def test_wrong_clust_mode(capsys):
"""
Test that when the given cluster mode does not exist, it returns the expected error message
"""
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(
parser, "-l lstinfo -n TEST4 -d dbpath -i 0.8 -o od -c 3".split())
_, err = capsys.readouterr()
assert "argument -c: invalid choice: 3 (choose from 0, 1, 2)" in err
def test_perc_id_nonum(capsys):
"""
Test that when the given percentage of identity is not a number, it returns the
expected error.
"""
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(
parser, "-l lstinfo -n TEST4 -d dbpath -i toto -o outdir".split())
_, err = capsys.readouterr()
assert "argument -i percentage_id: invalid float value: toto" in err
def test_big_perc_id(capsys):
"""
Test that when the given percentage of identity is greater than 1, it returns the
expected error.
"""
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(parser,
"-l lstinfo -n TEST4 -d dbpath -i 2 -o outdir".split())
_, err = capsys.readouterr()
assert "The minimum %% of identity must be in [0, 1]. Invalid value: 2" in err
def test_thread_neg(capsys):
"""
Test that when the given number of threads is negative,
it returns the expected error message.
"""
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(
parser, "-l lstinfo -n TEST4 -d dbpath -o od --threads -1".split())
_, err = capsys.readouterr()
assert "Please provide a positive number of threads (or 0 for all threads)" in err
def test_thread_no_int(capsys):
"""
Test that when the given number of threads is not an int, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(
parser,
"-l lstinfo -n TEST4 -d dbpath -o od --threads 1.5".split())
_, err = capsys.readouterr()
assert "argument --threads threads: invalid int value: 1.5" in err
def test_thread_too_many(capsys):
"""
Test that when the given number of threads is greater than the number of available threads,
it returns the expected error message.
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(
parser,
f"-l lstinfo -n TEST4 -d dbpath -o od --threads {nb*10}".split())
_, err = capsys.readouterr()
assert ("You have {} threads on your computer, you cannot ask for more: "
"invalid value: {}").format(nb, nb * 10) 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="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
with pytest.raises(SystemExit):
pangenome.parse(parser, "".split())
_, err = capsys.readouterr()
assert "usage: " in err
assert "-l LSTINFO_FILE -n DATASET_NAME -d DBPATH" in err
assert "[-i MIN_ID]" in err
assert " -o OUTDIR" in err
assert "[-f OUTFILE] [-c {0,1,2}]" in err
assert "[-s SPEDIR] [--threads THREADS] [-v]" in err
assert "[-q] [-h]" in err
assert "the following arguments are required: -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="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
options = pangenome.parse(parser,
"-l lstinfo -n TEST4 -d dbpath -o od".split())
assert options.lstinfo_file == "lstinfo"
assert options.dataset_name == "TEST4"
assert options.dbpath == "dbpath"
assert options.min_id == 0.8
assert options.outdir == "od"
assert options.clust_mode == 1
assert not options.spedir
assert options.threads == 1
assert not options.outfile
assert options.verbose == 0
assert not options.quiet
def test_parser_all_threads():
"""
Test that when run with the minimum required arguments, + '0' for the thread number,
all default values are as expected, and the number of threads is equal to the total
number of threads.
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Do pangenome",
add_help=False)
pangenome.build_parser(parser)
options = pangenome.parse(
parser, "-l lstinfo -n TEST4 -d dbpath -o od --threads 0".split())
assert options.lstinfo_file == "lstinfo"
assert options.dataset_name == "TEST4"
assert options.dbpath == "dbpath"
assert options.min_id == 0.8
assert options.outdir == "od"
assert options.clust_mode == 1
assert not options.spedir
assert options.threads == nb
assert not options.outfile
assert options.verbose == 0
assert not options.quiet