def prep_config(
config_file: Optional[str] = None,
results: Optional[WorkFlowResult] = None,
cores: Optional[int] = None,
memory: Optional[int] = None,
protocol: Optional[str] = None,
) -> WorkFlow:
"""A helper function to load the config file for the CLI and update common options.
Note:
If not config file path is given then we load the default workflow.
"""
if config_file is not None and protocol is not None:
raise RuntimeError(
"The `protocol` and `config` options are mutually exclusive please only supply one."
)
# load the local config
if config_file is not None:
workflow = WorkFlow.parse_file(config_file)
# load config from results
elif results is not None:
workflow = WorkFlow.from_results(results=results)
elif protocol is not None:
workflow = get_workflow_protocol(workflow_protocol=protocol)
else:
# use the basic workflow if no config given, model 0
workflow = get_workflow_protocol(workflow_protocol="0")
# update the workflow
workflow.local_resources.cores = cores or workflow.local_resources.cores
workflow.local_resources.memory = memory or workflow.local_resources.memory
return workflow
def test_build_results_optional(acetone):
"""
Test building a results object with an optional stage.
"""
model0 = get_workflow_protocol(workflow_protocol="0")
result = model0._build_initial_results(molecule=acetone)
assert result.results["virtual_sites"].stage_settings is None
def test_to_file(filename, tmpdir):
"""
Test writing to file.
"""
model = get_workflow_protocol(workflow_protocol="0")
with tmpdir.as_cwd():
model.to_file(filename=filename)
def test_results_round_trip(acetone, workflow_model):
"""
Test round tripping a workflow to and from results.
"""
workflow = get_workflow_protocol(workflow_protocol=workflow_model)
results = workflow._build_initial_results(molecule=acetone)
workflow_2 = WorkFlow.from_results(results=results)
assert workflow.json() == workflow_2.json()
def test_optional_stage_skip(skip_stages):
"""
Test adding the optional stages to the skip list.
"""
# has no vsite stage
model0 = get_workflow_protocol(workflow_protocol="0")
skips = model0._get_optional_stage_skip(skip_stages=skip_stages)
assert "virtual_sites" in skips
def test_config_prep_file(tmpdir):
"""
Make sure we can load a config file.
"""
with tmpdir.as_cwd():
workflow_0 = get_workflow_protocol(workflow_protocol="0")
workflow_0.to_file(filename="workflow.json")
workflow = prep_config(config_file="workflow.json")
assert workflow.json() == workflow_0.json()
def test_build_results(acetone):
"""
Make sure we can build a results object from the workflow which captures the correct settings.
"""
# get a model with all stages present
model5a = get_workflow_protocol(workflow_protocol="5a")
result = model5a._build_initial_results(molecule=acetone)
assert result.input_molecule.json() == acetone.json()
for result in result.results.values():
assert result.status == "waiting"
def test_validate(tmpdir, run_cli):
"""
Test validating a workflow via the cli.
"""
workflow = get_workflow_protocol(workflow_protocol="0")
workflow.to_file(filename="workflow.json")
output = run_cli.invoke(validate, args=["workflow.json"])
# gaussian is not installed so make sure we have the correct error
assert output.exit_code == 1
assert isinstance(output.exception, SpecificationError)
def test_validate_workflow(acetone):
"""
Make sure workflow validation correctly checks the specification and each stage.
"""
model0 = get_workflow_protocol(workflow_protocol="0")
# change to an rdkit spec which is available always
model0.qc_options.program = "rdkit"
model0.qc_options.method = "uff"
model0.qc_options.basis = None
# assuming no psi4 or gaussian
run_order = WorkFlow.get_running_order(skip_stages=["charges"])
model0.validate_workflow(workflow=run_order, molecule=acetone)
def create(filename: str, protocol: str) -> None:
"""Create a new config file using the standard workflow and write to file."""
w = get_workflow_protocol(workflow_protocol=protocol)
w.to_file(filename=filename)