feat: update gpu dependencies

[lwalew]

Description

• Update mlip to 0.1.6
• Update gpu optional dependency group to cuda for consistency with mlip. Additionally, do not manually reinstall jax[cuda12] and jaxlib but instead mlip[cuda].

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/mlipaudit
__init__.py	2	0	100%
benchmark.py	73	7	90%	128, 147, 213, 219–220, 230, 244
benchmarks_cli.py	109	109	0%	14–21, 23–26, 28–29, 33, 35, 37, 40–47, 52, 66–68, 70, 73, 88–90, 94–97, 102, 105, 119–124, 126, 128, 131, 158–159, 164–165, 167–168, 171, 178, 187–188, 190, 200, 202, 205, 212, 214–215, 217–219, 230, 234, 236, 246, 253–257, 261–262, 268, 271–277, 283, 285–287, 298, 301, 305–306, 317, 330–334, 342–343, 348, 356–358, 365
exceptions.py	1	0	100%
io.py	90	18	80%	115, 119, 147–150, 167–168, 170, 188–196
io_helpers.py	52	0	100%
run_mode.py	5	0	100%
scoring.py	21	0	100%
src/mlipaudit/benchmarks
__init__.py	25	0	100%
src/mlipaudit/benchmarks/bond_length_distribution
bond_length_distribution.py	88	1	98%	251
src/mlipaudit/benchmarks/conformer_selection
conformer_selection.py	88	0	100%
src/mlipaudit/benchmarks/dihedral_scan
dihedral_scan.py	100	0	100%
src/mlipaudit/benchmarks/folding_stability
folding_stability.py	98	4	95%	193, 241, 246, 302
helpers.py	35	0	100%
src/mlipaudit/benchmarks/noncovalent_interactions
noncovalent_interactions.py	149	4	97%	209, 212, 355, 369
src/mlipaudit/benchmarks/nudged_elastic_band
engine.py	126	94	25%	62, 81–82, 84–89, 91, 93, 95–96, 98–99, 101–103, 112–113, 115–116, 120–121, 123, 130, 132, 134–136, 138–139, 141, 143–145, 147–151, 153, 159–163, 165–167, 169–171, 173–175, 177–180, 182, 185, 189–190, 192, 194–195, 197, 201–202, 205–210, 212–213, 229, 234, 236–238, 240, 242–243, 246–247, 253, 256–257, 261–262, 267
nudged_elastic_band.py	105	1	99%	275
src/mlipaudit/benchmarks/reactivity
reactivity.py	103	0	100%
src/mlipaudit/benchmarks/ring_planarity
ring_planarity.py	93	4	95%	235, 238–239, 258
src/mlipaudit/benchmarks/sampling
helpers.py	60	4	93%	46, 67, 97, 129
sampling.py	212	11	94%	283–284, 318, 354, 357–359, 409, 676, 711, 735
src/mlipaudit/benchmarks/scaling
scaling.py	85	22	74%	113–115, 123–124, 126–129, 139–141, 178–181, 189–190, 192–193, 195, 241
src/mlipaudit/benchmarks/small_molecule_minimization
small_molecule_minimization.py	115	2	98%	284, 313
src/mlipaudit/benchmarks/solvent_radial_distribution
solvent_radial_distribution.py	98	8	91%	184–185, 187, 222, 227–228, 293, 315
src/mlipaudit/benchmarks/stability
stability.py	141	15	89%	142, 145, 177–178, 181–182, 184, 186, 189, 191, 401–402, 410, 492, 503
src/mlipaudit/benchmarks/tautomers
tautomers.py	78	0	100%
src/mlipaudit/benchmarks/water_radial_distribution
water_radial_distribution.py	92	2	97%	176, 256
src/mlipaudit/ui
__init__.py	16	0	100%
bond_length_distribution.py	58	9	84%	84–85, 142–143, 148, 151, 177, 189, 193
conformer_selection.py	62	4	93%	108–109, 166, 170
dihedral_scan.py	108	9	91%	134–135, 235–236, 285, 325, 327, 337, 341
folding_stability.py	93	5	94%	209–210, 220, 389, 393
leaderboard.py	72	10	86%	62, 69, 73, 80, 229–231, 233, 235, 238
noncovalent_interactions.py	153	14	90%	92–94, 99–100, 219–220, 230–231, 403, 408, 443, 464, 468
nudged_elastic_band.py	48	33	31%	35–38, 42, 44, 57–58, 60, 67, 74, 80–81, 84, 88–90, 92–93, 96, 98–101, 105, 107–108, 110, 121, 123, 133, 143, 147
page_wrapper.py	14	2	85%	36, 46
reactivity.py	54	5	90%	90–91, 109, 163, 167
ring_planarity.py	52	7	86%	66–67, 113–114, 150, 160, 164
sampling.py	83	7	91%	80, 123–124, 156, 224, 251, 255
scaling.py	46	4	91%	127–128, 150, 154
small_molecule_minimization.py	61	6	90%	124–125, 186, 213, 223, 227
solvent_radial_distribution.py	77	18	76%	107–108, 132, 138, 144–148, 150–151, 157, 160, 172, 179, 181, 193, 197
stability.py	62	10	83%	94–95, 118–119, 122, 132, 137, 148, 180, 184
tautomers.py	64	7	89%	69–70, 80–81, 89, 179, 183
utils.py	59	1	98%	109
water_radial_distribution.py	94	4	95%	127–128, 268, 272
src/mlipaudit/utils
__init__.py	4	0	100%
inference.py	16	1	93%	54
simulation.py	43	1	97%	131
stability.py	29	5	82%	56, 63, 87, 94, 98
trajectory_helpers.py	34	0	100%
unallowed_elements.py	10	0	100%
TOTAL	3656	468	87%

Tests	Skipped	Failures	Errors	Time
117	0 💤	0 ❌	0 🔥	14.799s ⏱️