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Merge pull request #2468 from e-kwsm/unittest

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test(python): modernize use of asserts
This commit is contained in:
Geoff Hutchison
2022-06-09 18:31:34 -04:00
committed by GitHub
parent cad234da89 0f4af753d4
commit 7ab11297bb
8 changed files with 79 additions and 78 deletions
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scripts/python/examples/dalke_test.py
+34 -34
View File
@@ -22,13 +22,14 @@ def testfile(name):
class MyTestCase(unittest.TestCase):
def assertClose(self, val, expect):
if expect > 0:
self.assertTrue((expect * 0.9999) < val < (expect * 1.0001), val)
else:
self.assertTrue((expect * 1.0001) < val < (expect * 0.9999), val)
a, b = 0.9999, 1.0001
if expect < 0:
a, b = b, a
self.assertLess(expect * a, val, val)
self.assertLess(val, expect * b, val)
def assertZero(self, val):
self.assertTrue(abs(val) < 0.00001, val)
self.assertLess(abs(val), 0.00001, val)
# Make a temporary directory for use during the "with" context block.
@@ -137,8 +138,7 @@ class TestIO(MyTestCase):
conv.CloseOutFile()
lines = open(tempdir("blah.smi"), "U").readlines()
self.assertTrue(lines[0] == "CCO\t#1\n" or
lines[0] == "OCC\t#1\n", repr(lines[0]))
self.assertIn(lines[0], ["CCO\t#1\n", "OCC\t#1\n"], repr(lines[0]))
self.assertTrue(lines[1] == "[NH4+]\tmol2\n", repr(lines[1]))
def test_write_sdf(self):
@@ -199,28 +199,28 @@ class TestPlugins(MyTestCase):
def test_known_types(self):
for name in TestPlugins.known_types:
s = ob.OBPlugin.ListAsString(name)
self.assertFalse("not a recognized" in s, s)
self.assertNotIn("not a recognized", s, s)
v = ob.vectorString()
ob.OBPlugin.ListAsVector(name, None, v)
self.assertTrue(len(v) > 0, list(v))
self.assertGreater(len(v), 0, list(v))
def test_as_string(self):
s = ob.OBPlugin.ListAsString("fingerprints")
self.assertTrue("FP2" in s, s)
self.assertTrue("FP3" in s, s)
self.assertTrue("MACCS" in s, s)
self.assertIn("FP2", s, s)
self.assertIn("FP3", s, s)
self.assertIn("MACCS", s, s)
def test_as_string_unknown_type(self):
s = ob.OBPlugin.ListAsString("qwerty.shrdlu")
self.assertTrue("\nfingerprints\n" in s, s)
self.assertTrue("\nloaders\n" in s, s)
self.assertIn("\nfingerprints\n", s, s)
self.assertIn("\nloaders\n", s, s)
def test_as_vector(self):
v = ob.vectorString()
ob.OBPlugin.ListAsVector("formats", None, v)
formats = set(v)
self.assertTrue("smiles -- SMILES format" in formats, formats)
self.assertIn("smiles -- SMILES format", formats, formats)
## def test_list(self):
## # XXX GRR! To capture requires passing a 3rd argument which is a std:ostream
@@ -243,7 +243,7 @@ class TestFingerprints(MyTestCase):
("FP4", "SMARTS patterns specified in the file SMARTS_InteLigand.txt" + P),
("MACCS", "SMARTS patterns specified in the file MACCS.txt" + P)):
fingerprinter = ob.OBFingerprint.FindFingerprint(name)
self.assertFalse(fingerprinter is None)
self.assertIsNotNone(fingerprinter)
self.assertEqual(fingerprinter.GetID(), name)
self.assertEqual(fingerprinter.Description(), expected_description)
