def flux_command(self):
"""
Returns a the flux version
"""
flux_bin = "flux"
if "flux_path" in self.expanded_spec.batch.keys():
flux_bin = os.path.join(self.expanded_spec.batch["flux_path"], "flux")
return get_flux_cmd(flux_bin, no_errors=self.no_errors)
def define_tests():
"""
Returns a dictionary of tests, where the key
is the test's name, and the value is a tuple
of (shell command, condition(s) to satisfy).
"""
celery_regex = r"(srun\s+.*)?celery\s+(-A|--app)\s+merlin\s+worker\s+.*"
# shortcut string variables
err_lvl = "-lvl error"
workers = f"merlin {err_lvl} run-workers"
run = f"merlin {err_lvl} run"
restart = f"merlin {err_lvl} restart"
purge = "merlin purge"
examples = "merlin/examples/workflows"
dev_examples = "merlin/examples/dev_workflows"
demo = f"{examples}/feature_demo/feature_demo.yaml"
remote_demo = f"{examples}/remote_feature_demo/remote_feature_demo.yaml"
demo_pgen = f"{examples}/feature_demo/scripts/pgen.py"
simple = f"{examples}/simple_chain/simple_chain.yaml"
slurm = f"{examples}/slurm/slurm_test.yaml"
slurm_restart = f"{examples}/slurm/slurm_par_restart.yaml"
flux = f"{examples}/flux/flux_test.yaml"
flux_restart = f"{examples}/flux/flux_par_restart.yaml"
lsf = f"{examples}/lsf/lsf_par.yaml"
black = "black --check --target-version py36"
config_dir = "./CLI_TEST_MERLIN_CONFIG"
release_dependencies = "./requirements/release.txt"
basic_checks = {
"merlin": ("merlin", HasReturnCode(1), "local"),
"merlin help": ("merlin --help", HasReturnCode(), "local"),
"merlin version": ("merlin --version", HasReturnCode(), "local"),
"merlin config": (
f"merlin config -o {config_dir}; rm -rf {config_dir}",
HasReturnCode(),
"local",
),
}
examples_check = {
"example list": (
"merlin example list",
HasReturnCode(),
"local",
),
}
run_workers_echo_tests = {
"run-workers echo simple_chain": (
f"{workers} {simple} --echo",
[HasReturnCode(), HasRegex(celery_regex)],
"local",
),
"run-workers echo feature_demo": (
f"{workers} {demo} --echo",
[HasReturnCode(), HasRegex(celery_regex)],
"local",
),
"run-workers echo slurm_test": (
f"{workers} {slurm} --echo",
[HasReturnCode(), HasRegex(celery_regex)],
"local",
),
"run-workers echo flux_test": (
f"{workers} {flux} --echo",
[HasReturnCode(), HasRegex(celery_regex)],
"local",
),
"run-workers echo override feature_demo": (
f"{workers} {demo} --echo --vars VERIFY_QUEUE=custom_verify_queue",
[HasReturnCode(), HasRegex("custom_verify_queue")],
"local",
),
}
wf_format_tests = {
"local minimum_format": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../{dev_examples}/minimum_format.yaml --local",
StepFileExists(
"step1",
"MERLIN_FINISHED",
"minimum_format",
OUTPUT_DIR,
params=False,
),
"local",
),
"local no_description": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_description.yaml --local",
HasReturnCode(1),
"local",
),
"local no_steps": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_steps.yaml --local",
HasReturnCode(1),
"local",
),
"local no_study": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_study.yaml --local",
HasReturnCode(1),
"local",
),
}
example_tests = {
"example failure":
("merlin example failure", HasRegex("not found"), "local"),
"example simple_chain": (
f"merlin example simple_chain ; {run} simple_chain.yaml --local --vars OUTPUT_PATH=./{OUTPUT_DIR} ; rm simple_chain.yaml",
HasReturnCode(),
"local",
),
}
restart_step_tests = {
"local restart_shell": (
f"{run} {dev_examples}/restart_shell.yaml --local --vars OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileExists(
"step2",
"MERLIN_FINISHED",
"restart_shell",
OUTPUT_DIR,
params=False,
),
"local",
),
"local restart": (
f"{run} {dev_examples}/restart.yaml --local --vars OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileExists(
"final_check_for_no_hard_fails",
