Bump pymatgen from 2020.11.11 to 2024.2.20

[dependabot[bot]]

Bumps pymatgen from 2020.11.11 to 2024.2.20.

Release notes

Sourced from pymatgen's releases.

v2024.2.20

What's Changed

This release addresses an important security issue that might affect some users of pymatgen who are parsing untrusted user input, for example a server using pymatgen to parse a user-uploaded CIF file. More information is available in the associated CVE. Thank you to William Khem-Marquez (@​SteakEnthusiast) for the discovery and responsible disclosure of this issue.

🐛 Bug Fixes

• Revert back TransformedStructure.__getattr__ by @​mjwen in materialsproject/pymatgen#3617
• Fixed Incar object to allow for ML_MODE vasp tag by @​davidwaroquiers in materialsproject/pymatgen#3625
• Add missing MPSCANRelaxSet.yaml parameters and alphabetize by @​Andrew-S-Rosen in materialsproject/pymatgen#3615
• Fix bader_analysis_from_path using warning as file path and reinstate test by @​janosh in materialsproject/pymatgen#3632

🛠 Enhancements

• Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates by @​jinlhr542 in materialsproject/pymatgen#3572
• Handle invalid selective dynamics info in POSCAR by @​DanielYang59 in materialsproject/pymatgen#3539
• Return self from all SiteCollection/Structure/Molecule in-place modification methods by @​janosh in materialsproject/pymatgen#3623
• Make the POTCAR setup instructions clearer by @​Andrew-S-Rosen in materialsproject/pymatgen#3630

🧹 House-Keeping

• Refactors + types + fix doc string returns to use Google format by @​janosh in materialsproject/pymatgen#3620

🚀 Performance

• Speeding up get_nn_info in local_env.py by @​ftherrien in materialsproject/pymatgen#3635

💥 Breaking Changes

• Lobsterenv improvements by @​naik-aakash in materialsproject/pymatgen#3624

🤷‍♂️ Other Changes

• Fix URL joining in OptimadeRester by @​rdamaral in materialsproject/pymatgen#3613
• Create a CODEOWNERS by @​Andrew-S-Rosen in materialsproject/pymatgen#3616
• Adds support for an MSONAtoms class that's an MSONable form of an ASE Atoms object by @​Andrew-S-Rosen in materialsproject/pymatgen#3619
• Lobster io improvements by @​naik-aakash in materialsproject/pymatgen#3627

New Contributors

• @​jinlhr542 made their first contribution in materialsproject/pymatgen#3572
• @​rdamaral made their first contribution in materialsproject/pymatgen#3613
• @​ftherrien made their first contribution in materialsproject/pymatgen#3635

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.2.8...v2024.2.20

v2024.2.8

What's Changed

🐛 Bug Fixes

• Fix Vasprun.get_potcars search method; tweak fake POTCARs by @​esoteric-ephemera in materialsproject/pymatgen#3587

🛠 Enhancements

• Aims input sets by @​tpurcell90 in materialsproject/pymatgen#3482
• Add SiteCollection.reduced_formula property by @​janosh in materialsproject/pymatgen#3610

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.2.20

This release addresses an important security issue that might affect some users of pymatgen who are parsing untrusted user input, for example a server using pymatgen to parse a user-uploaded CIF file. More information is available in the associated CVE. Thank you to William Khem-Marquez (@​SteakEnthusiast) for the discovery and responsible disclosure of this issue.

🐛 Bug Fixes

• Revert back TransformedStructure.__getattr__ by @​mjwen in materialsproject/pymatgen#3617
• Fixed Incar object to allow for ML_MODE vasp tag by @​davidwaroquiers in materialsproject/pymatgen#3625
• Add missing MPSCANRelaxSet.yaml parameters and alphabetize by @​Andrew-S-Rosen in materialsproject/pymatgen#3615
• Fix bader_analysis_from_path using warning as file path and reinstate test by @​janosh in materialsproject/pymatgen#3632

🛠 Enhancements

• Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates by @​jinlhr542 in materialsproject/pymatgen#3572
• Handle invalid selective dynamics info in POSCAR by @​DanielYang59 in materialsproject/pymatgen#3539
• Return self from all SiteCollection/Structure/Molecule in-place modification methods by @​janosh in materialsproject/pymatgen#3623
• Make the POTCAR setup instructions clearer by @​Andrew-S-Rosen in materialsproject/pymatgen#3630

🧹 House-Keeping

• Refactors + types + fix doc string returns to use Google format by @​janosh in materialsproject/pymatgen#3620

🚀 Performance

• Speeding up get_nn_info in local_env.py by @​ftherrien in materialsproject/pymatgen#3635

💥 Breaking Changes

• Lobsterenv improvements by @​naik-aakash in materialsproject/pymatgen#3624

🤷‍♂️ Other Changes

• Fix URL joining in OptimadeRester by @​rdamaral in materialsproject/pymatgen#3613
• Create a CODEOWNERS by @​Andrew-S-Rosen in materialsproject/pymatgen#3616
• Adds support for an MSONAtoms class that's an MSONable form of an ASE Atoms object by @​Andrew-S-Rosen in materialsproject/pymatgen#3619
• Lobster io improvements by @​naik-aakash in materialsproject/pymatgen#3627

New Contributors

• @​jinlhr542 made their first contribution in materialsproject/pymatgen#3572
• @​rdamaral made their first contribution in materialsproject/pymatgen#3613
• @​ftherrien made their first contribution in materialsproject/pymatgen#3635

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.2.8...v2024.2.20

v2024.2.8

🐛 Bug Fixes

• Fix Vasprun.get_potcars search method; tweak fake POTCARs by @​esoteric-ephemera in materialsproject/pymatgen#3587

🛠 Enhancements

• Aims input sets by @​tpurcell90 in materialsproject/pymatgen#3482
• Add SiteCollection.reduced_formula property by @​janosh in materialsproject/pymatgen#3610
• Add Entry.(formula|reduced_formula) by @​janosh in materialsproject/pymatgen#3611
• VASP IO copy() methods by @​janosh in materialsproject/pymatgen#3602

... (truncated)

Commits

• 013ccb5 v2024.2.20
• bde66a4 v2024.2.20
• 38b9b58 Speeding up get_nn_info in local_env.py (#3635)
• bd88e0d [WIP] Lobsterenv improvements (#3624)
• ff45527 Fix bader_analysis_from_path using warning as file path and reinstate test ...
• 5514ff5 Make the POTCAR setup instructions clearer (#3630)
• 170c701 Add missing MPSCANRelaxSet.yaml parameters and alphabetize (#3615)
• d44363e Fixed Incar object to allow for ML_MODE vasp tag (#3625)
• 988da0c Fix NotImplementedError messages in InputSet subclasses
• 0f474f6 Lobster io improvements (#3627)
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) You can disable automated security fix PRs for this repo from the Security Alerts page.