# Which supported platforms have non-32-bit integers?
@@ -489,8 +489,8 @@ class TestSmarts(MyTestCase):
self.assertEqual(pat.Match(mol, v), 1)
self.assertEqual(len(v), 2)
results = list(v)
self.assertTrue((5, 6, 7) in results, results)
self.assertTrue((1, 6, 7) in results, results)
self.assertIn((5, 6, 7), results, results)
self.assertIn((1, 6, 7), results, results)
def test_vector_match_with_one_unique_hit(self):
mol = parse_smiles("c1ccccc1O")
@@ -507,7 +507,7 @@ class TestSmarts(MyTestCase):
self.assertEqual(pat.Match(mol, v, ob.OBSmartsPattern.Single), 1)
self.assertEqual(len(v), 1)
result = v[0]
self.assertTrue(result == (5, 6, 7) or result == (1, 6, 7), result)
self.assertIn(result, ((5, 6, 7), (1, 6, 7)), result)
def test_vector_match_with_all_hits(self):
mol = parse_smiles("c1ccccc1O")
@@ -548,21 +548,21 @@ class TestDescriptors(MyTestCase):
#mol.AddHydrogens() # doesn't change the results
logp = calc_logp.Predict(mol)
self.assertTrue(abs(logp - 1.4008) <= 0.0001, logp)
self.assertLessEqual(abs(logp - 1.4008), 0.0001, logp)
def test_tpsa(self):
calc_tpsa = ob.OBDescriptor.FindType("TPSA")
mol = parse_smiles("Oc1ccccc1OC")
#mol.AddHydrogens() # doesn't change the results
tpsa = calc_tpsa.Predict(mol)
self.assertTrue(abs(tpsa - 29.460) <= 0.001, tpsa)
self.assertLessEqual(abs(tpsa - 29.460), 0.001, tpsa)
def test_mr(self):
calc_mr = ob.OBDescriptor.FindType("MR")
mol = parse_smiles("Oc1ccccc1OC")
#mol.AddHydrogens() # doesn't change the results
mr = calc_mr.Predict(mol)
self.assertTrue(abs(mr - 34.957) <= 0.001, mr)
self.assertLessEqual(abs(mr - 34.957), 0.001, mr)
def test_gotta_try_them_all(self):
v = ob.vectorString()
@@ -571,7 +571,7 @@ class TestDescriptors(MyTestCase):
for term in v:
name = term.split()[0]
prop_calculator = ob.OBDescriptor.FindType(name)
self.assertFalse(prop_calculator is None, "Could not find " + name)
self.assertIsNotNone(prop_calculator, "Could not find " + name)
prop_calculator.Predict(mol)
@@ -702,9 +702,9 @@ class TestAtomAndBond(MyTestCase):
mol = parse_smiles("[12CH4-]")
mol.SetTitle("Spam!")
atom = mol.GetAtom(0)
self.assertTrue(atom is None, "GetAtom(0)")
self.assertIsNone(atom, "GetAtom(0)")
atom = mol.GetAtom(1)
self.assertTrue(atom is not None, "GetAtom(1)")
self.assertIsNotNone(atom, "GetAtom(1)")
self.assertEqual(atom.GetAtomicNum(), 6)
self.assertEqual(atom.GetIsotope(), 12)
@@ -788,7 +788,7 @@ class TestAtomAndBond(MyTestCase):
self.assertClose(atom.GetPartialCharge(), -0.25658)
self.assertTrue(atom.GetParent().GetTitle() == mol.GetTitle(),
self.assertEqual(atom.GetParent().GetTitle(), mol.GetTitle(),
"parent is mol")
self.assertFalse(atom.IsAromatic())
@@ -816,7 +816,7 @@ class TestAtomAndBond(MyTestCase):
C = mol.GetAtom(1)
N = mol.GetAtom(2)
# XXX Why do bonds starts from 0 and not 1
self.assertTrue(mol.GetBond(1) is None)
self.assertIsNone(mol.GetBond(1))
bond = mol.GetBond(0)
self.assertEqual(bond.GetLength(), 0.0)
@@ -1041,7 +1041,7 @@ class TestAtomAndBond(MyTestCase):
class SpectorphoreTest(MyTestCase):
def assertWithin_0_001(self, val, expect):
assert val > 0
self.assertTrue(abs(val - expect) < 0.001, val)
self.assertLess(abs(val - expect), 0.001, val)
def _make_mol(self):
mol = ob.OBMol()
def new_atom(eleno):
@@ -1147,19 +1147,19 @@ class TestForceFields(MyTestCase):
# Huh. The plugin system uses case-insensitive lookup
names = [x.split()[0].lower() for x in v]
self.assertTrue("gaff" in names, names)
self.assertTrue("mmff94" in names, names)
self.assertTrue("uff" in names, names)
self.assertIn("gaff", names, names)
self.assertIn("mmff94", names, names)
self.assertIn("uff", names, names)
pFF1 = ob.OBForceField.FindForceField("GAFF")
pFF2 = ob.OBForceField.FindForceField("GafF")
self.assertFalse(pFF1 is None)
self.assertFalse(pFF2 is None)
self.assertIsNotNone(pFF1)
self.assertIsNotNone(pFF2)
self.assertEqual(pFF1.GetID(), pFF2.GetID())
def _test_energies(self, plugin_name, expected_results, filename = None):
pFF = ob.OBForceField.FindForceField(plugin_name)
