Nexus: Add PseudoSet class to improve pseudopotential handling for users.

[brockdyer03]

Proposed changes

This PR adds a class called PseudoSet to Nexus that will eventually replace the existing ppset class.

PseudoSet offers a more flexible and intuitive API for users that offers several advantages over the current ppset. Some notable advantages are:

• Ability to keep pseudopotentials in separate directories (no need to set pseudo_dir in settings).
• Ability to automatically read a set of pseudopotentials for a single code in a directory with PseudoSet.from_dir().
• Ability to automatically read a directory with pseudopotentials for multiple codes with PseudoSet.from_mixed_dir().
• Ability to automatically parse Z-valences from files with PseudoSet.get_Zeffs().
• Improved error messages, including, among other things, warnings for non-existent files and descriptive errors for duplicate pseudos for the same element.
• Support for gradual deprecation of ppset with PseudoSet._register_legacy_ppset().

Example usage

I've included some examples here so you don't need to pore through the code to see how the functions work.

The examples here assume the following contents of pseudo_dir

/tmp/pseudo_dir 
├── C
│   └── POTCAR
├── C.BFD.gms
├── C.ccECP.upf
├── C.ccECP.xml
├── C.USPP.upf
├── H
│   └── POTCAR
├── H.BFD.gms
├── H.ccECP.upf
├── H.ccECP.xml
└── H.USPP.upf

PseudoSet.from_dir()

>>> psps = PseudoSet.from_dir(pseudo_dir=pseudo_dir, code="qmcpack")
>>> for lbl, psp in psps.pseudos.items():
...     print(f"{lbl}: {psp}")
H: /tmp/pseudo_dir/H.ccECP.xml
C: /tmp/pseudo_dir/C.ccECP.xml

>>> psps = PseudoSet.from_dir(pseudo_dir=pseudo_dir, code="vasp")
>>> for lbl, psp in psps.pseudos.items():
...     print(f"{lbl}: {psp}")
C: /home/brock/tmp/pseudo_dir/C/POTCAR
H: /home/brock/tmp/pseudo_dir/H/POTCAR

>>> psps = PseudoSet.from_dir(
...     pseudo_dir=pseudo_dir,
...     code="espresso",
...     pattern="ccECP"
... )
>>> for lbl, psp in psps.pseudos.items():
...     print(f"{lbl}: {psp}")
C: /home/brock/tmp/pseudo_dir/C.ccECP.upf
H: /home/brock/tmp/pseudo_dir/H.ccECP.upf

PseudoSet.from_mixed_dir()

>>> psps = PseudoSet.from_mixed_dir(
...     pseudo_dir=pseudo_dir,
...     patterns={"espresso": "USPP"},
... )
>>> for code, ps_set in psps.items():
...     print(f"{code} pseudos:")
...     for lbl, psp in ps_set.pseudos.items():
...         print(f"  {lbl}: {psp}")
espresso pseudos:
C: /path/to/pseudo_dir/C.USPP.upf
H: /path/to/pseudo_dir/H.USPP.upf
gamess pseudos:
H: /path/to/pseudo_dir/H.BFD.gms
C: /path/to/pseudo_dir/C.BFD.gms
vasp pseudos:
C: /path/to/pseudo_dir/C/POTCAR
H: /path/to/pseudo_dir/H/POTCAR
qmcpack pseudos:
H: /path/to/pseudo_dir/H.ccECP.xml
C: /path/to/pseudo_dir/C.ccECP.xml

What type(s) of changes does this code introduce?

• New feature
• Testing changes (e.g. new unit/integration/performance tests)
• Documentation changes

Does this introduce a breaking change?

• No

What systems has this change been tested on?

Laptop, Fedora Linux 43 (KDE Plasma Desktop Edition)
AMD Ryzen 7 PRO 7840U (8 cores, 16 logical processors)

Python        3.14.5
uv            0.11.26
cif2cell      2.1.0
coverage      7.15.0
h5py          3.16.0
matplotlib    3.11.0
numpy         2.5.1
pycifrw       4.4.6
pydot         4.0.1
pytest        9.1.1
pytest-cov    7.1.0
pytest-order  1.5.0
scipy         1.18.0
seekpath      2.2.1
spglib        2.7.0
sphinx        9.1.0

Checklist

• • I have read the pull request guidance and develop docs
• • This PR is up to date with the current state of 'develop'
• • This PR adds tests to cover any new code, or to catch a bug that is being fixed
• • Documentation has been added (if appropriate)