"MERLIN_FINISHED",
"restart",
OUTPUT_DIR,
params=False,
),
"local",
),
}
restart_wf_tests = {
"restart local simple_chain": (
f"{run} {simple} --local --vars OUTPUT_PATH=./{OUTPUT_DIR} ; {restart} $(find ./{OUTPUT_DIR} -type d -name 'simple_chain_*') --local",
HasReturnCode(),
"local",
),
}
dry_run_tests = {
"dry feature_demo": (
f"{run} {demo} --local --dry --vars OUTPUT_PATH=./{OUTPUT_DIR}",
[
StepFileExists(
"verify",
"verify_*.sh",
"feature_demo",
OUTPUT_DIR,
params=True,
),
HasReturnCode(),
],
"local",
),
"dry launch slurm": (
f"{run} {slurm} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileHasRegex("runs", "*/runs.slurm.sh", "slurm_test",
OUTPUT_DIR, "srun "),
"local",
),
"dry launch flux": (
f"{run} {flux} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileHasRegex(
"runs",
"*/runs.slurm.sh",
"flux_test",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
"dry launch lsf": (
f"{run} {lsf} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileHasRegex("runs", "*/runs.slurm.sh", "lsf_par", OUTPUT_DIR,
"jsrun "),
"local",
),
"dry launch slurm restart": (
f"{run} {slurm_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileHasRegex(
"runs",
"*/runs.restart.slurm.sh",
"slurm_par_restart",
OUTPUT_DIR,
"srun ",
),
"local",
),
"dry launch flux restart": (
f"{run} {flux_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileHasRegex(
"runs_rs",
"*/runs_rs.restart.slurm.sh",
"flux_par_restart",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
}
other_local_tests = {
"local simple_chain": (
f"{run} {simple} --local --vars OUTPUT_PATH=./{OUTPUT_DIR}",
HasReturnCode(),
"local",
),
"local override feature_demo": (
f"{run} {demo} --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR} --local",
[
HasReturnCode(),
ProvenanceYAMLFileHasRegex(
regex=r"HELLO: \$\(SCRIPTS\)/hello_world.py",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="orig",
),
ProvenanceYAMLFileHasRegex(
regex=r"name: \$\(NAME\)",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="partial",
),
ProvenanceYAMLFileHasRegex(
regex="studies/feature_demo_",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="partial",
),
ProvenanceYAMLFileHasRegex(
regex="name: feature_demo",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
ProvenanceYAMLFileHasRegex(
regex=r"\$\(NAME\)",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
negate=True,
),
StepFileExists(
"verify",
"MERLIN_FINISHED",
"feature_demo",
OUTPUT_DIR,
params=True,
),
],
"local",
),
# "local restart expand name": (
# f"{run} {demo} --local --vars OUTPUT_PATH=./{OUTPUT_DIR} NAME=test_demo ; {restart} $(find ./{OUTPUT_DIR} -type d -name 'test_demo_*') --local",
# [
# HasReturnCode(),
# ProvenanceYAMLFileHasRegex(
# regex="name: test_demo",
# name="test_demo",
# output_path=OUTPUT_DIR,
# provenance_type="expanded",
# ),
# StepFileExists(
# "merlin_info", "test_demo.expanded.yaml", "test_demo", OUTPUT_DIR, params=True,
# ),
# ],
# "local",
# ),
"local csv feature_demo": (
f"echo 42.0,47.0 > foo_testing_temp.csv; merlin run {demo} --samplesfile foo_testing_temp.csv --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.csv",
[HasRegex("1 sample loaded."),
HasReturnCode()],
"local",
),
"local tab feature_demo": (
f"echo '42.0\t47.0\n7.0 5.3' > foo_testing_temp.tab; merlin run {demo} --samplesfile foo_testing_temp.tab --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.tab",
[HasRegex("2 samples loaded."),
HasReturnCode()],
"local",
),
"local pgen feature_demo": (
f"{run} {demo} --pgen {demo_pgen} --vars OUTPUT_PATH=./{OUTPUT_DIR} --local",
[
ProvenanceYAMLFileHasRegex(
regex=r"\[0.3333333",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
ProvenanceYAMLFileHasRegex(
regex=r"\[0.5",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
