Fix some issues noted by flake8

test/mdt_test.py

@@ -1,4 +1,3 @@
-import unittest
 from modeller.test import ModellerTest
 import modeller
 import mdt
@@ -7,6 +6,7 @@
 if sys.version_info[0] >= 3:
     from functools import reduce
 
+
 class MDTTest(ModellerTest):
 
     def get_mdt_library(self, **vars):
@@ -48,7 +48,7 @@ def assertMDTDataEqual(self, mdt1, mdt2):
         while self.roll_inds(inds, mdt1.shape, mdt1.offset):
             npoints += 1
             self.assertAlmostEqual(mdt1[inds], mdt2[inds], places=3)
-        self.assertEqual(npoints, reduce(lambda x,y: x*y, shape))
+        self.assertEqual(npoints, reduce(lambda x, y: x*y, shape))
 
     def assertMDTsEqual(self, mdt1, mdt2, check_pdf=True):
         """Make sure that two MDTs are equal"""

test/run-all-tests.py

@@ -1,5 +1,8 @@
 from __future__ import print_function
-import unittest, sys, os, re
+import unittest
+import sys
+import os
+import re
 from optparse import OptionParser
 import glob
 
@@ -24,6 +27,7 @@ def getDescription(self, test):
                     return doc_first_line
                 else:
                     return str(test)
+
         def _makeResult(self):
             return self._TestResult(self.stream, self.descriptions,
                                     self.verbosity)
@@ -83,9 +87,11 @@ def regressionTest():
     modnames = [os.path.splitext(f)[0] for f in files]
 
     modobjs = [__import__(m) for m in modnames]
-    tests = [unittest.defaultTestLoader.loadTestsFromModule(o) for o in modobjs]
+    tests = [unittest.defaultTestLoader.loadTestsFromModule(o)
+             for o in modobjs]
     return unittest.TestSuite(tests)
 
+
 def parse_options():
     parser = OptionParser()
     parser.add_option("-v", dest="verbose", action='store_true',
@@ -95,6 +101,7 @@ def parse_options():
                       help="directory to write HTML coverage info into")
     return parser.parse_args()
 
+
 if __name__ == "__main__":
     opts, args = parse_options()
     sys.argv = [sys.argv[0]] + args

test/test_bondlib.py

@@ -6,6 +6,7 @@
 import os
 import sys
 
+
 class BondLibTests(MDTTest):
 
     def get_test_mdt(self, mlib, features):
@@ -26,15 +27,15 @@ def test_write_bondlib(self):
         mlib.bond_classes.read('data/bndgrp.lib')
 
         bondtype = mdt.features.BondType(mlib)
-        bondlen = mdt.features.BondLength(mlib,
-                                      bins=mdt.uniform_bins(200, 1.0, 0.005))
+        bondlen = mdt.features.BondLength(
+            mlib, bins=mdt.uniform_bins(200, 1.0, 0.005))
         m = self.get_test_mdt(mlib, [bondtype, bondlen])
         with open('test.out', 'w') as fh:
             mdt.write_bondlib(fh, m)
 
         # Make sure that valid Python code was produced
         with open('test.out') as fh:
-            code = compile(fh.read(), 'test.out', 'exec')
+            _ = compile(fh.read(), 'test.out', 'exec')
         os.unlink('test.out')
 
     def test_bad_bin_name_write_bondlib(self):
@@ -61,7 +62,7 @@ def test_write_anglelib(self):
 
         # Make sure that valid Python code was produced
         with open('test.out') as fh:
-            code = compile(fh.read(), 'test.out', 'exec')
+            _ = compile(fh.read(), 'test.out', 'exec')
         os.unlink('test.out')
 
     def test_write_improperlib(self):
@@ -77,23 +78,23 @@ def test_write_improperlib(self):
 
         # Make sure that valid Python code was produced
         with open('test.out') as fh:
-            code = compile(fh.read(), 'test.out', 'exec')
+            _ = compile(fh.read(), 'test.out', 'exec')
         os.unlink('test.out')
 
     def test_write_splinelib(self):
         """Test the write_splinelib function"""
         mlib = self.get_mdt_library()
 
         restype = mdt.features.ResidueType(mlib)
-        ang = mdt.features.Chi1Dihedral(mlib,
-                                        bins=mdt.uniform_bins(180, -180.0, 4.0))
+        ang = mdt.features.Chi1Dihedral(
+            mlib, bins=mdt.uniform_bins(180, -180.0, 4.0))
         m = self.get_test_mdt(mlib, [restype, ang])
         with open('test.out', 'w') as fh:
             mdt.write_splinelib(fh, m, 'chi1')
 
         # Make sure that valid Python code was produced
         with open('test.out') as fh:
-            code = compile(fh.read(), 'test.out', 'exec')
+            _ = compile(fh.read(), 'test.out', 'exec')
         os.unlink('test.out')
 
     def test_write_2dsplinelib(self):
@@ -111,7 +112,7 @@ def test_write_2dsplinelib(self):
 
