19443270205

Committed 17 Nov 2025 08:17PM UTC coverage: 93.197% (+0.1%) from 93.08%

Build # 19443270205

Build Type

Pull #58

github

Committed by

web-flow

Commit Message

Merge c0fd25661 into 9e2caaae9

Pull Request Pull Request #58: Bugfix job database.iterate jobs

Run Details

142 of 155 branches covered (91.61%)

Branch coverage included in aggregate %.

23 of 26 new or added lines in 8 files covered. (88.46%)

20 existing lines in 2 files now uncovered.

1543 of 1653 relevant lines covered (93.35%)

2.8 hits per line

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67.92

/tests/test_api.py

import multiprocessing
import time
from unittest import mock

import pytest

from slurmise.api import Slurmise
from slurmise.job_data import JobData
from slurmise.job_database import JobDatabase


def slurmise_record(toml, process_id, error_queue):
    def mock_metadata(kwargs):
        return {
            "slurm_id": kwargs["slurm_id"],
            "job_name": "nupack",
            "state": "COMPLETED",
            "partition": "",
            "elapsed_seconds": 97201,
            "CPUs": 1,
            "memory_per_cpu": 0,
            "memory_per_node": 0,
            "max_rss": 232,
            "step_id": "external",
        }

    try:
        time.sleep(process_id * 0.1)
        with mock.patch(
            "slurmise.slurm.parse_slurm_job_metadata",
            side_effect=lambda *args, **kwargs: mock_metadata(kwargs),
        ):
            slurmise = Slurmise(toml)
            time.sleep(process_id * 0.1)
            for i in range(10):
                slurmise.record("nupack monomer -T 2 -C simple", slurm_id=str(process_id * 100 + i))
                time.sleep(process_id * 0.1)
    except Exception as e:  # noqa: BLE001
        error_queue.put(f"PID {process_id}: {e}")


def test_multiple_slurmise_instances(simple_toml):
    processes = []
    error_queue = multiprocessing.Queue()
    for i in range(10):
        p = multiprocessing.Process(target=slurmise_record, args=(simple_toml.toml, i, error_queue))
        processes.append(p)
        p.start()

    [p.join() for p in processes]

    if not error_queue.empty():
        while not error_queue.empty():
            print(error_queue.get())
        pytest.fail("Child prcess had error")


def test_job_data_from_dict(simple_toml):
    slurmise = Slurmise(simple_toml.toml)
    result = slurmise.job_data_from_dict(
        {"threads": 3, "complexity": "simple"},
        "nupack",
    )
    assert result.categorical == {"complexity": "simple"}
    assert result.numerical == {"threads": 3}


def test_update_all_models_empty_database(simple_toml):
    slurmise = Slurmise(simple_toml.toml)
    slurmise.update_all_models()


# TODO avoid rewriting duplicated logic to fixtures in tests/test_job_database.py
def test_update_all_models(simple_toml, tmp_path):
    hdf5_path = tmp_path / "test_db.h5"
    slurmise = Slurmise(simple_toml.toml)
    slurmise.configuration.db_filename = str(hdf5_path)

    with JobDatabase.get_database(hdf5_path) as db:
        for job_id in range(50):
            db.record(
                JobData(
                    job_name="nupack",
                    slurm_id=str(job_id),
                    categorical={"complexity": "simple"},
                    numerical={"threads": 2},
                    memory=200,
                    runtime=3600,
                )
            )

    slurmise.update_all_models()

1	import multiprocessing	3✔
2	import time	3✔
3	from unittest import mock	3✔
4
5	import pytest	3✔
6
7	from slurmise.api import Slurmise	3✔
8	from slurmise.job_data import JobData	3✔
9	from slurmise.job_database import JobDatabase	3✔
10
11
12	def slurmise_record(toml, process_id, error_queue):	3✔
UNCOV 13	def mock_metadata(kwargs):	×
UNCOV 14	return {	×
15	"slurm_id": kwargs["slurm_id"],
16	"job_name": "nupack",
17	"state": "COMPLETED",
18	"partition": "",
19	"elapsed_seconds": 97201,
20	"CPUs": 1,
21	"memory_per_cpu": 0,
22	"memory_per_node": 0,
23	"max_rss": 232,
24	"step_id": "external",
25	}
26
27	try:	×
UNCOV 28	time.sleep(process_id * 0.1)	×
UNCOV 29	with mock.patch(	×
30	"slurmise.slurm.parse_slurm_job_metadata",
31	side_effect=lambda args, *kwargs: mock_metadata(kwargs),
32	):
33	slurmise = Slurmise(toml)	×
34	time.sleep(process_id * 0.1)	×
35	for i in range(10):	×
36	slurmise.record("nupack monomer -T 2 -C simple", slurm_id=str(process_id * 100 + i))	×
37	time.sleep(process_id * 0.1)	×
UNCOV 38	except Exception as e: # noqa: BLE001	×
UNCOV 39	error_queue.put(f"PID {process_id}: {e}")	×
40
41
42	def test_multiple_slurmise_instances(simple_toml):	3✔
43	processes = []	3✔
44	error_queue = multiprocessing.Queue()	3✔
45	for i in range(10):	3✔
46	p = multiprocessing.Process(target=slurmise_record, args=(simple_toml.toml, i, error_queue))	3✔
47	processes.append(p)	3✔
48	p.start()	3✔
49
50	[p.join() for p in processes]	3✔
51
52	if not error_queue.empty():	3✔
53	while not error_queue.empty():	×
UNCOV 54	print(error_queue.get())	×
UNCOV 55	pytest.fail("Child prcess had error")	×
56
57
58	def test_job_data_from_dict(simple_toml):	3✔
59	slurmise = Slurmise(simple_toml.toml)	3✔
60	result = slurmise.job_data_from_dict(	3✔
61	{"threads": 3, "complexity": "simple"},
62	"nupack",
63	)
64	assert result.categorical == {"complexity": "simple"}	3✔
65	assert result.numerical == {"threads": 3}	3✔
66
67
68	def test_update_all_models_empty_database(simple_toml):	3✔
69	slurmise = Slurmise(simple_toml.toml)	3✔
70	slurmise.update_all_models()	3✔
71
72
73	# TODO avoid rewriting duplicated logic to fixtures in tests/test_job_database.py
74	def test_update_all_models(simple_toml, tmp_path):	3✔
75	hdf5_path = tmp_path / "test_db.h5"	3✔
76	slurmise = Slurmise(simple_toml.toml)	3✔
77	slurmise.configuration.db_filename = str(hdf5_path)	3✔
78
79	with JobDatabase.get_database(hdf5_path) as db:	3✔
80	for job_id in range(50):	3✔
81	db.record(	3✔
82	JobData(
83	job_name="nupack",
84	slurm_id=str(job_id),
85	categorical={"complexity": "simple"},
86	numerical={"threads": 2},
87	memory=200,
88	runtime=3600,
89	)
90	)
91
92	slurmise.update_all_models()	3✔

PrincetonUniversity / slurmise / 19443270205

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