Use no-argument form of super()

Now that we require Python 3, we can use
the simpler and less error-prone no-argument
form of super() to access the Python base class.

modules/core/test/test_direction.py

@@ -12,7 +12,7 @@ class DirectionRestraint(IMP.Restraint):
     """Harmonically restrain a Direction to a vector."""
 
     def __init__(self, m, pi, v, k):
-        super(DirectionRestraint, self).__init__(m, "DirectionRestraint%1%")
+        super().__init__(m, "DirectionRestraint%1%")
         self.pi, self.u = pi, v.get_unit_vector()
         self.uf = IMP.core.Cosine(k, 1, 0)
 

modules/core/test/test_direction_angle.py

@@ -12,7 +12,7 @@ class AngleRestraint(IMP.Restraint):
     """Harmonically restrain an angle between two directions to a value."""
 
     def __init__(self, m, pi, a, k):
-        super(AngleRestraint, self).__init__(m, "AngleRestraint%1%")
+        super().__init__(m, "AngleRestraint%1%")
         self.pi = pi
         self.a = a
         self.k = k

modules/core/test/test_hierarchy.py

@@ -5,7 +5,7 @@
 
 class TestVisitor(IMP.core.HierarchyVisitor):
     def __init__(self, descend=True):
-        super(TestVisitor, self).__init__()
+        super().__init__()
         self.descend = descend
         self.seen = []
     def __call__(self, h):

modules/kernel/pyext/IMP_kernel.argparse.i

@@ -65,7 +65,7 @@ class ArgumentParser(argparse.ArgumentParser):
     def __init__(self, *args, **kwargs):
         # Don't add --help option (since the Boost option parser handles it)
         kwargs['add_help'] = False
-        super(ArgumentParser, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         for ntoken in (0, 1):
             flags = _get_all_flags(ntoken)
             for f in flags:
@@ -85,7 +85,7 @@ class ArgumentParser(argparse.ArgumentParser):
            @returns   args
         """
         self._boost_command_line = [sys.argv[0]]
-        ret = super(ArgumentParser, self).parse_args(args, namespace)
+        ret = super().parse_args(args, namespace)
         if len(self._boost_command_line) > 1:
             self._handle_boost()
         return ret

modules/mmcif/pyext/src/data.py

@@ -84,7 +84,7 @@ class _EntityMapper(dict):
        share sequence."""
     def __init__(self, system):
         self.system = system
-        super(_EntityMapper, self).__init__()
+        super().__init__()
         self._sequence_dict = {}
         self._entities = []
         self._alphabet_map = {
@@ -165,7 +165,7 @@ def __init__(self, entity, asym_id, name):
 class _ComponentMapper:
     """Handle mapping from IMP Chains to CIF AsymUnits."""
     def __init__(self, system):
-        super(_ComponentMapper, self).__init__()
+        super().__init__()
         self.system = system
         self._used_entities = set()
         self._all_components = []
@@ -385,12 +385,12 @@ class _StartingModel(ihm.startmodel.StartingModel):
 
     def __init__(self, asym_unit, struc_prov):
         self.filename = struc_prov[0].get_filename()
-        super(_StartingModel, self).__init__(
-                asym_unit=asym_unit(0, 0),  # will update in _add_residue()
-                # will fill in later with _set_sources_datasets()
-                dataset=None,
-                asym_id=struc_prov[0].get_chain_id(),
-                offset=struc_prov[0].get_residue_offset())
+        super().__init__(
+            asym_unit=asym_unit(0, 0),  # will update in _add_residue()
+            # will fill in later with _set_sources_datasets()
+            dataset=None,
+            asym_id=struc_prov[0].get_chain_id(),
+            offset=struc_prov[0].get_residue_offset())
 
     def _add_residue(self, resind):
         # Update seq_id_range to accommodate this residue
@@ -519,7 +519,7 @@ def _get_starting_model(sp, resind):
 class _Datasets:
     """Store all datasets used."""
     def __init__(self, system):
-        super(_Datasets, self).__init__()
+        super().__init__()
         self._datasets = {}
         self._groups = {}
         self.system = system
@@ -563,7 +563,7 @@ class _AllSoftware:
     def __init__(self, system):
         self.system = system
         self._by_namever = {}
-        super(_AllSoftware, self).__init__()
+        super().__init__()
 
     def add_hierarchy(self, h, top_h=None):
         # todo: if no SoftwareProvenance available, use RMF producer field
@@ -627,18 +627,18 @@ def __init__(self, prov, num_models_begin, assembly, all_software):
         method = prov.get_method()
         if prov.get_number_of_replicas() > 1:
             method = "Replica exchange " + method
-        super(_ProtocolStep, self).__init__(
-                assembly=assembly,
-                # todo: fill in useful value for dataset_group
-                dataset_group=None,
-                method=method, name='Sampling',
-                num_models_begin=num_models_begin,
-                num_models_end=prov.get_number_of_frames(),
-                # todo: support multiple states, time ordered
-                multi_state=False, ordered=False,
-                # todo: revisit assumption all models are multiscale
-                multi_scale=True,
-                software=all_software._add_previous_provenance(prov))
+        super().__init__(
+            assembly=assembly,
+            # todo: fill in useful value for dataset_group
+            dataset_group=None,
+            method=method, name='Sampling',
+            num_models_begin=num_models_begin,
+            num_models_end=prov.get_number_of_frames(),
+            # todo: support multiple states, time ordered
+            multi_state=False, ordered=False,
+            # todo: revisit assumption all models are multiscale
+            multi_scale=True,
+            software=all_software._add_previous_provenance(prov))
 
