Pymatgen

* Use joblib to speed up expensive enumeration energy computations.
* Minor cleanups.

* Use lru_cache to speed up get_el_sp by 400x (v1kko).
* Related to lru_cache of get_el_sp, Species.properties is now deprecated in favor of setting Species(spin=5). The rationale is
that spin is the only supported property for Species anyway. Species and DummySpecies is now mostly immutable, i.e., setting specie.spin = 5 have no effect. This is as intended since the first version of pymatgen.
* PR 3111 from xjf729 fix-MoleculeGraph-draw_graph
* PR 3030 from lbluque Remove superfluous structure argument docstring from `SQSTransformation` init
* PR 3031 from kavanase Quick fix to allow direct initialisation of the `DictSet` class.
* PR 3015 from lbluque Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.

* PR 3062 from Andrew-S-Rosen asefix
Closes 3061. JaGeo
* PR 3030 from lbluque master
Remove superfluous structure argument docstring from `SQSTransformation` init
* PR 3031 from kavanase master
This is a quick fix to allow direct initialisation of the `DictSet` class, which was possible before but broke in <https://github.com/materialsproject/pymatgen/pull/2972> due to the `Yb_2` check querying `self.CONFIG`, which is only defined if `DictSet` was being initialised from a subclass and not directly.
* PR 3015 from lbluque neighbors
Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.

* Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" [3022](https://github.com/materialsproject/pymatgen/pull/3022)
* Unignore ruff PD011 [3020](https://github.com/materialsproject/pymatgen/pull/3020)
* Tweak variable names [3019](https://github.com/materialsproject/pymatgen/pull/3019)
* MaterialsProjectCompatibility issue silencable deprecation warning [3017](https://github.com/materialsproject/pymatgen/pull/3017)
* Optimize cython find_points_in \_spheres [3015](https://github.com/materialsproject/pymatgen/pull/3015)
* Cp2k 2.0 [2672](https://github.com/materialsproject/pymatgen/pull/2672)
* Added methods to compute and compare DOS fingerprints [2772](https://github.com/materialsproject/pymatgen/pull/2772)
* Breaking: Overhaul class PymatgenTest [3014](https://github.com/materialsproject/pymatgen/pull/3014)
* Fix ValueError when structure.selective_dynamics has type np.array [3012](https://github.com/materialsproject/pymatgen/pull/3012)
* Clean up [3010](https://github.com/materialsproject/pymatgen/pull/3010)
* Update .pytest-split-durations [3005](https://github.com/materialsproject/pymatgen/pull/3005)
* Lookup MPRester API key in settings if None provided as arg [3004](https://github.com/materialsproject/pymatgen/pull/3004)
* Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) [3003](https://github.com/materialsproject/pymatgen/pull/3003)
* Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None [3002](https://github.com/materialsproject/pymatgen/pull/3002)
* Species parse oxi state from symbol str [2998](https://github.com/materialsproject/pymatgen/pull/2998)
* Re-export SiteCollection + DummySpecies from pymatgen.core [2995](https://github.com/materialsproject/pymatgen/pull/2995)
* Orbital-resolved icohplist [2993](https://github.com/materialsproject/pymatgen/pull/2993)
* Hide all type-hint-only imports behind if TYPE_CHECKING [2992](https://github.com/materialsproject/pymatgen/pull/2992)
* Add type hints for pymatgen.io.ase module [2991](https://github.com/materialsproject/pymatgen/pull/2991)
* Enable ruff doc rules in CI [2990](https://github.com/materialsproject/pymatgen/pull/2990)
* Suspected Typo Fix in pymatgen.io.vasp.optics [2989](https://github.com/materialsproject/pymatgen/pull/2989)
* Doc strings [2987](https://github.com/materialsproject/pymatgen/pull/2987)
* Fix average error [2986](https://github.com/materialsproject/pymatgen/pull/2986)
* Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports [2981](https://github.com/materialsproject/pymatgen/pull/2981)
* Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (3022) [3022](https://github.com/materialsproject/pymatgen/pull/3022)
* fix unwanted x margins in get_elt_projected_plots_color (closes 562) [562](https://github.com/materialsproject/pymatgen/issues/562)
* Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (3002) [2756](https://github.com/materialsproject/pymatgen/issues/2756)
* add doc str explaining need for class ElementBase (closes 2999) [2999](https://github.com/materialsproject/pymatgen/issues/2999)
* Update docs. `3e3c31c <https://github.com/materialsproject/pymatgen/commit/3e3c31c8d342c84f2c6bbb961c321e458b9accb9>`\_
* ruff set isort.split-on-trailing-comma = false `c0ec534 <https://github.com/materialsproject/pymatgen/commit/c0ec53452c3dc87c6cca5edc1c6b2b6218f15569>`\_

* Fix mem leak in pbc_shortest_vector cython code. (stichri)
* Set all cython code to language level 3.

