nix updates

[sheepforce]

This Nix PR adds the compiled pysisyphus addons with sympleints, adds thermoanalysis module, the missing numba and optuna dependencies, and forces usage of ORCA 5.0.4 instead of the current 6.0.1 release.

[sheepforce]

@eljost the test_diabatization_driver[DiaKind.EDMISTON_RUEDENBERG] and test_diabatization_driver[DiaKind.BOYS] are still failing, now with file not found errors. Looks like the others that had problems with gitignore.

[eljost]

The required files are now mentioned explicitly in .gitignore. It seems as if the wildcard(s) in .gitignore don't work.

[sheepforce]

1 solved, 1 to go, still a missing file:

pysisyphus> =================================== FAILURES ===================================
pysisyphus> ____________ test_diabatization_driver[DiaKind.EDMISTON_RUEDENBERG] ____________
pysisyphus> 
pysisyphus> dia_kinds = <DiaKind.EDMISTON_RUEDENBERG: 1>
pysisyphus> this_dir = PosixPath('/build/ffpjvwb1cwdarpjcaz9nxsnjbhzy74v4-source/tests/test_diabatization')
pysisyphus> 
pysisyphus>     @pytest.mark.parametrize(
pysisyphus>         "dia_kinds",
pysisyphus>         (
pysisyphus>             pytest.param(
pysisyphus>                 dia_driver.DiaKind.EDMISTON_RUEDENBERG, marks=using("pysisyphus_addons")
pysisyphus>             ),
pysisyphus>             (dia_driver.DiaKind.BOYS),
pysisyphus>         ),
pysisyphus>     )
pysisyphus>     def test_diabatization_driver(dia_kinds, this_dir):
pysisyphus>         """Example from http://dx.doi.org/10.1063/1.3148777 (BeNa2 cation)."""
pysisyphus>         inp_dir = this_dir / "00_bena2_cat"
pysisyphus>         out_dir = this_dir / "00_bena2_cat_out"
pysisyphus>         base = inp_dir / "00_bena2_dcat.log"
pysisyphus>         base_name = base.stem
pysisyphus>         wf, all_ens, Xa, Ya, Xb, Yb = dia_driver.parse_orca(base)
pysisyphus>         states = [1, 2]
pysisyphus>     
pysisyphus>         dia_inp = dia_driver.DiaInput(
pysisyphus>             wf=wf,
pysisyphus>             all_ens=all_ens,
pysisyphus>             Xa=Xa,
pysisyphus>             Ya=Ya,
pysisyphus>             Xb=Xb,
pysisyphus>             Yb=Yb,
pysisyphus>             states=states,
pysisyphus>             base_name=base_name,
pysisyphus>         )
pysisyphus>         # Update states by calculating overlaps if requested
pysisyphus> >       dia_results, cube_fns = dia_driver.run_dia(
pysisyphus>             dia_inp,
pysisyphus>             dia_kinds=dia_kinds,
pysisyphus>             cube_kinds=dia_driver.CubeKind.NONE,
pysisyphus>             out_dir=out_dir,
pysisyphus>             force=True,
pysisyphus>             h5_fn=out_dir / "00_bena2_cat_dia_result.h5",
pysisyphus>         )
pysisyphus> 
pysisyphus> tests/test_diabatization/test_diabatization.py:48: 
pysisyphus> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysisyphus> /nix/store/h3i0acpmr8mrjx07519xxmidv8mpax4y-python3-3.12.5/lib/python3.12/functools.py:907: in wrapper
pysisyphus>     return dispatch(args[0].__class__)(*args, **kw)
pysisyphus> pysisyphus/diabatization/driver.py:970: in _
pysisyphus>     return run_dia(
pysisyphus> /nix/store/h3i0acpmr8mrjx07519xxmidv8mpax4y-python3-3.12.5/lib/python3.12/functools.py:907: in wrapper
pysisyphus>     return dispatch(args[0].__class__)(*args, **kw)
pysisyphus> pysisyphus/diabatization/driver.py:853: in run_dia
pysisyphus>     er_dia_result = run_coulomb_dia(
pysisyphus> pysisyphus/diabatization/driver.py:414: in run_coulomb_dia
pysisyphus>     aux_shells = shells.from_basis(aux_basis_fn)
pysisyphus> pysisyphus/wavefunction/shells.py:463: in from_basis
pysisyphus>     return shells_with_basis(
pysisyphus> /nix/store/h3i0acpmr8mrjx07519xxmidv8mpax4y-python3-3.12.5/lib/python3.12/functools.py:907: in wrapper
pysisyphus>     return dispatch(args[0].__class__)(*args, **kw)
pysisyphus> pysisyphus/wavefunction/Basis.py:182: in shells_with_basis
pysisyphus>     basis = basis_from_json(name)
pysisyphus> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysisyphus> 
pysisyphus> name = 'def2-universal-jfit.json'
pysisyphus> 
pysisyphus>     def basis_from_json(name):
pysisyphus>         basis_path = Path(name).with_suffix(".json")
pysisyphus>         if not basis_path.is_absolute():
pysisyphus>             basis_path = BASIS_LIB_DIR / basis_path
pysisyphus>     
pysisyphus> >       with open(basis_path) as handle:
pysisyphus> E       FileNotFoundError: [Errno 2] No such file or directory: '/build/ffpjvwb1cwdarpjcaz9nxsnjbhzy74v4-source/pysisyphus/basis_library/def2-universal-jfit.json'
pysisyphus> 
pysisyphus> pysisyphus/wavefunction/Basis.py:22: FileNotFoundError