def test_parser_thread_notint(capsys):
"""
Test that when the number of threads given is not an int, it returns an error message
"""
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
with pytest.raises(SystemExit):
align.parse(
parser,
"-l listgenome -n dname -d dbpath -o outdir --threads 1.5".split())
_, err = capsys.readouterr()
assert "argument --threads threads: invalid int value: 1.5" in err
def test_parser_thread_neg(capsys):
"""
Test that when the number of threads given is a negative number, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
with pytest.raises(SystemExit):
align.parse(
parser,
"-l listgenome -n dname -d dbpath -o outdir --threads -5".split())
_, err = capsys.readouterr()
assert (
"Please provide a positive number of threads (or 0 for all threads): "
"Invalid value: -5") in err
def test_parser_thread_toomany(capsys):
"""
Test that when the number of threads given is higher than the total number of threads,
it returns the expected error message
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
with pytest.raises(SystemExit):
align.parse(
parser, "-l listgenome -n dname -d dbpath -o outdir "
"--threads {}".format(nb + 3).split())
_, err = capsys.readouterr()
assert ("You have {} threads on your computer, you cannot ask for more: "
"invalid value: {}".format(nb, nb + 3)) in err
def test_parser_noarg(capsys):
"""
Test that when the script is called without any argument, an error message appears,
indicating the required arguments.
"""
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
with pytest.raises(SystemExit):
align.parse(parser, "".split())
_, err = capsys.readouterr()
assert "usage: " in err
assert "-c COREPERS -l LIST_GENOMES -n DATASET_NAME -d DBPATH" in err
assert "-o OUTDIR" in err
assert "[--threads THREADS] [-F] [-P] [-v] [-q] [-h]" in err
assert "[-h]" in err
assert "the following arguments are required: -c, -l, -n, -d, -o" in err
def test_parser_default():
"""
Test that when run with the minimum required arguments, all default values are
as expected.
"""
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
options = align.parse(
parser, "-c cp -l listgenome -n dname -d dbpath -o outdir".split())
assert options.corepers == "cp"
assert options.list_genomes == "listgenome"
assert options.dataset_name == "dname"
assert options.dbpath == "dbpath"
assert options.outdir == "outdir"
assert options.threads == 1
assert options.force is False
assert options.verbose == 0
assert options.quiet is False
assert options.prot_ali is False
def test_parser_all_ok():
"""
Test that when all arguments given are ok, it builds expected parser
"""
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
options = align.parse(
parser, "-c cp -l listgenome -n dname -d dbpath -o outdir "
"--threads 1 -P".split())
assert options.corepers == "cp"
assert options.list_genomes == "listgenome"
assert options.dataset_name == "dname"
assert options.dbpath == "dbpath"
assert options.outdir == "outdir"
assert options.threads == 1
assert options.force is False
assert options.verbose == 0
assert options.quiet is False
assert options.prot_ali is True
def test_parser_allthreads():
"""
Test that when run with 0 for --threads option, it returns the total number of threads in
computer
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Align families",
add_help=False)
align.build_parser(parser)
options = align.parse(
parser, "-c cp -l listgenome -n dname -d dbpath -o outdir "
"--threads 0".split())
assert options.corepers == "cp"
assert options.list_genomes == "listgenome"
assert options.dataset_name == "dname"
assert options.dbpath == "dbpath"
assert options.outdir == "outdir"
assert options.threads == nb
assert options.force is False
assert options.verbose == 0
assert options.quiet is False
assert options.prot_ali is False