Bump pymatgen from 2019.7.30 to 2021.2.13

[dependabot[bot]]

Bumps pymatgen from 2019.7.30 to 2021.2.13.

Release notes

Sourced from pymatgen's releases.

v2021.2.13

• Misc bug fixes.

v2021.2.12

• Misc bug fixes.

v2021.2.8

• Addition of new job types to Q-Chem IO (@​espottesmith, #2055), note metal_edge_extender has been moved into local_env for this change
• Improvements to string utils, new Stringify mixin with to_pretty_string(), to_latex_string(), to_unicode_string(), to_html_string() (@​shyuep)
• Improvements to build system (@​shyuep, @​ltalirz, see #2046)
• Entry is now immutable, removing "in_place" option for normalize (@​mkhorton, @​mattmcdermott, #2060)
• Bug fix for co-ordination geometry finder (@​davidwaroquiers, #2035)
• Bug fix for GibbsComputedStructureEntry (@​mattmcdermott)

v2021.1.28

• Ability to read Lobster wavefunctions (@​JaGeo, #2034)
• Method to estimate number of bands for VASP calculation (@​rwoodsrobinson, #2044)
• Q-Chem cube file plotting and improvements to output parsring (@​samblau, #2032)
• Improvements to PhaseDiagram hashing and equality checking (@​CompRhys, #2014)
• Improvements to pymatgen import speed (@​mkhorton, #2031)
• Bug fix for k-path generation (@​munrojm, #2037)
• Bug fix for parsing of core potentials from VASP (@​utf, #2033)

v2020.12.31

• End of 2020 release with minor bug fixes for cli scripts.

v2020.12.18

• New IsayevNN nearest-neighbor algorithm (@​utf, #2011)
• Improvements to electrode objects (@​jmmshn, #2016)
• Improvements to Element and PhaseDiagram (@​jmmshn, #2005)
• Bug fix to increase minimum version of setuptools which was causing incompatible versions of numpy to be installed for some users (@​shyuep, see issue #2010)
• Bug fix to VASP run type detection (@​rkingsbury, #2007)

v2020.12.3

• Site insertion algorithm based on charge density (@​jmmshn, #1997)
• Allow calculation of Fermi level from occupancies in VASP calculation (@​rkingsbury, #2000)
• Improvement to legibility of 3D phase diagram plots (@​bayesfactor, #1999)
• Improvement to allow general input for exciting (@​vorwerkc, #1975)
• Improvements to code formatting (@​mkhorton, #2008)
• Bug fix for VASP run type detection (@​rkingsbury, #1996)

v2020.11.11

• Bug fix for PhononBandStructureSymmLine. (@​gpetretto)
• Improved robustness in ABINIT input generation. (@​gpetretto)
• Other minor bug fixes.

v2020.10.20

1. Cp2K support (@​nwinner)

... (truncated)

Changelog

Sourced from pymatgen's changelog.

Change log

v2023.2.22

• PR #2848 from @​ml-evs ml-evs/update_optimade_aliases Currently OptimadeRester defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means they will not be used if the user provides their own filtered list of aliases, without doing some extra work. This PR refreshes the vendored list of aliases (which should be much more stable now since their initial addition 2 years ago), and also adds the option to refresh the aliases on initialization of the class. This currently affects the pymatgen OPTIMADE tutorials at https://github.com/Materials-Consortia/optimade-tutorial-exercises.

v2023.1.30

• PR #2806 from @​samblau qchem
  • Major changes to Q-Chem IO (inputs.py and outputs.py) to accommodate differences and new features in version 6+
  • Additional parsing capabilities for HOMO/LUMO, dipoles, NBO info (hyperbonds and 3C bonds) in outputs.py
  • Utility for processing a parsed binary Hessian scratch file
  • Overdue updates to default values in sets.py and new defaults associated with differences and new features in Q-Chem 6+
• PR #2814 from @​jmmshn patch_dos

  Added Convenience to obtain the normalized CompleteDos object

  Added tests to make sure calling it multiple time still only gives one result.

v2023.1.20

• Passthrough kwargs support for Structure.from_file and Structure.from_str
• Allow the frac_tolerance to be specified for rounding coordinates in CifParser.
• PR #2803 from @​amkrajewski add_weightbasedfunctions When working with metallic alloys, weight-fraction-based notations such as Ti64 / Ti-6V-4Al or NiTiNOL60 / Ni-40Ti are commonly employed in both industrial specifications and scientific literature. Regardless of the numerous downsides of this situation, including errors in scientific experiments or NLP-parsing when they are mistaken for atomic fractions or chemical formulas, being able to create a Composition object from them (under correct interpretation) would be a useful pymatgen feature.
  • Composition class method to initialize it from a dictionary of weight fractions
  • Composition property giving a dictionary of weight fractions
  • concise tests for the two above were added QChem: translate DMSO name in smd_solvent

v2023.1.9

• PR #2792 from @​JaGeo bug_fix
• PR #2773 from @​ab5424 cbar
• PR #2776 from @​MichaelWolloch master
• PR #2762 from @​MichaelWolloch master
• PR #2774 from @​dgaines2 fix-poscar
• PR #2667 from @​nwinner volumetric-data-patch
• PR #2764 from @​naik-aakash lobster_lsodos
• PR #2215 from @​rkingsbury cmirs
• PR #2742 from @​materialsproject pip-dependabot
• PR #2741 from @​materialsproject resurrect-req-txt
• PR #2735 from @​njzjz patch-1

v2022.11.7

• PR #2724 from @​janosh: raise ValueError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries
• PR #2720 by @​utf: Fix tensor mapping

... (truncated)

Commits

• 60fe733 Update docs
• 250f620 Remove discourse posting
• 1a99a19 Update docs
• d71e117 Seriously annoyed at the workflow version.
• a339275 Update docs
• 480f9c7 Fix deprecated tests.
• 6b09c4a Fix missing req.
• 2d31697 Abandon py39 testing for now.
• 11e4d08 Remove irritating netCDF4 requirement that prevents py39 support.
• 17f0252 Remove py36 test and support. Add py39.
• Additional commits viewable in compare view

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