self.assertFalse(pFF is None, "Cannot load " + plugin_name)
self.assertIsNotNone(pFF, "Cannot load " + plugin_name)
if filename is None:
filename = testfile("forcefield.sdf")
scripts/python/examples/testpybel.py
+9 -8
View File
@@ -256,7 +256,7 @@ M END
# (even those that are supposed to be immune like TPSA)
self.mols[1].addh()
desc = self.mols[1].calcdesc()
self.assertTrue(len(desc) > 3)
self.assertGreater(len(desc), 3)
self.assertAlmostEqual(desc[self.tpsaname], 26.02, 2)
self.assertRaises(ValueError, self.RFdesctest)
@@ -273,24 +273,25 @@ M END
newvalues = {'hey':'there', 'yo':1}
data.update(newvalues)
self.assertEqual(data['yo'], '1')
self.assertTrue('there' in data.values())
self.assertIn('there', data.values())
def testMDglobalaccess(self):
"""Check out the keys"""
data = self.head[0].data
self.assertFalse('Noel' in data)
self.assertNotIn('Noel', data)
self.assertEqual(len(data), len(self.datakeys))
for key in data:
self.assertEqual(key in self.datakeys, True)
self.assertIn(key, self.datakeys)
r = repr(data)
self.assertTrue(r[0]=="{" and r[-2:]=="'}", r)
self.assertEqual(r[0], "{", r)
self.assertEqual(r[-2:], "'}", r)
def testMDdelete(self):
"""Delete some keys"""
data = self.head[0].data
self.assertTrue('NSC' in data)
self.assertIn('NSC', data)
del data['NSC']
self.assertFalse('NSC' in data)
self.assertNotIn('NSC', data)
data.clear()
self.assertEqual(len(data), 0)
@@ -358,7 +359,7 @@ class TestPybel(TestToolkit):
def testMDcomment(self):
"""Mess about with the comment field"""
data = self.head[0].data
self.assertEqual('Comment' in data, True)
self.assertIn('Comment', data)
self.assertEqual(data['Comment'], 'CORINA 2.61 0041 25.10.2001')
data['Comment'] = 'New comment'
self.assertEqual(data['Comment'], 'New comment')
test/testbabel.py
+8 -8
View File
@@ -115,15 +115,15 @@ class TestOBabel(BaseTest):
"""Ensure that this does not segfault (PR#1818)"""
self.canFindExecutable("obabel")
output, error = run_exec("obabel -i")
self.assertTrue(len(output) > 1, "Did not generate output")
self.assertTrue(len(error) > 1, "Did not generate error message")
self.assertGreater(len(output), 1, "Did not generate output")
self.assertGreater(len(error), 1, "Did not generate error message")
def testShortOutfileName(self):
# Test that -O can handle short file names
# if not the command will show warning on 2D coords
self.canFindExecutable("obabel")
_, errormsg = run_exec("CCC", "obabel -ismi -omol -Otf --gen2D")
self.assertFalse("No 2D or 3D coordinates" in errormsg)
self.assertNotIn("No 2D or 3D coordinates", errormsg)
def testSMItoInChI(self):
self.canFindExecutable("obabel")
@@ -142,7 +142,7 @@ class TestOBabel(BaseTest):
errors = ["reactant", "agent", "product"]
for rsmi, error in zip(data, errors):
output, errormsg = run_exec('obabel -:%s -irsmi -orsmi' % rsmi)
self.assertTrue(error in errormsg)
self.assertIn(error, errormsg)
def sort(self, rsmi):
# TODO: Change OBMol.Separate to preserve the order. This
@@ -164,10 +164,10 @@ class TestOBabel(BaseTest):
"c%(000001)ccccc%(000001)", "c%(51)ccccc%(15)"]
for smi in data:
output, error = run_exec("obabel -:%s -osmi" % smi)
self.assertTrue("0 molecules converted" in error)
self.assertIn("0 molecules converted", error)
# Now test writing of %(NNN) notation
output, error = run_exec("obabel %s -osmi" % self.getTestFile("102Uridine.smi"))
self.assertTrue("%(100)" in output)
self.assertIn("%(100)", output)
def testPDBQT(self):
self.canFindExecutable("obabel")
@@ -250,7 +250,7 @@ TORSDOF 5
else:
os.environ.pop("BABEL_LIBDIR")
self.assertTrue('BABEL_LIBDIR' in msg)
self.assertIn('BABEL_LIBDIR', msg)
def testCOFtoCAN(self):
self.canFindExecutable("obabel")
@@ -430,7 +430,7 @@ TORSDOF 5
other mol2 test here'''
mol2file = self.getTestFile('5sun_protein.mol2')
outputerr = run_exec( "obabel -imol2 %s -osdf" % mol2file)
self.assertTrue(len(outputerr[0]) > 0, "Did not generate output")
self.assertGreater(len(outputerr[0]), 0, "Did not generate output")
def testXYZph(self):
'''This is a bug report from Stefano Forli on the openbabel-devel list.