negate=True,
),
HasReturnCode(),
],
"local",
),
}
provenence_equality_checks = { # noqa: F841
"local provenance spec equality": (
f"{run} {simple} --vars OUTPUT_PATH=./{OUTPUT_DIR} --local ; cp $(find ./{OUTPUT_DIR}/simple_chain_*/merlin_info -type f -name 'simple_chain.expanded.yaml') ./{OUTPUT_DIR}/FILE1 ; rm -rf ./{OUTPUT_DIR}/simple_chain_* ; {run} ./{OUTPUT_DIR}/FILE1 --vars OUTPUT_PATH=./{OUTPUT_DIR} --local ; cmp ./{OUTPUT_DIR}/FILE1 $(find ./{OUTPUT_DIR}/simple_chain_*/merlin_info -type f -name 'simple_chain.expanded.yaml')",
HasReturnCode(),
"local",
),
}
style_checks = { # noqa: F841
"black check merlin": (f"{black} merlin/", HasReturnCode(), "local"),
"black check tests": (f"{black} tests/", HasReturnCode(), "local"),
}
dependency_checks = {
"deplic no GNU": (
f"deplic {release_dependencies}",
[HasRegex("GNU", negate=True),
HasRegex("GPL", negate=True)],
"local",
),
}
distributed_tests = { # noqa: F841
"run and purge feature_demo": (
f"{run} {demo} ; {purge} {demo} -f",
HasReturnCode(),
),
"remote feature_demo": (
f"{run} {remote_demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers ; {workers} {remote_demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers",
[
HasReturnCode(),
ProvenanceYAMLFileHasRegex(
regex="cli_test_demo_workers:",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
StepFileExists(
"verify",
"MERLIN_FINISHED",
"feature_demo",
OUTPUT_DIR,
params=True,
),
],
),
# this test is deactivated until the --spec option for stop-workers is active again
# "stop workers for distributed feature_demo": (
# f"{run} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers ; {workers} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers ; sleep 20 ; merlin stop-workers --spec {demo}",
# [
# HasReturnCode(),
# ProvenanceYAMLFileHasRegex(
# regex="cli_test_demo_workers:",
# name="feature_demo",
# output_path=OUTPUT_DIR,
# provenance_type="expanded",
# ),
# StepFileExists(
# "verify",
# "MERLIN_FINISHED",
# "feature_demo",
# OUTPUT_DIR,
# params=True,
# ),
# ],
# ),
}
# combine and return test dictionaries
all_tests = {}
for test_dict in [
basic_checks,
examples_check,
run_workers_echo_tests,
wf_format_tests,
example_tests,
restart_step_tests,
restart_wf_tests,
dry_run_tests,
other_local_tests,
# provenence_equality_checks, # omitting provenance equality check because it is broken
# style_checks, # omitting style checks due to different results on different machines
dependency_checks,
distributed_tests,
]:
all_tests.update(test_dict)
return all_tests
def define_tests():
"""
Returns a dictionary of tests, where the key
is the test's name, and the value is a tuple
of (shell command, condition(s) to satisfy).
"""
celery_regex = r"(srun\s+.*)?celery\s+worker\s+(-A|--app)\s+merlin\s+.*"
# shortcut string variables
workers = "merlin run-workers"
run = "merlin run"
restart = "merlin restart"
purge = "merlin purge"
examples = "merlin/examples/workflows"
demo = f"{examples}/feature_demo/feature_demo.yaml"
simple = f"{examples}/simple_chain/simple_chain.yaml"
slurm = f"{examples}/slurm/slurm_test.yaml"
slurm_restart = f"{examples}/slurm/slurm_par_restart.yaml"
flux = f"{examples}/flux/flux_test.yaml"
flux_restart = f"{examples}/flux/flux_par_restart.yaml"
lsf = f"{examples}/lsf/lsf_par.yaml"
black = "black --check --target-version py36"
config_dir = "./CLI_TEST_MERLIN_CONFIG"
return {
"merlin": ("merlin", ReturnCodeCond(1), "local"),
"merlin help": ("merlin --help", ReturnCodeCond(), "local"),
"merlin version": ("merlin --version", ReturnCodeCond(), "local"),
"merlin config": (
f"merlin config -o {config_dir}; rm -rf {config_dir}",
ReturnCodeCond(),
"local",
),
"run-workers echo simple_chain": (
f"{workers} {simple} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo feature_demo": (
