d115 JDFTXOutfileSlice.trajectory revision (#4425)
• 2b3510a Bump requests from 2.32.3 to 2.32.4 (#4434)
• 98bdb66 Single source of truth for POTCAR directory structure (#4431)
• 5a4046b Speed up symmetry functions with faster is_periodic_image algorithm (#4433)
• ec1b63b Fingerprint sources (#4432)
• aa08052 Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_m...
• Additional commits viewable in compare view

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Superseded by #566.