test/testbindings.py
+16 -16
View File
@@ -39,7 +39,7 @@ except ImportError:
class PythonBindings(unittest.TestCase):
def setUp(self):
self.assertTrue(ob is not None, "Failed to import the openbabel module")
self.assertIsNotNone(ob, "Failed to import the openbabel module")
class TestPythonBindings(PythonBindings):
def testSimple(self):
@@ -51,7 +51,7 @@ class TestPythonBindings(PythonBindings):
class PybelWrapper(PythonBindings):
def testDummy(self):
self.assertTrue(pybel is not None, "Failed to import the Pybel module")
self.assertIsNotNone(pybel, "Failed to import the Pybel module")
class TestSuite(PythonBindings):
@@ -208,7 +208,7 @@ $end"""
self.assertEqual(res, atomorder)
mol = pybel.readstring("smi", "CC")
mol.write("can")
self.assertFalse("SMILES Atom Order" in mol.data)
self.assertNotIn("SMILES Atom Order", mol.data)
def testECFP(self):
data = [
@@ -224,7 +224,7 @@ $end"""
ecfp2 = mol.calcfp("ecfp2").bits
self.assertEqual(len(ecfp2), numB)
for bit in ecfp0:
self.assertTrue(bit in ecfp2)
self.assertIn(bit, ecfp2)
def testOldRingInformationIsWipedOnReperception(self):
"""Previously, the code that identified ring atoms and bonds
@@ -380,10 +380,10 @@ H 0.74700 0.50628 -0.64089
changed = neutralize.Do(mol, option)
result = pybel.Molecule(mol).write("smi").rstrip()
self.assertEqual(ans, result)
if not option:
self.assertEqual(True, changed)
if not option or after:
self.assertTrue(changed)
else:
self.assertEqual(True if after else False, changed)
self.assertFalse(changed)
def testImplicitCisDblBond(self):
"""Ensure that dbl bonds in rings of size 8 or less are always
@@ -393,12 +393,12 @@ H 0.74700 0.50628 -0.64089
ringsize = i + 4
ringsmi = smi + "1"
roundtrip = pybel.readstring("smi", ringsmi).write("smi")
self.assertTrue("/" not in roundtrip)
self.assertNotIn("/", roundtrip)
smi += "C"
ringsize = 9
ringsmi = smi + "1"
roundtrip = pybel.readstring("smi", ringsmi).write("smi")
self.assertTrue("/" in roundtrip)
self.assertIn("/", roundtrip)
def testKekulizationOfHypervalents(self):
# We should support hypervalent aromatic S and N (the latter
@@ -638,7 +638,7 @@ H -0.26065 0.64232 -2.62218
# Check whether the element is available as a constant
self.assertEqual(N, getattr(ob, ob.GetName(N)))
self.assertTrue(N > 100)
self.assertGreater(N, 100)
def testElementsSpecifiedByAtomicNumberInSmiles(self):
smis = [
@@ -678,7 +678,7 @@ H -0.26065 0.64232 -2.62218
for a, b in itertools.combinations(mol.atoms, 2)
]
mindist = min(dists)
self.assertTrue(mindist > 0.00001)
self.assertGreater(mindist, 0.00001)
def testRegressionBenzene2D(self):
"""Check that benzene is given a correct layout, see #1900"""
@@ -884,16 +884,16 @@ class AcceptStereoAsGiven(PythonBindings):
# Should preserve stereo
tet = "[C@@H](Br)(Br)Br"
out = pybel.readstring("smi", tet).write("smi")
self.assertTrue("@" in out)
self.assertIn("@", out)
cistrans = r"C/C=C(\C)/C"
out = pybel.readstring("smi", cistrans).write("smi")
self.assertTrue("/" in out)
self.assertIn("/", out)
# Should wipe stereo
out = pybel.readstring("smi", tet, opt={"S": True}).write("smi")
self.assertFalse("@" in out)
self.assertNotIn("@", out)
cistrans = r"C/C=C(\C)/C"
out = pybel.readstring("smi", cistrans, opt={"S": True}).write("smi")
self.assertFalse("/" in out)
self.assertNotIn("/", out)
class OBMolCopySubstructure(PythonBindings):