f"{workers} {demo} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo slurm_test": (
f"{workers} {slurm} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo flux_test": (
f"{workers} {flux} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo override feature_demo": (
f"{workers} {demo} --echo --vars VERIFY_QUEUE=custom_verify_queue",
[ReturnCodeCond(),
RegexCond("custom_verify_queue")],
"local",
),
"run feature_demo": (f"{run} {demo}", ReturnCodeCond()),
"purge feature_demo": (f"{purge} {demo} -f", ReturnCodeCond()),
"dry feature_demo": (
f"{run} {demo} --local --dry --vars OUTPUT_PATH=./{OUTPUT_DIR}",
[
StepFileExistsCond("verify", "*/verify_*.sh", "feature_demo",
OUTPUT_DIR),
ReturnCodeCond(),
],
"local",
),
"local simple_chain": (
f"{run} {simple} --local --vars OUTPUT_PATH=./{OUTPUT_DIR}",
ReturnCodeCond(),
"local",
),
"example failure":
(f"merlin example failure", RegexCond("not found"), "local"),
"example simple_chain": (
f"merlin example simple_chain ; {run} simple_chain.yaml --local --vars OUTPUT_PATH=./{OUTPUT_DIR} ; rm simple_chain.yaml",
ReturnCodeCond(),
"local",
),
# "restart local simple_chain": (
# f"{restart} --local $(find studies/ -type d -name 'simple_chain_*')",
# [ReturnCodeCond(), NoStderrCond()],
# ),
"dry launch slurm": (
f"{run} {slurm} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond("runs", "*/runs.slurm.sh", "slurm_test",
OUTPUT_DIR, "srun "),
"local",
),
"dry launch flux": (
f"{run} {flux} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs",
"*/runs.slurm.sh",
"flux_test",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
"dry launch lsf": (
f"{run} {lsf} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond("runs", "*/runs.slurm.sh", "lsf_par",
OUTPUT_DIR, "jsrun "),
"local",
),
"dry launch slurm restart": (
f"{run} {slurm_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs",
"*/runs.restart.slurm.sh",
"slurm_par_restart",
OUTPUT_DIR,
"srun ",
),
"local",
),
"dry launch flux restart": (
f"{run} {flux_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs_rs",
"*/runs_rs.restart.slurm.sh",
"flux_par_restart",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
"local override feature_demo": (
f"{run} {demo} --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR} --local",
[
ReturnCodeCond(),
ProvenanceCond(regex=" -n 2 -outfile",
name="feature_demo",
output_path=OUTPUT_DIR),
StepFileExistsCond("verify", "MERLIN_FINISHED", "feature_demo",
OUTPUT_DIR),
],
# "local",
),
"local csv feature_demo": (
f"echo 42.0,47.0 > foo_testing_temp.csv; {run} {demo} --samples foo_testing_temp.csv --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.csv",
[RegexCond("1 sample loaded."),
ReturnCodeCond()],
# "local",
),
"local tab feature_demo": (
f"echo '42.0\t47.0\n7.0 5.3' > foo_testing_temp.tab; {run} {demo} --samples foo_testing_temp.tab --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.tab",
[RegexCond("2 samples loaded."),
ReturnCodeCond()],
# "local",
),
"distributed feature_demo": (
f"{run} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers ; {workers} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers",
[
ReturnCodeCond(),
ProvenanceCond(
regex="cli_test_demo_workers:",
name="feature_demo",
output_path=OUTPUT_DIR,
),
StepFileExistsCond("verify", "MERLIN_FINISHED", "feature_demo",
OUTPUT_DIR),
],
),
# "black check merlin": (f"{black} merlin/", ReturnCodeCond(), "local"),
# "black check tests": (f"{black} tests/", ReturnCodeCond(), "local"),
"deplic no GNU": (
f"deplic ./",
[RegexCond("GNU", negate=True),
RegexCond("GPL", negate=True)],
"local",
),
}
def define_tests():
"""
Returns a dictionary of tests, where the key
is the test's name, and the value is a tuple
of (shell command, condition(s) to satisfy).
