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Bump pymatgen from 2024.9.17.1 to 2024.11.13 #1191

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@dependabot dependabot bot commented on behalf of github Nov 18, 2024

Bumps pymatgen from 2024.9.17.1 to 2024.11.13.

Release notes

Sourced from pymatgen's releases.

v2024.11.13

  • CP2K fixes (@​janosh)
  • Fix borg.hive.SimpleVaspToComputedEntryDrone.assimilate ValueError when core file missing (@​DanielYang59)
  • Revert breaking analysis.local_env default_op_params/cn_opt_params rename (@​DanielYang59)
  • Added new Flag for AutoOxiStateDecorationTransformation (@​jmmshn)
  • Fixed execution of packmol in relative path. (@​davidwaroquiers)
  • Improve element mismatch handling with POTCAR for Poscar.from_file/str (@​DanielYang59)
  • Preprocess Structure Reduction Before Bulk Match (@​lan496)
  • Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop (@​DanielYang59)

v2024.10.29

  • VaspDir has been renamed and moved to pymatgen.io.common.PMGDir for more general support of all IO classes. Note that this is a backwards incompatible change. It should not affect many users since VaspDir was introduced only in the last one week.
  • Fixed execution of packmol in relative path. (@​davidwaroquiers)
  • VaspDoc.get_incar_tags: Use Mediawiki API (@​yantar92)
  • Fix comment pass in Kpoints constructors (@​DanielYang59)

v2024.10.27

  • Bug fix for parsing of dielectric calculations from vasprun.xml.

v2024.10.25

  • VaspDir now supports nest directories. Also, supports non-object string returns.
  • Bug fix for parsing of BSE vaspruns.xml.

v2024.10.22

  • New pyamtgen.io.vasp.VaspDir class for easy navigation of VASP directories as pymatgen objects.
  • Fix gaussian input parser (@​sio-salt)
  • Fix: preserve site properties over cell transform (@​Lattay)
  • Make Incar keys case insensitive, fix init Incar from dict val processing for str/float/int (@​DanielYang59)
  • Fix: Preserve PBC info in AseAtomsAdaptor (@​jsukpark)
  • Migrate ext.COD from mysql to REST API (@​DanielYang59)
  • Fix: Parsing bugs in io.pwscf.PWInput (@​jsukpark)
  • Fix arg passing in inverse property of SymmOp (@​DanielYang59)
  • Add support for use_structure_charge keyword in FHI-aims input generator (@​ansobolev)
  • Fix: savefig in pmg.cli.plot (@​DanielYang59)
  • Fix: Volumetric data and XDATCAR parsing for monatomic structures (@​esoteric-ephemera)
  • Support to aims format from Structure instance (@​ansobolev)
  • Fix: Bugfix for Ion CO2(aq) reduced formula (@​rkingsbury)
  • Replace deprecated ExpCellFilter with FrechetCellFilter (@​ab5424)

v2024.10.3

Changelog

Sourced from pymatgen's changelog.

2024.11.13

  • CP2K fixes (@​janosh)
  • Fix borg.hive.SimpleVaspToComputedEntryDrone.assimilate ValueError when core file missing (@​DanielYang59)
  • Revert breaking analysis.local_env default_op_params/cn_opt_params rename (@​DanielYang59)
  • Added new Flag for AutoOxiStateDecorationTransformation (@​jmmshn)
  • Fixed execution of packmol in relative path. (@​davidwaroquiers)
  • Improve element mismatch handling with POTCAR for Poscar.from_file/str (@​DanielYang59)
  • Preprocess Structure Reduction Before Bulk Match (@​lan496)
  • Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop (@​DanielYang59)

2024.10.29

  • VaspDir has been renamed and moved to pymatgen.io.common.PMGDir for more general support of all IO classes. Note that this is a backwards incompatible change. It should not affect many users since VaspDir was introduced only in the last one week.
  • Fixed execution of packmol in relative path. (@​davidwaroquiers)
  • VaspDoc.get_incar_tags: Use Mediawiki API (@​yantar92)
  • Fix comment pass in Kpoints constructors (@​DanielYang59)

v2024.10.27

  • Bug fix for parsing of dielectric calculations from vasprun.xml.

v2024.10.25

  • VaspDir now supports nested directories. Also, supports returning strings where a parser is not defined.
  • Bug fix for parsing of BSE vaspruns.xml.

v2024.10.21

  • New pyamtgen.io.vasp.VaspDir class for easy navigation of VASP directories as pymatgen objects.
  • Fix gaussian input parser (@​sio-salt)
  • Fix: preserve site properties over cell transform (@​Lattay)
  • Make Incar keys case insensitive, fix init Incar from dict val processing for str/float/int (@​DanielYang59)
  • Fix: Preserve PBC info in AseAtomsAdaptor (@​jsukpark)
  • Migrate ext.COD from mysql to REST API (@​DanielYang59)
  • Fix: Parsing bugs in io.pwscf.PWInput (@​jsukpark)
  • Fix arg passing in inverse property of SymmOp (@​DanielYang59)
  • Add support for use_structure_charge keyword in FHI-aims input generator (@​ansobolev)
  • Fix: savefig in pmg.cli.plot (@​DanielYang59)
  • Fix: Volumetric data and XDATCAR parsing for monatomic structures (@​esoteric-ephemera)
  • Support to aims format from Structure instance (@​ansobolev)
  • Fix: Bugfix for Ion CO2(aq) reduced formula (@​rkingsbury)
  • Replace deprecated ExpCellFilter with FrechetCellFilter (@​ab5424)

v2024.10.3

Commits
  • aab23ff Update docs
  • 910e037 Merge branch 'master' of github.com:materialsproject/pymatgen
  • 05fcb53 Update changelog.
  • 5049409 Revert breaking analysis.local_env default_op_params/cn_opt_params rename...
  • 08dc6eb is_subgroup() modifications in SpaceGroup and PointGroup (#3941)
  • 704c9c9 Use binary distribution (wheels) to install pymatgen in test suite (#4073)
  • 179cdeb bump monty to use the monty.json import speedup patch, add import time re...
  • 65f52ea Add min "thickness" check in CifParser to filter invalid structure which le...
  • 40100e9 Improve element mismatch handling with POTCAR for Poscar.from_file/str (#4143)
  • cc63b81 Replace hard-coded np.allclose/isclose and math.isclose (for complex expr...
  • Additional commits viewable in compare view

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@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Nov 18, 2024
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Binder 👈 Launch a binder notebook on branch pyiron/pyiron_contrib/dependabot/pip/pymatgen-2024.11.13

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pmrv commented Jan 6, 2025

https://github.com/dependabot recreate

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.9.17.1 to 2024.11.13.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](materialsproject/pymatgen@v2024.9.17.1...v2024.11.13)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot force-pushed the dependabot/pip/pymatgen-2024.11.13 branch from 34103f7 to 885763a Compare January 6, 2025 12:55
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codacy-production bot commented Jan 6, 2025

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation Diff coverage
+0.00% (target: -1.00%)
Coverage variation details
Coverable lines Covered lines Coverage
Common ancestor commit (4e31537) 10200 1280 12.55%
Head commit (33cf97d) 10200 (+0) 1280 (+0) 12.55% (+0.00%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details
Coverable lines Covered lines Diff coverage
Pull request (#1191) 0 0 ∅ (not applicable)

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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github-actions bot commented Jan 6, 2025

Pull Request Test Coverage Report for Build 12632900181

Details

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage remained the same at 12.549%

Totals Coverage Status
Change from base Build 12632421988: 0.0%
Covered Lines: 1280
Relevant Lines: 10200

💛 - Coveralls

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