refactor: merge cli

[lwalew]

Merge both cli commands into a single one.

[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	74	74	0%	15–19, 21–24, 26–27, 31, 33, 35, 38–45, 50, 60–62, 67, 69, 72, 87–89, 93–96, 101, 104, 118–123, 125, 127, 130, 142–143, 148, 150, 155–157, 159, 161–164, 166, 168, 173–174, 176–178, 180, 183, 189–191, 193–194, 199
exceptions.py	1	0	100%
io.py	90	18	80%	111, 115, 143–146, 163–165, 183–191
io_helpers.py	45	0	100%
run_mode.py	5	0	100%
scoring.py	21	0	100%
src/mlipaudit/benchmarks
__init__.py	24	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%	195, 243, 248, 304
helpers.py	35	0	100%
src/mlipaudit/benchmarks/noncovalent_interactions
noncovalent_interactions.py	149	4	97%	209, 212, 355, 369
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	9	95%	301–302, 336, 372, 375–377, 427, 694
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%	286, 315
src/mlipaudit/benchmarks/solvent_radial_distribution
solvent_radial_distribution.py	98	8	91%	184–185, 187, 222, 227–228, 289, 311
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	79	2	97%	166, 219
src/mlipaudit/ui
__init__.py	15	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%	133–134, 234–235, 284, 324, 326, 336, 340
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, 399, 404, 439, 460, 464
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%	126–127, 188, 215, 225, 229
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	103	4	96%	99–100, 278, 282
src/mlipaudit/utils
__init__.py	4	0	100%
inference.py	16	1	93%	54
simulation.py	39	1	97%	108
stability.py	29	5	82%	56, 63, 87, 94, 98
trajectory_helpers.py	34	0	100%
unallowed_elements.py	10	0	100%
TOTAL	3325	303	90%

Tests	Skipped	Failures	Errors	Time
116	0 💤	0 ❌	0 🔥	15.406s ⏱️