Test with flux

[jan-janssen]

No description provided.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
__init__.py	19	0	100%
io_utils.py	57	20	64%	106–111, 135–142, 144, 171–172, 181, 185–186
mass.py	4	0	100%
neighbors.py	34	0	100%
shared.py	16	0	100%
structure.py	365	124	66%	88, 106–107, 125–126, 144–145, 148, 218, 268, 270–271, 273–275, 278, 280–281, 305–306, 308–309, 325–327, 332–333, 339–340, 361–362, 369–370, 376, 380–382, 388–390, 393–394, 400–401, 410–411, 415–423, 507, 516, 518–519, 522, 524–532, 534–541, 552–553, 689–691, 700–701, 707, 714–715, 721–722, 727, 742, 760, 780, 793, 795–796, 799, 801, 803–806, 809–813, 985–986, 988–991, 994–1000, 1002–1004, 1007
analysis
__init__.py	0	0	100%
bond_angle_distribution.py	32	1	96%	79
cavities.py	19	0	100%
cte.py	30	27	10%	57, 71–78, 80–81, 83–88, 90–91, 93–94, 126–128, 131–132, 134
qn_network_connectivity.py	30	2	93%	103–104
radial_distribution_functions.py	68	18	73%	57–60, 62–63, 65–67, 69–71, 73–77, 79
rings.py	40	2	95%	88, 122
potentials
__init__.py	0	0	100%
bjp_potential.py	34	29	14%	45–46, 49, 56–58, 60, 68, 71–74, 77, 85–93, 95–99, 101, 103
pmmcs_potential.py	38	34	10%	56–57, 60–63, 65–66, 68–69, 71–73, 75, 84, 86–89, 91, 99–105, 109–113, 117, 119
potential.py	13	4	69%	29, 31, 34–35
shik_potential.py	84	5	94%	114–115, 143, 146–147
workflows
__init__.py	0	0	100%
cte.py	205	184	10%	28–29, 32–33, 36–37, 40, 42, 117–118, 121, 148–150, 152, 154, 159, 176–178, 180–187, 189–192, 194, 210–212, 214–219, 221–226, 228–233, 235–240, 242–247, 337, 340, 343, 345–346, 349, 352, 366, 369, 376, 383, 390, 399–410, 439–447, 449–451, 453–454, 462–465, 467–473, 475–483, 485–492, 494, 520–522, 547–548, 550–553, 555, 659, 662, 667, 670, 673, 676, 679–680, 683, 686, 702, 718–720, 723–726, 729–730, 733, 749–751, 754, 765–777, 780–781, 783
elastic_mod.py	80	66	17%	84–85, 88, 91, 119, 121, 143–144, 146, 149, 151, 193–196, 199–202, 204, 230–233, 235–238, 240–241, 243, 311, 313–314, 322, 327, 342, 346–348, 350, 353, 367–368, 371–377, 380–387, 389, 391, 394–397, 399
md.py	21	13	38%	76–77, 80, 83, 111, 113, 166, 168–169, 177, 182, 197, 199
meltquench.py	37	28	24%	82–83, 86, 90–91, 93–94, 96, 98, 100, 127, 129, 154–156, 159, 161, 221–223, 225, 228–231, 234, 251, 253
meltquench_protocols.py	37	29	21%	54, 65, 75, 83, 92, 101, 108, 129, 140, 151, 160, 170, 179, 186, 207, 218, 227, 237, 242, 252, 261, 271, 279, 332–335, 337–338
shared.py	11	10	9%	21–25, 27–29, 31–32
structural_analysis.py	242	118	51%	113–114, 116–118, 121, 123–128, 130–132, 134, 155–160, 162–163, 165–167, 169–176, 178, 180, 197–198, 201–204, 206–209, 211, 213–221, 223–227, 229, 245, 248–251, 253, 255–259, 261, 263–267, 269, 271–275, 278–281, 283, 285–286, 289–293, 297–301, 303–304, 307–308, 310, 314–321, 323, 476
viscosity.py	147	55	62%	80–81, 84, 87, 115, 117, 166, 168–169, 177, 182, 197, 212, 225, 227, 269, 315–316, 318–319, 321–322, 326–331, 337, 349, 351, 356–358, 360–361, 363–365, 367–368, 370–372, 374, 377–378, 382, 384, 409, 430–431, 454–455, 505
TOTAL	1663	769	53%

[jan-janssen]

@ltalirz I do not really have an explanation but everything seems to be working fine when using the FluxClusterExecutor for testing rather than the TestClusterExecutor. My assumption is that the test environment struggles with the orphan processes which are created by the TestClusterExecutor to execute the calculation in the background resulting in the process to hang.

[ltalirz]

I see - interesting... and thanks for looking into the issue.

I'll merge this in a bit.

Maybe I then actually want to use SingleNodeExecutor as the fallback rather than the TestClusterExecutor. Let me try that as well

[ltalirz]

hm... that was indeed a bit too good to be true:

the way you start flux here appears not to be correct.
the API server then also does not manage to start and the test is skipped.

Run flux start  amorphouspy_INTEGRATION=1 uvicorn amorphouspy_api.app:app --port 8002 & pytest -m integration -s --durations=0 --cov=src/amorphouspy_api --cov-report=xml --cov-report=term --cov-append
Feb 09 11:00:27.911219 UTC 2026 broker.err[0]: rc2.0: amorphouspy_INTEGRATION=1 uvicorn amorphouspy_api.app:app --port 8002 error launching process: No such file or directory (rc=127) 0.0s
2026-02-09 11:00:32,743 - amorphouspy_api.app - INFO - Using amorphouspy version: 0.0.12
2026-02-09 11:00:32,743 - amorphouspy_api.app - INFO - Using default project directory: /home/runner/work/amorphouspy/amorphouspy/amorphouspy_api/projects
2026-02-09 11:00:32,744 - amorphouspy_api.app - INFO - No API base URL configured, using relative paths
2026-02-09 11:00:32,744 - amorphouspy_api.app - INFO - Ensured projects directory exists: /home/runner/work/amorphouspy/amorphouspy/amorphouspy_api/projects
2026-02-09 11:00:32,744 - amorphouspy_api.app - INFO - Task store database path: /home/runner/work/amorphouspy/amorphouspy/amorphouspy_api/projects/tasks.db
2026-02-09 11:00:32,744 - amorphouspy_api.app - INFO - Directory exists: True, Directory writable: True

I'll make sure this results in a failed test going forward