❗ The Yb_2 deprecation release ❗

This release changes the Ytterbium (Yb) pseudo-potential (PSP) from Yb_2 to Yb_3 for all PBE_54 VASP input sets.

Background: The `A-lab <https://newscenter.lbl.gov/2023/04/17/meet-the-autonomous-lab-of-the-future>` revealed that as a result of using Yb_2 the energy on Yb compounds is off by a lot, resulting in supposedly stable things being unsynthesizable. While an unfortunate mistake, it's also great to see how experiment can help surface simulation errors.

On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results for most systems since Yb is most often in oxidation state Yb3+.

Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds.

For more details see [2968](https://github.com/materialsproject/pymatgen/pull/2968)and [#2969](https://github.com/materialsproject/pymatgen/pull/2969).

What's Changed

* Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by janosh in [2907](https://github.com/materialsproject/pymatgen/pull/2907)
* Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by janosh in [2908](https://github.com/materialsproject/pymatgen/pull/2908)
* Fix VolumetricData.to_cube() not preserving structure dimensions by janosh in [2909](https://github.com/materialsproject/pymatgen/pull/2909)
* Update team.rst by jmmshn in [2912](https://github.com/materialsproject/pymatgen/pull/2912)
* Faff by janosh in [2915](https://github.com/materialsproject/pymatgen/pull/2915)
* Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by kavanase in [2916](https://github.com/materialsproject/pymatgen/pull/2916)
* Modified dosplotter by kaueltzen in [2844](https://github.com/materialsproject/pymatgen/pull/2844)
* auto version by jmmshn in [2925](https://github.com/materialsproject/pymatgen/pull/2925)
* bug fix for potcar parsing by jmmshn in [2910](https://github.com/materialsproject/pymatgen/pull/2910)
* Fix breaking changes from pandas v2 by janosh in [2935](https://github.com/materialsproject/pymatgen/pull/2935)
* add kwarg to MoleculeGraph method and fix PackmolSet bug by orionarcher in [2927](https://github.com/materialsproject/pymatgen/pull/2927)
* fix on reading multiple route in Gaussian input file by Ameyanagi in [2939](https://github.com/materialsproject/pymatgen/pull/2939)
* Fix CI errors by janosh in [2940](https://github.com/materialsproject/pymatgen/pull/2940)
* Add ResParser support for reading files with spin values by ScottNotFound in [2941](https://github.com/materialsproject/pymatgen/pull/2941)
* Ignore bad unicode characters in Structure.from_file() by janosh in [2948](https://github.com/materialsproject/pymatgen/pull/2948)
* Minor modification for symmetrically distinct Miller index generation by fyalcin in [2949](https://github.com/materialsproject/pymatgen/pull/2949)
* Fixed Wulff shape for new versions of matplotlib by CifLord in [2950](https://github.com/materialsproject/pymatgen/pull/2950)
* Test figure returned by WulffShape.get_plot() contains single Axes3D by janosh in [2953](https://github.com/materialsproject/pymatgen/pull/2953)
* Fix Cp2kOutput.spin_polarized() likely not doing what author intended by janosh in [2954](https://github.com/materialsproject/pymatgen/pull/2954)
* For MPcules: Molecule Trajectory and graph hashes by espottesmith in [2945](https://github.com/materialsproject/pymatgen/pull/2945)
* self.assertArrayEqual->assert by janosh in [2955](https://github.com/materialsproject/pymatgen/pull/2955)
* fix GaussianOutput bug with multiple route lines by xjf729 in [2937](https://github.com/materialsproject/pymatgen/pull/2937)
* Fix ValueError when passing selective_dynamics to Poscar by chiang-yuan in [2951](https://github.com/materialsproject/pymatgen/pull/2951)
* Link /addons from new subsection on /contributing page by janosh in [2967](https://github.com/materialsproject/pymatgen/pull/2967)
* Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by janosh in [2969](https://github.com/materialsproject/pymatgen/pull/2969)
* fix recursion error by adding copy and deepcopy dunder methods by orionarcher in [2973](https://github.com/materialsproject/pymatgen/pull/2973)
* Revert to Yb_2 on pre-PBE_54 input sets by janosh in [2972](https://github.com/materialsproject/pymatgen/pull/2972)