def test_creates_substitution():
cmd = "test {var1} {creates}"
creates = "test.out"
variables = {"var1": "1.0"}
command = Command(cmd=cmd, creates=creates, variables=variables)
assert command.cmd == [cmd.format(creates=creates, **variables)]
assert str(command) == cmd.format(creates=creates, **variables)
def test_requires_substitution():
cmd = "test {var1} {requires}"
requires = "test.in"
variables = {"var1": "1.0"}
command = Command(cmd=cmd, requires=requires, variables=variables)
assert command.cmd == [cmd.format(requires=requires, **variables)]
assert str(command) == cmd.format(requires=requires, **variables)
def test_command_equality():
"""Test that equality compares classes not just values."""
class Subcommand(Command):
def __init__(self, cmd):
super().__init__(cmd)
assert Subcommand("test") != Command("test")
def test_job_length_depends(tmp_dir):
file = tmp_dir / "test.txt"
file.write_text("test")
assert file.exists()
job = Job([Command("echo", creates="test.txt")],
directory=tmp_dir,
use_dependencies=True)
assert len(job) == 0
def test_dependencies(tmp_dir):
command = Command(cmd="echo contents > {creates}", creates="test")
jobs = [Job([command], directory=Path(tmp_dir), use_dependencies=True)]
create_file = tmp_dir / "test"
create_file.write_text("success")
run_bash_jobs(jobs, tmp_dir)
assert "success" in create_file.read_text()
jobs[0].use_dependencies = False
run_bash_jobs(jobs, tmp_dir)
assert "contents" in create_file.read_text()
def test_dependencies_list(tmp_dir):
commands = [
Command(cmd=f"echo contents{i} > {{creates}}", creates=f"test{i}")
for i in range(5)
]
jobs = [Job(commands, directory=Path(tmp_dir), use_dependencies=True)]
create_files = [tmp_dir / f"test{i}" for i in range(5)]
create_files[1].write_text("success")
run_bash_jobs(jobs, tmp_dir)
for i in range(5):
if i == 1:
assert "success" in create_files[i].read_text()
else:
assert f"contents{i}" in create_files[i].read_text()
def test_command_substitution():
cmd = "test {var1}"
variables = {"var1": "1.0"}
command = Command(cmd=cmd, variables=variables)
assert command.cmd == [cmd.format(**variables)]
assert str(command) == cmd.format(**variables)
def test_command_simple():
cmd = "test"
command = Command(cmd=cmd)
assert command.cmd == [cmd]
assert str(command) == cmd
def test_default_files(scheduler, expected):
assert create_scheduler_file(scheduler,
Job([Command("echo 1")])) == expected
def test_get_variables_empty():
result = Command("test").get_variables()
assert result == set()
def test_get_variables(variables):
format_string = "{" + "}{".join(variables) + "}"
result = Command(format_string, {i: None
for i in variables}).get_variables()
print(format_string)
assert sorted(set(variables)) == sorted(result)
def _create_jobs(command: str) -> Iterator[Job]:
yield Job([Command(command)])
def test_dry_run(tmp_dir):
command = Command(cmd="echo contents > {creates}", creates="test")
jobs = [Job([command], directory=Path(tmp_dir))]
create_file = tmp_dir / "test"
run_bash_jobs(jobs, tmp_dir, dry_run=True)
assert not create_file.exists()
def test_hashable_command():
cmd = "test"
command = Command(cmd=cmd)
assert hash(command) == hash((cmd, ))
cmd_dict = {command: "Success"}
assert cmd_dict.get(command) == "Success"
def test_command_init():
Command("test")
with pytest.raises(ValueError):
Command("{test}")
with pytest.raises(ValueError):
Command("{test1} {test2}", variables={"test1": ""})
def test_uniqueify_command():
cmd_list = [Command(cmd="test") for _ in range(5)]
unique_commands = uniqueify(cmd_list)
assert len(unique_commands) == 1
def test_job_length():
job = Job([Command("echo")])
assert len(job) == 1
def test_cmd_list():
command = Command(cmd=["test"] * 5)
assert command.cmd == ["test"] * 5
assert str(command) == " && ".join(["test"] * 5)
#SBATCH --time 1:00
SLURM_ARRAY_TASK_ID=0
cd "$SLURM_SUBMIT_DIR"
COMMAND=( \\
"echo 1" \\
)
${COMMAND[$SLURM_ARRAY_TASK_ID]}
"""
@pytest.mark.parametrize("job, result", [
(Job([Command("echo 1")]), '( \\\n"echo 1" \\\n)'),
(
Job([Command("echo 1"), Command("echo 2")]),
'( \\\n"echo 1" \\\n"echo 2" \\\n)',
),
],
ids=["single", "list"])
def test_jobs_as_bash_array(job, result):
assert job.as_bash_array() == result
@pytest.mark.parametrize('scheduler, expected', [('pbs', DEFAULT_PBS),
('slurm', DEFAULT_SLURM)],
ids=["PBS", "SLURM"])
def test_default_files(scheduler, expected):
assert create_scheduler_file(scheduler,