"""Tests for copying a component of an OBMol"""
@@ -1126,7 +1126,7 @@ class AtomClass(PythonBindings):
smi = "[*:6]C"
mol = pybel.readstring("smi", smi)
molfile = mol.write("mol")
self.assertTrue("M RGP 1 1 6" in molfile)
self.assertIn("M RGP 1 1 6", molfile)
molb = pybel.readstring("mol", molfile)
out = mol.write("smi", opt={"a":True, "n":True, "nonewline":True})
self.assertEqual(smi, out)
test/testcdjsonformat.py
+4 -4
View File
@@ -74,8 +74,8 @@ class TestCdJsonFormat(PybelWrapper):
output = json.loads(mols[0].write('cdjson'))
self.assertEqual(len(output['m'][0]['a']), 4)
for a in output['m'][0]['a']:
self.assertTrue('x' in a)
self.assertTrue('y' in a)
self.assertIn('x', a)
self.assertIn('y', a)
def test_write_bonds(self):
"""Test writing bonds."""
@@ -87,9 +87,9 @@ class TestCdJsonFormat(PybelWrapper):
"""Test writing minified output."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
output = mols[0].write('cdjson', opt={'m': None})
self.assertTrue('\n' not in output)
self.assertNotIn('\n', output)
output = mols[0].write('cdjson')
self.assertTrue('\n' in output)
self.assertIn('\n', output)
if __name__ == "__main__":
test/testobconv_writers.py
+2 -2
View File
@@ -108,7 +108,7 @@ def get_mol(test_case, mol):
mol = ob.OBMol()
if not _smi_conv.ReadString(mol, smiles):
test_case.assert_("Cannot parse SMILES %r" % (smiles,))
test_case.fail("Cannot parse SMILES %r" % (smiles,))
mol.SetTitle(title)
return mol
@@ -120,7 +120,7 @@ def get_mol(test_case, mol):
def get_converter(test_case, output_format, options=None):
conv = ob.OBConversion()
if not conv.SetInAndOutFormats("smi", output_format):
test_case.assert_("Cannot set output format %r" % (output_format,))
test_case.fail("Cannot set output format %r" % (output_format,))
if options:
# Can pass in a dictionary ...
test/testpcjsonformat.py
+3 -3
View File
@@ -83,7 +83,7 @@ class TestPcJsonFormat(PybelWrapper):
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_2244_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(len(output['PC_Compounds']), 1)
self.assertTrue('id' in output['PC_Compounds'][0])
self.assertIn('id', output['PC_Compounds'][0])
self.assertEqual(output['PC_Compounds'][0]['id']['id']['cid'], '2244')
def test_write_atoms(self):
@@ -99,9 +99,9 @@ class TestPcJsonFormat(PybelWrapper):
"""Test writing minified output."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
output = mols[0].write('pcjson', opt={'m': None})
self.assertTrue('\n' not in output)
self.assertNotIn('\n', output)
output = mols[0].write('pcjson')
self.assertTrue('\n' in output)
self.assertIn('\n', output)
def test_write_complex_bonds(self):
"""Test writing complex bonds."""
test/testroundtrip.py
+3 -3
View File
@@ -174,7 +174,7 @@ def roundtripFile(fname):
class TestSuite(unittest.TestCase):
def setUp(self):
self.assertTrue(ob is not None, "Failed to import the openbabel module")
self.assertIsNotNone(ob, "Failed to import the openbabel module")
def canFindFile(self, filename):
self.assertTrue(os.path.exists(filename),
@@ -210,11 +210,11 @@ class TestSuite(unittest.TestCase):
if ret != None:
print(i,fname)
print(ret)
self.assertTrue(ret == None, ret)
self.assertIsNone(ret, ret)
except TimeoutError:
print(i,fname)
print("Timeout or segfault")
self.assertTrue(False,"Timeout or segfault with %s"%fname)
self.fail("Timeout or segfault with %s"%fname)