def test_swarm_notexec():
"""Error thrown if swarm not executable"""
try:
cluster = swarm.Swarm("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_swarm_exec_notexist():
"""Error thrown if swarm executable does not exist"""
try:
cluster = swarm.Swarm(os.path.join(".", "swarm"))
except NotExecutableError:
return True
else:
return False
def test_metapy_exec_notexist():
"""Error thrown if metapy.py executable does not exist"""
try:
# using swarm module here just to check it is present
cluster = swarm.Swarm(os.path.join(".", "metapy.py"))
except NotExecutableError:
return True
else:
return False
def test_swarm_exec():
"""swarm clusters test data"""
cluster = swarm.Swarm("swarm")
parameters = swarm.Parameters(t=1, d=1)
result = cluster.run(INFILE, OUTDIR, parameters)
parser = swarm.SwarmParser()
target = parser.read(TARGET)
swarms = parser.read(result.outfilename)
assert_equal(target, swarms)
def test_swarm_exec():
"""Run swarm on test data
TODO: We need a Swarm parser. Members of a group may be reported in any
order, so we cannot rely on output files being identical on all
systems, or after all runs.
"""
cluster = swarm.Swarm("swarm")
try:
shutil.rmtree(OUTDIR)
except FileNotFoundError:
pass
os.makedirs(OUTDIR, exist_ok=True)
parameters = swarm.Parameters(t=1, d=1)
result = cluster.run(INFILE, OUTDIR, parameters)
parser = swarm.SwarmParser()
target = parser.read(TARGET)
swarms = parser.read(result.outfilename)
print('\n'.join([', '.join(c.amplicons) for c in target.swarms]))
print('\n'.join([', '.join(c.amplicons) for c in swarms.swarms]))
print(target == swarms)
def test_metapy():
"""metapy instantiates with cmd-line if metapy.py is in $PATH"""
# using swarm module here just to check it is present
cluster = swarm.Swarm("metapy.py")
def test_swarm_cmd():
"""swarm instantiates and returns correct form of cmd-line"""
cluster = swarm.Swarm("swarm")
target = ' '.join(["swarm -t 1 -d 1", "-o {0}".format(OUTFILE), INFILE])
parameters = swarm.Parameters(t=1, d=1)
assert_equal(cluster.run(INFILE, OUTDIR, parameters, dry_run=True), target)
def test_swarm():
"""swarm instantiates with cmd-line if swarm is in $PATH"""
cluster = swarm.Swarm("swarm")
def test_swarm():
"""swarm executable is in $PATH"""
cluster = swarm.Swarm("swarm")
