def clients(tmpdir):
c1 = util.temporary_directory(tmpdir)
c2 = util.temporary_directory(tmpdir)
server = util.temporary_directory(tmpdir)
util.initialize_bare_repository(server)
util.clone_repository(server, c1 / '.')
util.clone_repository(server, c2 / '.')
util.make_file(c1 / 'foo.json')
c1 = GitSyncer(c1)
c2 = GitSyncer(c2)
return c1, c2
def test_nup133_modeller(self):
"""Test the Nup133 example Modeller script"""
with util.temporary_directory() as td:
testdir = os.path.join(td, 'nup133')
shutil.copytree(FOXSDIR, testdir)
c = [sys.executable, 'add-missing-residues.py']
print(" ".join(c))
subprocess.check_call(c, shell=False, cwd=testdir)
expected = ['3KFO-fill.ini', '3KFO-fill.rsr', '3KFO-fill.sch']
for i in range(1, 6):
for pattern in ('3KFO-fill.D0000000%d', '3KFO-fill.V9999000%d',
'3KFO-fill.B9999000%d.pdb'):
expected.append(pattern % i)
for e in expected:
os.unlink(os.path.join(testdir, e))
def test_rpa(self):
"""Test the MultiFoXS RPA example"""
with util.temporary_directory() as td:
topdir = os.path.join(td, 'top')
testdir = os.path.join(topdir, 'multi_foxs', 'rpa')
shutil.copytree(TOPDIR, topdir)
subprocess.check_call("./multifoxs.sh", shell=True, cwd=topdir)
expected = [
'cluster_representatives.txt', 'multi_state_model_1_1_1.dat',
'multi_state_model_1_2_1.dat', 'multi_state_model_1_3_1.dat',
'ensembles_size_1.txt', 'multi_state_model_2_1_1.dat',
'multi_state_model_2_2_1.dat', 'ensembles_size_2.txt',
'multi_state_model_3_1_1.dat', 'ensembles_size_3.txt'
]
for e in expected:
os.unlink(os.path.join(testdir, e))
def filesystem(tmpdir):
root = util.temporary_directory(tmpdir)
(root / 'server').mkdir()
util.initialize_bare_repository(root / 'server')
(root / 'client_1').mkdir()
util.clone_repository(root / 'server', root / 'client_1')
(root / 'client_2').mkdir()
util.clone_repository(root / 'server', root / 'client_2')
(root / 'repo').mkdir()
util.initialize_repository(root / 'repo')
(root / 'notrepo').mkdir()
return root
def test_nup133(self):
"""Test the FoXS Nup133 example"""
with util.temporary_directory() as td:
topdir = os.path.join(td, 'top')
testdir = os.path.join(topdir, 'foxs', 'nup133')
shutil.copytree(TOPDIR, topdir)
subprocess.check_call("./foxs.sh", shell=True, cwd=topdir)
with open(os.path.join(testdir, '3KFO_23922_merge.dat')) as fh:
lines = fh.readlines()
self.assertIn('Chi^2 = 8.76', lines[1])
with open(
os.path.join(testdir,
'3KFO-fill.B99990005_23922_merge.dat')) as fh:
lines = fh.readlines()
self.assertIn('Chi^2 = 1.31', lines[1])
expected = [
'3KFO_23922_merge.dat', '3KFO-fill.B99990005_23922_merge.dat',
'fit.plt', 'profiles.plt', 'fit.png'
]
for e in expected:
os.unlink(os.path.join(testdir, e))
def database_path(data, tmpdir):
path = util.temporary_directory(tmpdir) / 'database.json'
with path.open('w') as database_file:
serialize(database_file, data)
return path