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python: replace IOError with OSError

Browse Source 
https://peps.python.org/pep-3151/
This commit is contained in:
Eisuke Kawashima
2022-04-25 16:35:39 +09:00
parent f3ed2a9a51
commit 77530fb0aa
4 changed files with 21 additions and 21 deletions
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14
scripts/python/examples/testpybel.py
View File

@@ -101,7 +101,7 @@ class TestToolkit(myTestCase):
def testRSformaterror(self):
"""Test that invalid formats raise an error"""
self.assertRaises(ValueError, self.toolkit.readstring, "noel", "jkjk")
self.assertRaises(IOError, self.toolkit.readstring, "smi", "&*)(%)($)")
self.assertRaises(OSError, self.toolkit.readstring, "smi", "&*)(%)($)")
def testselfconversion(self):
"""Test that the toolkit can eat its own dog-food."""
@@ -189,7 +189,7 @@ M END
def testRFmissingfile(self):
"""Test that reading from a non-existent file raises an error."""
self.assertRaises(IOError, self.RFreaderror)
self.assertRaises(OSError, self.RFreaderror)
def RFformaterror(self):
mol = getattr(self.toolkit.readfile("noel", "head.sdf"), nextmethod)()
@@ -225,7 +225,7 @@ M END
filecontents = input.readlines()[0].split("\t")[0].strip()
input.close()
self.assertEqual(filecontents, test)
self.assertRaises(IOError, mol.write, "smi", "testoutput.txt")
self.assertRaises(OSError, mol.write, "smi", "testoutput.txt")
os.remove("testoutput.txt")
self.assertRaises(ValueError, mol.write, "noel", "testoutput.txt")
@@ -235,8 +235,8 @@ M END
with self.toolkit.Outputfile("sdf", "testoutput.txt") as outputfile:
for mol in self.head:
outputfile.write(mol)
self.assertRaises(IOError, outputfile.write, mol)
self.assertRaises(IOError, self.toolkit.Outputfile, "sdf", "testoutput.txt")
self.assertRaises(OSError, outputfile.write, mol)
self.assertRaises(OSError, self.toolkit.Outputfile, "sdf", "testoutput.txt")
input = open("testoutput.txt", "r")
numdollar = len([x for x in input.readlines()
if x.rstrip() == "$$$$"])
@@ -314,7 +314,7 @@ M END
self.assertEqual(str(self.atom), test)
def invalidSMARTStest(self):
# Should raise IOError
# Should raise OSError
return self.toolkit.Smarts("[#NOEL][#NOEL]")
def testSMARTS(self):
@@ -324,7 +324,7 @@ M END
ans = smarts.findall(mol)
self.assertEqual(len(ans), 3)
self.toolkit.ob.obErrorLog.SetOutputLevel(self.toolkit.ob.obError)
self.assertRaises(IOError, self.invalidSMARTStest)
self.assertRaises(OSError, self.invalidSMARTStest)
self.toolkit.ob.obErrorLog.SetOutputLevel(self.toolkit.ob.obWarning)
def testAddh(self):