"""
celery_regex = r"(srun\s+.*)?celery\s+(-A|--app)\s+merlin\s+worker\s+.*"
# shortcut string variables
workers = "merlin run-workers"
run = "merlin run"
restart = "merlin restart"
purge = "merlin purge"
examples = "merlin/examples/workflows"
dev_examples = "merlin/examples/dev_workflows"
demo = f"{examples}/feature_demo/feature_demo.yaml"
demo_pgen = f"{examples}/feature_demo/scripts/pgen.py"
simple = f"{examples}/simple_chain/simple_chain.yaml"
slurm = f"{examples}/slurm/slurm_test.yaml"
slurm_restart = f"{examples}/slurm/slurm_par_restart.yaml"
flux = f"{examples}/flux/flux_test.yaml"
flux_restart = f"{examples}/flux/flux_par_restart.yaml"
lsf = f"{examples}/lsf/lsf_par.yaml"
black = "black --check --target-version py36"
config_dir = "./CLI_TEST_MERLIN_CONFIG"
return {
"merlin": ("merlin", ReturnCodeCond(1), "local"),
"merlin help": ("merlin --help", ReturnCodeCond(), "local"),
"merlin version": ("merlin --version", ReturnCodeCond(), "local"),
"merlin config": (
f"merlin config -o {config_dir}; rm -rf {config_dir}",
ReturnCodeCond(),
"local",
),
"local minimum_format": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../{dev_examples}/minimum_format.yaml --local",
StepFileExistsCond(
"step1",
"MERLIN_FINISHED",
"minimum_format",
OUTPUT_DIR,
params=False,
),
"local",
),
"local no_description": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_description.yaml --local",
ReturnCodeCond(1),
"local",
),
"local no_steps": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_steps.yaml --local",
ReturnCodeCond(1),
"local",
),
"local no_study": (
f"mkdir {OUTPUT_DIR} ; cd {OUTPUT_DIR} ; merlin run ../merlin/examples/dev_workflows/no_study.yaml --local",
ReturnCodeCond(1),
"local",
),
"run-workers echo simple_chain": (
f"{workers} {simple} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo feature_demo": (
f"{workers} {demo} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo slurm_test": (
f"{workers} {slurm} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo flux_test": (
f"{workers} {flux} --echo",
[ReturnCodeCond(), RegexCond(celery_regex)],
"local",
),
"run-workers echo override feature_demo": (
f"{workers} {demo} --echo --vars VERIFY_QUEUE=custom_verify_queue",
[ReturnCodeCond(),
RegexCond("custom_verify_queue")],
"local",
),
"run feature_demo": (f"{run} {demo}", ReturnCodeCond()),
"purge feature_demo": (f"{purge} {demo} -f", ReturnCodeCond()),
"dry feature_demo": (
f"{run} {demo} --local --dry --vars OUTPUT_PATH=./{OUTPUT_DIR}",
[
StepFileExistsCond(
"verify",
"verify_*.sh",
"feature_demo",
OUTPUT_DIR,
params=True,
),
ReturnCodeCond(),
],
"local",
),
"restart local simple_chain": (
f"{run} {simple} --local --vars OUTPUT_PATH=./{OUTPUT_DIR} ; {restart} $(find ./{OUTPUT_DIR} -type d -name 'simple_chain_*') --local",
ReturnCodeCond(),
"local",
),
"local simple_chain": (
f"{run} {simple} --local --vars OUTPUT_PATH=./{OUTPUT_DIR}",
ReturnCodeCond(),
"local",
),
"example failure":
(f"merlin example failure", RegexCond("not found"), "local"),
"example simple_chain": (
f"merlin example simple_chain ; {run} simple_chain.yaml --local --vars OUTPUT_PATH=./{OUTPUT_DIR} ; rm simple_chain.yaml",
ReturnCodeCond(),
"local",
),
"dry launch slurm": (
f"{run} {slurm} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond("runs", "*/runs.slurm.sh", "slurm_test",
OUTPUT_DIR, "srun "),
"local",
),
"dry launch flux": (
f"{run} {flux} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs",
"*/runs.slurm.sh",
"flux_test",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
"dry launch lsf": (
f"{run} {lsf} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond("runs", "*/runs.slurm.sh", "lsf_par",
OUTPUT_DIR, "jsrun "),
"local",
),
