python: replace IOError with OSError

https://peps.python.org/pep-3151/

scripts/python/examples/testpybel.py

@@ -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(OSError, outputfile.write, mol)
-        self.assertRaises(IOError, self.toolkit.Outputfile, "sdf", "testoutput.txt")
+        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):

scripts/python/openbabel/pybel.py

@@ -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.

scripts/python/setup.py

@@ -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.')
 
 

test/testbindings.py

@@ -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"