Bump pymatgen from 2024.8.9 to 2024.10.29

dependabot[bot] commented 3 weeks ago

Bumps pymatgen from 2024.8.9 to 2024.10.29.

Release notes

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

Enable parsing of "SCF energy" and "Total energy" from QCOutput for Q-chem 6.1.1+. (@Jaebeom-P)

Fix dict equality check with numpy array (@DanielYang59)

Fix usage of strict=True for zip in cp2k.outputs (@DanielYang59)

Fix bug with species defaults (@tpurcell90)

SLME Bug Fixes (@kavanase)

v2024.9.17.1

Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @yang-ruoxi for fixing.)

v2024.9.17

Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @yang-ruoxi for fixing.)

v2024.9.10

💥 Breaking: NumPy/Cython integer type changed from np.long/np.int_ to int64 on Windows to align with NumPy 2.x, changing the default integer type to int64 on Windows 64-bit systems in favor of the platform-dependent np.int_ type. Recommendation: Please explicitly declare dtype=np.int64 when initializing a NumPy array if it's passed to a Cythonized pymatgen function like find_points_in_spheres. You may also want to test downstream packages with NumPy 1.x on Windows in CI pipelines.

🛠 Enhancements

... (truncated)

Changelog

Sourced from pymatgen's changelog.

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

Enable parsing of "SCF energy" and "Total energy" from QCOutput for Q-chem 6.1.1+. (@Jaebeom-P)

Fix dict equality check with numpy array (@DanielYang59)

Fix usage of strict=True for zip in cp2k.outputs (@DanielYang59)

Fix bug with species defaults (@tpurcell90)

SLME Bug Fixes (@kavanase)

v2024.9.17.1

Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @yang-ruoxi for fixing.)

v2024.9.17

Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @yang-ruoxi for fixing.)

v2024.9.10

💥 Breaking: NumPy/Cython integer type changed from np.long/np.int_ to int64 on Windows to align with NumPy 2.x, changing the default integer type to int64 on Windows 64-bit systems in favor of the platform-dependent np.int_ type.

... (truncated)

Commits

5404615 Update docs
5dd8c74 Update changelog.
7719515 VaspDoc.get_incar_tags: Use Mediawiki API (#4141)
91a5b65 Fixed execution of packmol in relative path. (#4145)
c600ffc Bump rexml from 3.3.6 to 3.3.9 in /docs (#4147)
a3dfc8e Update changelog.
6311a81 Merge branch 'master' of github.com:materialsproject/pymatgen
89969ba Rename VaspDir to PMGDir and move it to pymatgen.io.common since it is
e85d73b Silly me, just use relative_to in pathlib.
22b6a7f Fix VaspDir.files.
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github-actions[bot] commented 3 weeks ago

:point_left: Launch a binder notebook on branch _pyiron/pyironnodes/dependabot/pip/pymatgen-2024.10.29

codacy-production[bot] commented 3 weeks ago

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
:white_check_mark: +0.00% (target: -1.00%)	:white_check_mark: ∅

Coverage variation details

| | Coverable lines | Covered lines | Coverage | | ------------- | ------------- | ------------- | ------------- | | Common ancestor commit (bb4a4c8cc4a57c2c028a591131e76c0d19fa3956) | 2187 | 654 | 29.90% | | | Head commit (6e0be8f7fa63d093e24c77b341fd33ca695e4bad) | 2187 (+0) | 654 (+0) | 29.90% (**+0.00%**) | **Coverage variation** is the difference between the coverage for the head and common ancestor commits of the pull request branch: ` - `

Diff coverage details

| | Coverable lines | Covered lines | Diff coverage | | ------------- | ------------- | ------------- | ------------- | | Pull request (#103) | 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: `/ * 100%`

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_{Codacy stopped sending the deprecated coverage status on June 5th, 2024. Learn more}

coveralls commented 3 weeks ago

Pull Request Test Coverage Report for Build 11668170959

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 29.904%

Totals
Change from base Build 11427646139:	0.0%
Covered Lines:	654
Relevant Lines:	2187

💛 - Coveralls

dependabot[bot] commented 1 week ago

Superseded by #107.

pyiron / pyiron_nodes