"dry launch slurm restart": (
f"{run} {slurm_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs",
"*/runs.restart.slurm.sh",
"slurm_par_restart",
OUTPUT_DIR,
"srun ",
),
"local",
),
"dry launch flux restart": (
f"{run} {flux_restart} --dry --local --no-errors --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR}",
StepFileContainsCond(
"runs_rs",
"*/runs_rs.restart.slurm.sh",
"flux_par_restart",
OUTPUT_DIR,
get_flux_cmd("flux", no_errors=True),
),
"local",
),
"local override feature_demo": (
f"{run} {demo} --vars N_SAMPLES=2 OUTPUT_PATH=./{OUTPUT_DIR} --local",
[
ReturnCodeCond(),
ProvenanceCond(
regex="PREDICT: \$\(SCRIPTS\)/predict.py",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="orig",
),
ProvenanceCond(
regex="name: \$\(NAME\)",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="partial",
),
ProvenanceCond(
regex="studies/feature_demo_",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="partial",
),
ProvenanceCond(
regex="name: feature_demo",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
ProvenanceCond(
regex="\$\(NAME\)",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
negate=True,
),
StepFileExistsCond(
"verify",
"MERLIN_FINISHED",
"feature_demo",
OUTPUT_DIR,
params=True,
),
],
"local",
),
# "local restart expand name": (
# f"{run} {demo} --local --vars OUTPUT_PATH=./{OUTPUT_DIR} NAME=test_demo ; {restart} $(find ./{OUTPUT_DIR} -type d -name 'test_demo_*') --local",
# [
# ReturnCodeCond(),
# ProvenanceCond(
# regex="name: test_demo",
# name="test_demo",
# output_path=OUTPUT_DIR,
# provenance_type="expanded",
# ),
# StepFileExistsCond(
# "merlin_info", "test_demo.expanded.yaml", "test_demo", OUTPUT_DIR, params=True,
# ),
# ],
# "local",
# ),
"local csv feature_demo": (
f"echo 42.0,47.0 > foo_testing_temp.csv; {run} {demo} --samples foo_testing_temp.csv --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.csv",
[RegexCond("1 sample loaded."),
ReturnCodeCond()],
"local",
),
"local tab feature_demo": (
f"echo '42.0\t47.0\n7.0 5.3' > foo_testing_temp.tab; {run} {demo} --samples foo_testing_temp.tab --vars OUTPUT_PATH=./{OUTPUT_DIR} --local; rm -f foo_testing_temp.tab",
[RegexCond("2 samples loaded."),
ReturnCodeCond()],
"local",
),
"local pgen feature_demo": (
f"{run} {demo} --pgen {demo_pgen} --vars OUTPUT_PATH=./{OUTPUT_DIR} --local",
[
ProvenanceCond(
regex="\[0.3333333",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
ProvenanceCond(
regex="\[0.5",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
negate=True,
),
ReturnCodeCond(),
],
"local",
),
# "local provenance spec equality": (
# f"{run} {simple} --vars OUTPUT_PATH=./{OUTPUT_DIR} --local ; cp $(find ./{OUTPUT_DIR}/simple_chain_*/merlin_info -type f -name 'simple_chain.expanded.yaml') ./{OUTPUT_DIR}/FILE1 ; rm -rf ./{OUTPUT_DIR}/simple_chain_* ; {run} ./{OUTPUT_DIR}/FILE1 --vars OUTPUT_PATH=./{OUTPUT_DIR} --local ; cmp ./{OUTPUT_DIR}/FILE1 $(find ./{OUTPUT_DIR}/simple_chain_*/merlin_info -type f -name 'simple_chain.expanded.yaml')",
# ReturnCodeCond(),
# "local",
# ),
# "black check merlin": (f"{black} merlin/", ReturnCodeCond(), "local"),
# "black check tests": (f"{black} tests/", ReturnCodeCond(), "local"),
"deplic no GNU": (
f"deplic ./",
[RegexCond("GNU", negate=True),
RegexCond("GPL", negate=True)],
"local",
),
"distributed feature_demo": (
f"{run} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers ; {workers} {demo} --vars OUTPUT_PATH=./{OUTPUT_DIR} WORKER_NAME=cli_test_demo_workers",
[
ReturnCodeCond(),
ProvenanceCond(
regex="cli_test_demo_workers:",
name="feature_demo",
output_path=OUTPUT_DIR,
provenance_type="expanded",
),
StepFileExistsCond(
"verify",
"MERLIN_FINISHED",
"feature_demo",
OUTPUT_DIR,
params=True,
),
],
),
}