Pymatgen

* Misc bug fixes.
* Enable Structure relaxations with TrajectoryObserver (janosh)
* Breaking: Rename `gen_sl_transform_matrices->gen_sl_transform_matrices` (2894)

* PR 2882 substrate-optimizations for speed up (mkhorton)
* Fix very fragile POTCAR parsing.

* 69a548e210 revert adding ubuntu-latest to release job matrix
* e63cab3620 add 3.11 to release job python-versions
* c03dacb94d use `cibuildwheel` to build linux wheels (2800)
* fe2597d92e Merge setup.cfg into pyproject.toml (2858)
* 40cbf1d7c4 del class AtomicFile, \_maketemp(), ask_yesno() from pymatgen/util/io_utils.py (2860)
* 0b16987f2c fix reduced formula in Ion (2864)

* 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Currently `OptimadeRester` defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means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>.

* 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.

* 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