def test_parser_threadnotint(capsys):
"""
Test that when the number of threads given is not an int, it returns an error message
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align -o outdir --threads 1.2".split())
_, err = capsys.readouterr()
assert "argument --threads threads: invalid int value: 1.2" in err
def test_parser_boot_notenough(capsys):
"""
Test that when the number of threads given is a negative number, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align -b 10 -o outdir".split())
_, err = capsys.readouterr()
assert ("With IQtree, number of replicates for bootstraps must be >= 1000") in err
def test_parser_iqtree_writeboot_fast(capsys):
"""
Test that when soft is fasttree, and we ask to write bootstraps, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-o outdir -a align -B -fast".split())
_, err = capsys.readouterr()
assert "-fast option is available only for IQtree, and not compatible with '-B' and '--boot' options (bootstraps)" in err
def test_parser_fastme_memory(capsys):
"""
Test that when soft is fastme, and we ask for a memory amount, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-o outdir -a align -s fastme --mem 10GB".split())
_, err = capsys.readouterr()
assert "'--mem' option is only available for IQtree" in err
def test_parser_fasttree_writeboot(capsys):
"""
Test that when soft is fasttree, and we ask to write bootstraps, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-o outdir -a align -s fasttree -B".split())
_, err = capsys.readouterr()
assert "'-B' option is only available with FastME and IQtree" in err
def test_parser_quicktree_parallel(capsys):
"""
Test that when soft is quicktree, and e ask for more than 1 thread, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align -s quicktree --threads 2 -o outdir".split())
_, err = capsys.readouterr()
assert ("You cannot run quicktree with multiple threads. Choose another software, or remove "
"the --threads option.") 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="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align --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_iqtree_wrongmodel(capsys):
"""
Test that when soft is fasttree, and we ask for RY model, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align -o outdir -s iqtree -m toto".split())
_, err = capsys.readouterr()
assert ("toto is not an available model for iqtree. Please choose an available DNA model (see "
"-h for more details)") in err
def test_parser_quicktree_model(capsys):
"""
Test that when soft is quicktree, and we ask for a specific model, it returns the expected
error message.
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-o outdir -a align -s quicktree -m F84".split())
_, err = capsys.readouterr()
assert ("Quicktree only runs the NJ algorithm. You cannot choose a DNA substitution "
"model.") 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="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "-a align --threads {} -o outdir".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="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
tree.parse(parser, "".split())
_, err = capsys.readouterr()
assert "usage: " in err
assert "-a ALIGNMENT -o OUTDIR" in err
assert "[-s {fasttree,fastme,quicktree,iqtree,iqtree2}] [-b BOOT]" in err
assert "[--threads THREADS] [-m MODEL]" in err
assert "[-B] [--mem MEMORY" in err
assert "[-v]" in err
assert "[-q] [-h]" in err
assert "the following arguments are required: -a, -o" in err
def test_parser_default():
"""
Test that when giving only align file, it returns the expected values for all other arguments
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
args = tree.parse(parser, "-a align -o outdir".split())
assert args.alignment == "align"
assert args.boot is None
assert args.outdir == "outdir"
assert args.soft == "iqtree2"
assert args.model == "GTR"
assert args.write_boot is False
assert args.threads == 1
assert args.verbose == 0
assert args.quiet == False
def test_parser_fasttree_jc():
"""
Test that when giving align file, using fasttree, with JC model, it returns expected
values for all arguments
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
args = tree.parse(parser, "-a align -o outdir -s fasttree -m JC".split())
assert args.alignment == "align"
assert args.boot is None
assert args.outdir == "outdir"
assert args.soft == "fasttree"
assert args.model == ""
assert args.write_boot is False
assert args.threads == 1
assert args.verbose == 0
assert args.quiet == False
def test_parser_threads_ok():
"""
Test that when giving align file and a correct number of threads (positive int), it returns the
expected values for all arguments
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
import multiprocessing
nb = multiprocessing.cpu_count()
args = tree.parse(parser, f"-a align -o outdir --threads {nb}".split())
assert args.alignment == "align"
assert args.boot is None
assert args.outdir == "outdir"
assert args.soft == "iqtree2"
assert args.model == "GTR"
assert args.write_boot is False
assert args.threads == nb
assert args.verbose == 0
assert args.quiet == False
def test_parser_all_threads():
"""
Test that when giving alignment file, and 0 to use all threads, it returns expected values
for all arguments
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
args = tree.parse(parser, "-a align -o outdir --threads 0".split())
assert args.alignment == "align"
assert args.boot is None
assert args.outdir == "outdir"
assert args.soft == "iqtree2"
assert args.model == "GTR"
assert args.write_boot is False
assert args.threads == nb
assert args.verbose == 0
assert args.quiet == False
