def main(args):
if args.test:
import run_tests
run_tests.run()
else:
cm = charmatrix.charmatrix(args.datafile)
cm.print_summary()
if args.algorithm == 'exhaustive':
import exhaustive
trees = exhaustive.exhaustive_search(cm)
for tree in trees:
print tree.to_string(cm)
elif args.algorithm in ('bnb', 'branch-and-bound'):
import branchnbound
trees = branchnbound.branchnbound_search(cm)
for tree in trees:
print tree.to_string(cm)
else:
import parallel_search
comm = parallel_search.communicator(cm, args.time, args.interval)
if args.algorithm == 'nni':
import nni
nni.nni_search(cm, comm)
elif args.algorithm == 'spr':
import spr
spr.spr_search(cm, comm)
elif args.algorithm == 'tbr':
import tbr
tbr.tbr_search(cm, comm)
elif args.algorithm == 'mixed':
import mixed
mixed.mixed_search(cm, comm)
def run(self):
matches = []
for root, dirnames, filenames in os.walk('tests'):
for filename in fnmatch.filter(filenames, '*.py'):
matches.append(os.path.join(root, filename).split('.py')[0])
[importlib.import_module('.'.join(m.split('/'))) for m in matches]
run_tests.run()
def test_countFP_anon():
paramfile = "params_anonadds_CountFPMatch_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[8,168])
results2, networkspec = run(paramfile,netfile)
assert (results == results2)
def test_countFP_anon():
paramfile = "params_anonadds_CountFPMatch_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[8,168])
results2, networkspec = run(paramfile,netfile)
assert (results == results2)
def test_patternmatch_path_wavepool():
paramfile = "params_patternmatch_path_domaingraph_wavepool.json"
results, networkspec = run(paramfile,"good_wavepool.txt","query_results_PathMatchInDomainGraph_wt1_microarray_coregenes_lifepoints_interpol_trim.json")
print(networkspec)
print(results)
assert(results=={'SWI4 : (NDD1)(~YOX1) : E\nHCM1 : SWI4 : E\nNDD1 : HCM1 : E\nYOX1 : SWI4 : E': [[0.0, 0, 14], [0.01, 8, 14], [0.05, 5, 14]]})
results, networkspec = run(paramfile,"good_wavepool.txt","query_results_PathMatchInStableFullCycle_wt1_microarray_coregenes_lifepoints_interpol_trim.json")
print(networkspec)
print(results)
assert(results=={'SWI4 : (NDD1)(~YOX1) : E\nHCM1 : SWI4 : E\nNDD1 : HCM1 : E\nYOX1 : SWI4 : E': [[0.0, 0, 2, 14], [0.01, 2, 2, 14], [0.05, 1, 2, 14]]})
def test_patternmatch_path():
paramfile = "params_patternmatch_path_domaingraph_X1X2X3.json"
results, networkspec = run(paramfile,netfile,"query_results_PathMatchInDomainGraph_no_time_series_file.json")
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[[0.0, 58, 168], [0.1, 80, 168]])
def test_patternmatch_stable():
paramfile = "params_patternmatch_stable_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[[0.0, 40, 168], [0.1, 54, 168]])
def test_patternmatch_path():
paramfile = "params_patternmatch_path_domaingraph_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[[0.0, 58, 168], [0.1, 80, 168]])
def test_patternmatch2():
paramfile = "params_empty2.json"
results, networkspec = run(
paramfile, netfile,
"query_results_PathMatchInDomainGraph_no_time_series_file.json")
print(results)
assert (len(results) == 3)
def test_countFC():
paramfile = "params_CountStableFC_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[76,168])
def test_patternmatch_stable():
paramfile = "params_patternmatch_stable_X1X2X3.json"
results, networkspec = run(paramfile,netfile,"query_results_CycleMatchInStableMorseSet_no_time_series_file.json")
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results=={'X1 : (X1)(~X3) : E\nX2 : (X1 + X3) : E\nX3 : (X1 + X2) : E\n': [[0.0, 205, 2352], [0.1, 317, 2352]], 'X1 : (X1)(~X3) : E\nX2 : (X1) : E\nX3 : (X1 + X2) : E\n': [[0.0, 40, 168], [0.1, 54, 168]], 'X1 : (X1)(~X3) : E\nX2 : (X3)(~X1) : E\nX3 : (X1 + X2) : E\n': [[0.0, 0, 2352], [0.1, 0, 2352]]})
def test_countFC():
paramfile = "params_CountStableFC_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
print(results)
assert(len(results)==3)
assert(networkspec in results)
assert(results[networkspec]==[76,168])
def test_patternmatch_path_badwavepool():
paramfile = "params_patternmatch_path_domaingraph_badwavepool.json"
with warnings.catch_warnings(record=True) as w:
# Trigger a warning.
_ = run(paramfile,"bad_wavepool.txt")
# Verify some things
print(w)
assert(len(w) == 0)
def test_patternmatch_path_badwavepool():
paramfile = "params_patternmatch_path_domaingraph_badwavepool.json"
with warnings.catch_warnings(record=True) as w:
# Trigger a warning.
_ = run(paramfile,"bad_wavepool.txt","query_results_PathMatchInDomainGraph_wt1_microarray_coregenes_lifepoints_interpol_trim.json")
# Verify some things
print(w)
assert(len(w) == 0)
def test_countFP_remove_with_filter():
paramfile = "params_remove_CountFPMatch_with_filter_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
print(results)
assert(len(results)==6)
assert(networkspec in results)
assert(results[networkspec]==[8,168])
assert(results=={'X1 : (X1)(~X3) : E\nX2 : (X1) : E\nX3 : (X2) : E\n': [4, 14], 'X1 : (X1)(~X3) : E\nX2 : (X1) : E\nX3 : (X1 + X2 + x4) : E\nx4 : (X1) : E\n': [120, 4968], 'X1 : (X1)(~X3) : E\nX2 : (X1) : E\nX3 : (X1 + X2) : E\n': [8, 168], 'X1 : (X1 + X3) : E\nX2 : (X1) : E\nX3 : (X1 + X2) : E\n': [24, 168], 'X1 : (X1)(~X3) : E\nX2 : (X3) : E\nX3 : (X1 + X2 + x4) : E\nx4 : (~X2) : E\n': [0, 4872], 'X1 : (X1)(~X3) : E\nX2 : (X1)(~X3) : E\nX3 : (X1 + X2) : E\n': [48, 2352]})
def worker(u, i):
username = getusername(u)
# if even, do write first, else do reads first
query = ["run_tests.py", username]
query.extend(task)
query.extend([getuserfile(basehtml, u, i),getuserfile(basecookie, u, i)])
if u % 2 == 0:
query.append("1") # do reads first
else:
query.append("0") # do writes first
assert len(query) == 10, "wrong number of arguments"
stat.set(u)
assert stat.worker != 0, "not a worker :-("
res = run_tests.run(query,stat)
workerFinish()
'arguments': '$IN_FILE$'
}
directory = ''
if ADDRESS_STYLE == 'PARENT':
folder = input(colored('Input folder name: ', 'blue'))
if folder != '':
folder = '/' + folder + '/'
path = Path(__file__).resolve().parents[1].as_posix()
directory = path + folder
elif ADDRESS_STYLE == 'CURRENT':
folder = input(colored('Input folder name: ', 'blue'))
if folder != '':
folder = '/' + folder + '/'
path = Path(__file__).resolve().parents[0].as_posix()
directory = path + folder
elif ADDRESS_STYLE == 'ABSOLUTE':
directory = input(colored('Input folder\'s absolute path: ', 'blue'))
if directory[-1] != '/':
directory += '/'
if directory != '':
config = settings.open_settings(default_settings=DEFAULT_SETTINGS, directory=directory)
files = find_file.find_files(directory=directory)
if not build.build(files, directory=directory, settings=config):
run_tests.run(directory=directory, settings=config)
if config['style_check']:
style_check.check(files, directory=directory)
if config['cleanup']:
cleanup.cleanup(directory=directory, settings=config)
def test_patternmatch_path_wavepool():
paramfile = "params_patternmatch_path_domaingraph_wavepool.json"
results, networkspec = run(paramfile,"good_wavepool.txt")
print(networkspec)
print(results)
assert(results=={'SWI4 : (NDD1)(~YOX1) : E\nHCM1 : SWI4 : E\nNDD1 : HCM1 : E\nYOX1 : SWI4 : E': [[0.0, 0, 14], [0.01, 8, 14], [0.05, 5, 14]]})
#!/usr/bin/env python2.7
import run_tests
run_tests.run("examples", "prod")
def test_countFP_remove():
paramfile = "params_remove_CountFPMatch_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
assert(len(results)==6)
assert(networkspec in results)
assert(results[networkspec]==[8,168])
def test_countFP_remove():
paramfile = "params_remove_CountFPMatch_X1X2X3.json"
results, networkspec = run(paramfile,netfile)
assert(len(results)==6)
assert(networkspec in results)
assert(results[networkspec]==[8,168])
def run_tests(self):
import shlex
from run_tests import run
run(args=[shlex.split(self.runtests_args)])
def run_tests(self):
import shlex
from run_tests import run
run(args=[shlex.split(self.runtests_args)])