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Revert "updates test_submit.py for ccad2 submission"
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This reverts commit 794824f.
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@jsanjak
jsanjak committed Sep 7, 2023
1 parent 794824f commit 8013666
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170 changes: 170 additions & 0 deletions poetryinstall.output
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Installing dependencies from lock file

Package operations: 123 installs, 25 updates, 0 removals

• Updating certifi (2023.5.7 -> 2021.10.8)
• Updating charset-normalizer (3.1.0 /home/conda/feedstock_root/build_artifacts/charset-normalizer_1678108872112/work -> 2.0.12)
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• Installing markupsafe (2.0.1)
• Installing pyparsing (3.0.9)
• Installing pytz (2022.1)
• Updating six (1.16.0 /home/conda/feedstock_root/build_artifacts/six_1620240208055/work -> 1.16.0)
• Updating urllib3 (1.26.15 /home/conda/feedstock_root/build_artifacts/urllib3_1678635778344/work -> 1.26.9)
• Updating zipp (3.15.0 /home/conda/feedstock_root/build_artifacts/zipp_1677313463193/work -> 3.8.0)
• Installing alabaster (0.7.12)
• Installing asttokens (2.0.5)
• Installing babel (2.10.1)
• Installing docutils (0.16)
• Updating attrs (23.1.0 /home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work -> 21.4.0)
• Installing imagesize (1.3.0)
• Installing iniconfig (1.1.1)
• Installing jinja2 (2.11.3)
• Updating packaging (23.1 /home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work -> 21.3)
• Installing parso (0.8.3)
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• Installing pure-eval (0.2.2)
• Updating importlib-resources (5.12.0 /home/conda/feedstock_root/build_artifacts/importlib_resources_1676919000169/work -> 5.7.1)
• Installing pygments (2.12.0)
• Updating pyrsistent (0.19.3 /home/conda/feedstock_root/build_artifacts/pyrsistent_1672681475076/work -> 0.18.1)
• Updating ptyprocess (0.7.0 /home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl -> 0.7.0)
• Installing py (1.11.0)
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• Updating requests (2.31.0 /home/conda/feedstock_root/build_artifacts/requests_1684774241324/work -> 2.27.1)
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• Installing sphinxcontrib-serializinghtml (1.1.5)
• Installing toml (0.10.2)
• Updating tomli (2.0.1 /home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work -> 2.0.1)
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• Updating platformdirs (3.5.1 /home/conda/feedstock_root/build_artifacts/platformdirs_1683850015520/work -> 2.5.2)
• Updating numpy (1.24.3 /home/conda/feedstock_root/build_artifacts/numpy_1682210232610/work -> 1.22.3)
• Installing regex (2022.4.24)
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• Installing black (20.8b1)
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• Updating importlib-metadata (6.6.0 /home/conda/feedstock_root/build_artifacts/importlib-metadata_1682176699712/work -> 1.7.0)
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• Updating virtualenv (20.23.0 /home/conda/feedstock_root/build_artifacts/virtualenv_1682674264573/work -> 20.14.1)
• Installing ruamel-std-pathlib (0.9.2)
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• Installing jupyter-client (7.3.1)
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• Installing ipykernel (5.5.6)
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• Updating more-itertools (9.1.0 /home/conda/feedstock_root/build_artifacts/more-itertools_1677514956219/work -> 8.13.0)
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• Installing pytest-mock (3.7.0)
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• Installing snakefmt (0.4.2)
• Installing sphinx-click (3.1.0)
• Installing sphinx-pydantic (0.1.1)
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• Installing sphinxcontrib-mermaid (0.4.0)
• Installing typer (0.3.2)
• Installing ptvsd (4.3.2)
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
Connection pool is full, discarding connection: pypi.org. Connection pool size: 10

Installing the current project: cgr_gwas_qc (0.1.2)
64 changes: 13 additions & 51 deletions tests/cli/test_submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,42 +5,30 @@
from cgr_gwas_qc.testing.data import FakeData


# [(True, False, None), (False, True, None), (False, False, "./test")],
@pytest.mark.parametrize(
"cgems,biowulf,ccad2,cluster_profile",
[
(True, False, False, None),
(False, True, False, None),
(False, False, True, None),
(False, False, False, "./test"),
],
"cgems,biowulf,cluster_profile",
[(True, False, None), (False, True, None), (False, False, "./test")],
)
def test_check_exclusive_options_no_error(cgems, biowulf, ccad2, cluster_profile):
def test_check_exclusive_options_no_error(cgems, biowulf, cluster_profile):
from cgr_gwas_qc.cli.submit import check_exclusive_options

check_exclusive_options(cgems, biowulf, ccad2, cluster_profile)
check_exclusive_options(cgems, biowulf, cluster_profile)


# [(True, True, "./test"), (True, True, None), (True, False, "./test"), (False, True, "./test")],
@pytest.mark.parametrize(
"cgems,biowulf,ccad2,cluster_profile",
[
(True, True, True, "./test"),
(True, True, True, None),
(True, False, False, "./test"),
(False, True, False, "./test"),
],
"cgems,biowulf,cluster_profile",
[(True, True, "./test"), (True, True, None), (True, False, "./test"), (False, True, "./test")],
)
def test_check_exclusive_options_raises_error(cgems, biowulf, ccad2, cluster_profile):
def test_check_exclusive_options_raises_error(cgems, biowulf, cluster_profile):
from click.exceptions import Exit as ClickExit

from cgr_gwas_qc.cli.submit import check_exclusive_options

with pytest.raises(ClickExit):
check_exclusive_options(cgems, biowulf, ccad2, cluster_profile)
check_exclusive_options(cgems, biowulf, cluster_profile)


@pytest.mark.parametrize("cluster", ["cgems", "biowulf", "ccad2"])
@pytest.mark.parametrize("cluster", ["cgems", "biowulf"])
def test_get_profile(cluster):
from pathlib import Path

Expand Down Expand Up @@ -144,44 +132,19 @@ def test_create_submission_script_biowulf(tmp_path):


@pytest.mark.parametrize(
"cluster,cmd",
[("cgems", "qsub"), ("biowulf", "sbatch"), ("ccad2", "sbatch"), ("custom", "pbs")],
"cluster,cmd", [("cgems", "qsub"), ("biowulf", "sbatch"), ("custom", "pbs")]
)
def test_run_submit_with_right_command(cluster, cmd, tmp_path, mocker: MockerFixture):
from cgr_gwas_qc.cli import submit

if cluster == "cgems":
cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = (
True,
False,
False,
None,
None,
None,
)
cgems, biowulf, cluster_profile, queue, submission_cmd = True, False, None, None, None
elif cluster == "biowulf": # Biowulf
cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = (
False,
True,
False,
None,
None,
None,
)
elif cluster == "ccad2":
cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = (
False,
False,
True,
None,
None,
None,
)
cgems, biowulf, cluster_profile, queue, submission_cmd = False, True, None, None, None
else:
profile_dir = tmp_path / "test_profile"
profile_dir.mkdir()
cgems, biowulf, ccad2, cluster_profile, queue, submission_cmd = (
False,
cgems, biowulf, cluster_profile, queue, submission_cmd = (
False,
False,
profile_dir,
Expand All @@ -195,7 +158,6 @@ def test_run_submit_with_right_command(cluster, cmd, tmp_path, mocker: MockerFix
submit.main(
cgems=cgems,
biowulf=biowulf,
ccad2=ccad2,
cluster_profile=cluster_profile,
subworkflow=None,
time_hr=12,
Expand Down
2 changes: 1 addition & 1 deletion tests/data
Submodule data updated from 73eddd to 5def84

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