12
scripts/python/openbabel/pybel.py
View File

@@ -158,7 +158,7 @@ def readfile(format, filename, opt=None):
if not formatok:
raise ValueError("%s is not a recognised Open Babel format" % format)
if not os.path.isfile(filename):
raise IOError("No such file: '%s'" % filename)
raise OSError("No such file: '%s'" % filename)
def filereader():
obmol = ob.OBMol()
@@ -206,7 +206,7 @@ def readstring(format, string, opt=None):
success = obconversion.ReadString(obmol, string)
if not success:
raise IOError("Failed to convert '%s' to format '%s'" % (
raise OSError("Failed to convert '%s' to format '%s'" % (
string, format))
return Molecule(obmol)
@@ -242,7 +242,7 @@ class Outputfile(object):
self.format = format
self.filename = filename
if not overwrite and os.path.isfile(self.filename):
raise IOError(
raise OSError(
"%s already exists. Use 'overwrite=True' to overwrite it." %
self.filename)
@@ -272,7 +272,7 @@ class Outputfile(object):
molecule
"""
if not self.filename:
raise IOError("Outputfile instance is closed.")
raise OSError("Outputfile instance is closed.")
if self.total == 0:
self.obConversion.WriteFile(molecule.OBMol, self.filename)
@@ -554,7 +554,7 @@ class Molecule(object):
if filename:
if not overwrite and os.path.isfile(filename):
raise IOError(("%s already exists. Use 'overwrite=True' to "
raise OSError(("%s already exists. Use 'overwrite=True' to "
"overwrite it.") % filename)
obconversion.WriteFile(self.OBMol, filename)
obconversion.CloseOutFile()
@@ -952,7 +952,7 @@ class Smarts(object):
self.obsmarts = ob.OBSmartsPattern()
success = self.obsmarts.Init(smartspattern)
if not success:
raise IOError("Invalid SMARTS pattern")
raise OSError("Invalid SMARTS pattern")
def findall(self, molecule):
"""Find all matches of the SMARTS pattern to a particular molecule.

2
scripts/python/setup.py
View File

@@ -26,7 +26,7 @@ def find_version():
if version_match:
return version_match.group(1)
raise Exception('Could not find version string in openbabel/__init__.py.')
except IOError:
except OSError:
raise Exception('Could not find openbabel/__init__.py.')

14
test/testbindings.py
View File

@@ -323,7 +323,7 @@ $end"""
mol = pybel.readstring("smi", smi)
self.assertTrue(mol.OBMol.GetData(ob.StereoData))
for smi in bad:
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
for smi in alsobad:
mol = pybel.readstring("smi", smi)
self.assertTrue(mol.OBMol.GetData(ob.StereoData))
@@ -356,7 +356,7 @@ H 0.74700 0.50628 -0.64089
smis = [r"\0", "&0", "=&",
"[H][S][S][S@S00]0[S][S@S00H](0[S@S00][S])0n"]
for smi in smis:
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
smis = ["c0C[C@H](B)00O0"] # warning and stereo ignored
for smi in smis:
@@ -461,7 +461,7 @@ M END
data += " [C@,](Br)(Cl)(I)F C1,CC1 C%1,1CC%11 C%(1,1)CC%11"
data += " C=,C"
for smi in data.split(" "):
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
def testOBMolAssignTotalChargeToAtoms(self):
"""Run the test cases described in the source code"""
@@ -499,7 +499,7 @@ M END
mol = pybel.readstring("smi", smi)
self.assertEqual(charge, mol.atoms[0].formalcharge)
for smi in bad:
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
def testReadingBenzyne(self):
"""Check that benzyne is read correctly"""
@@ -544,7 +544,7 @@ M END
for smi in smis:
mol = pybel.readstring("smi", smi)
self.assertEqual(mol.write("smi").rstrip(), smi)
self.assertRaises(IOError, pybel.readstring, "smi", "[11111C]")
self.assertRaises(OSError, pybel.readstring, "smi", "[11111C]")
mol = pybel.readstring("smi", "[C]")
mol.atoms[0].OBAtom.SetIsotope(65535)
self.assertEqual(mol.write("smi").rstrip(), "[C]")
@@ -652,7 +652,7 @@ H -0.26065 0.64232 -2.62218
for smi, rt in smis:
if rt==-1:
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
continue
if rt is None:
rt = smi
@@ -731,7 +731,7 @@ class NewReactionHandling(PythonBindings):
self.assertEqual(smi, nsmi)
badsmis = ["C>>N>O", ">>>", "C>N>O>", ">", ">N", "N>"]
for smi in badsmis:
self.assertRaises(IOError, pybel.readstring, "smi", smi)
self.assertRaises(OSError, pybel.readstring, "smi", smi)
def testFacade(self):
parts = "CNO"