     def add_combine(self, prov):
         self.num_models_end = prov.get_number_of_frames()

modules/mmcif/pyext/src/restraint.py

@@ -120,7 +120,7 @@ def __init__(self, imp_restraint, info, components, system):
         self._asyms = tuple(asyms)
         p = IMP.mmcif.metadata._GMMParser()
         r = p.parse_file(info['filename'])
-        super(_EM3DRestraint, self).__init__(
+        super().__init__(
             dataset=r['dataset'], assembly=assembly,
             number_of_gaussians=r['number_of_gaussians'],
             fitting_method='Gaussian mixture model')
@@ -157,7 +157,7 @@ def __init__(self, imp_restraint, info, components, image_number):
                 details="Electron microscopy class average")
         dataset = ihm.dataset.EM2DClassDataset(loc)
 
-        super(_EM2DRestraint, self).__init__(
+        super().__init__(
             dataset=dataset, assembly=assembly,
             segment=False,
             number_raw_micrographs=info['micrographs number'] or None,
@@ -203,7 +203,7 @@ def __init__(self, imp_restraint, info, components, system):
         loc = ihm.location.InputFileLocation(
             info['filename'], details='SAXS profile')
         dataset = ihm.dataset.SASDataset(loc)
-        super(_SAXSRestraint, self).__init__(
+        super().__init__(
             dataset=dataset, assembly=assembly,
             segment=False, fitting_method='IMP SAXS restraint',
             fitting_atom_type=info['form factor type'],
@@ -232,7 +232,7 @@ def __init__(self, imp_restraint, info, components, system):
             smiles_canonical=info.get('linker smiles canonical'),
             inchi=info.get('linker inchi'),
             inchi_key=info.get('linker inchi key'))
-        super(_CrossLinkRestraint, self).__init__(
+        super().__init__(
             dataset=dataset, linker=linker)
         # Map from IMP/RMF chain names to ihm.Entity
         cmap = {e.description: e for e in system.entities}
@@ -292,7 +292,7 @@ class _GeometricRestraint(ihm.restraint.GeometricRestraint):
     def __init__(self, imp_restraint, info, components, system):
         self._info = info
         asym = _AsymMapper(imp_restraint.get_model(), components)
-        super(_GeometricRestraint, self).__init__(
+        super().__init__(
             dataset=None,
             geometric_object=self._geom_object,
             feature=asym.get_feature(

modules/test/pyext/src/__init__.py

@@ -834,7 +834,7 @@ def __del__(self):
 class _TestResult(unittest.TextTestResult):
 
     def __init__(self, stream=None, descriptions=None, verbosity=None):
-        super(_TestResult, self).__init__(stream, descriptions, verbosity)
+        super().__init__(stream, descriptions, verbosity)
         self.all_tests = []
 
     def stopTestRun(self):
@@ -851,10 +851,10 @@ def stopTestRun(self):
                 fname = Path("Z:") / fname
             with open(str(fname), 'wb') as fh:
                 pickle.dump(self.all_tests, fh, protocol)
-        super(_TestResult, self).stopTestRun()
+        super().stopTestRun()
 
     def startTest(self, test):
-        super(_TestResult, self).startTest(test)
+        super().startTest(test)
         test.start_time = datetime.datetime.now()
 
     def _test_finished(self, test, state, detail=None):
@@ -884,27 +884,27 @@ def _test_finished(self, test, state, detail=None):
 
     def addSuccess(self, test):
         self._test_finished(test, 'OK')
-        super(_TestResult, self).addSuccess(test)
+        super().addSuccess(test)
 
     def addError(self, test, err):
         self._test_finished(test, 'ERROR', err)
-        super(_TestResult, self).addError(test, err)
+        super().addError(test, err)
 
     def addFailure(self, test, err):
         self._test_finished(test, 'FAIL', err)
-        super(_TestResult, self).addFailure(test, err)
+        super().addFailure(test, err)
 
     def addSkip(self, test, reason):
         self._test_finished(test, 'SKIP', reason)
-        super(_TestResult, self).addSkip(test, reason)
+        super().addSkip(test, reason)
 
     def addExpectedFailure(self, test, err):
         self._test_finished(test, 'EXPFAIL', err)
-        super(_TestResult, self).addExpectedFailure(test, err)
+        super().addExpectedFailure(test, err)
 
     def addUnexpectedSuccess(self, test):
         self._test_finished(test, 'UNEXPSUC')
-        super(_TestResult, self).addUnexpectedSuccess(test)
+        super().addUnexpectedSuccess(test)
 
     def getDescription(self, test):
         doc_first_line = test.shortDescription()