         # Make sure that valid Python code was produced
         with open('test.out') as fh:
-            code = compile(fh.read(), 'test.out', 'exec')
+            _ = compile(fh.read(), 'test.out', 'exec')
         os.unlink('test.out')
 
     def test_write_statpot(self):
@@ -123,9 +124,9 @@ def test_write_statpot(self):
         d = mdt.features.AtomDistance(mlib, bins=mdt.uniform_bins(5, 0, 0.5))
         a1 = mdt.features.AtomType(mlib)
         a2 = mdt.features.AtomType(mlib, pos2=True)
-        m = mdt.Table(mlib, features=(d,a1,a2))
+        m = mdt.Table(mlib, features=(d, a1, a2))
         # Remove undefined bin
-        m = m.reshape((d,a1,a2), m.offset, (-1, -1, -1))
+        m = m.reshape((d, a1, a2), m.offset, (-1, -1, -1))
         with open('test.out', 'w') as fh:
             mdt.write_statpot(fh, m)
         # Check size of file
@@ -134,9 +135,10 @@ def test_write_statpot(self):
         self.assertEqual(len(lines), 7)
         self.assertEqual(len(lines[-1].split()), 21)
         # Make sure Modeller can read the file
-        g = modeller.group_restraints(env, 'test/data/atmcls-tiny.lib',
+        _ = modeller.group_restraints(env, 'test/data/atmcls-tiny.lib',
                                       'test.out')
         os.unlink('test.out')
 
+
 if __name__ == '__main__':
     unittest.main()

test/test_bondsep.py

@@ -5,6 +5,7 @@
 import modeller
 import os
 
+
 class BondSeparationFeatureTests(MDTTest):
 
     def build_mdt_from_sequence(self, mlib, features, seq, **keys):
@@ -29,24 +30,25 @@ def get_all_libraries(self):
     def test_chain_span(self):
         """Atom pairs spanning chains should not be connected"""
         mlib = self.get_all_libraries()
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
         m = self.build_mdt_from_sequence(mlib, bsep, 'C/C',
-                                         residue_span_range=(-999,-1,1,999))
+                                         residue_span_range=(-999, -1, 1, 999))
         # All atom pairs should be undefined, since chains are not connected
         self.assertEqual(m.sample_size, 49.0)
         self.assertEqual(m[-1], 49.0)
 
     def test_unknown_atom_type(self):
         """Atoms of unknown type should count as undefined"""
         mlib = self.get_all_libraries()
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                 bins=mdt.uniform_bins(10, -1000, 1000.0))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(10, -1000, 1000.0))
         m = self.build_mdt_from_sequence(mlib, bsep, 'C',
-                                         residue_span_range=(0,0,0,0))
-        # The OXT atom is not referenced in the bond library, so bond separation
-        # to any of the other 6 atoms should count as undefined (even though
-        # the raw "distance" of -1 would otherwise fall in the first bin)
+                                         residue_span_range=(0, 0, 0, 0))
+        # The OXT atom is not referenced in the bond library, so bond
+        # separation to any of the other 6 atoms should count as undefined
+        # (even though the raw "distance" of -1 would otherwise fall in the
+        # first bin)
         self.assertEqual(m[-1], 6.0)
 
     def test_unconnected_internal(self):
@@ -67,10 +69,10 @@ def test_unconnected_internal(self):
 
         attyp1 = mdt.features.AtomType(mlib)
         attyp2 = mdt.features.AtomType(mlib, pos2=True)
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
-        m = self.build_mdt_from_sequence(mlib, [attyp1, attyp2, bsep],
-                        'A', residue_span_range=(0,0,0,0))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
+        m = self.build_mdt_from_sequence(
+            mlib, [attyp1, attyp2, bsep], 'A', residue_span_range=(0, 0, 0, 0))
         atom_types = {}
         for n, b in enumerate(m.features[0].bins):
             atom_types[b.symbol] = n
@@ -105,10 +107,11 @@ def test_unconnected_external(self):
 
         attyp1 = mdt.features.AtomType(mlib)
         attyp2 = mdt.features.AtomType(mlib, pos2=True)
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
-        m = self.build_mdt_from_sequence(mlib, [attyp1, attyp2, bsep],
-                        'AA', residue_span_range=(-1,-1,1,1))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
+        m = self.build_mdt_from_sequence(
+            mlib, [attyp1, attyp2, bsep], 'AA',
+            residue_span_range=(-1, -1, 1, 1))
         atom_types = {}
         for n, b in enumerate(m.features[0].bins):
             atom_types[b.symbol] = n
@@ -133,10 +136,11 @@ def test_internal(self):
         mlib = self.get_all_libraries()
         attyp1 = mdt.features.AtomType(mlib)
         attyp2 = mdt.features.AtomType(mlib, pos2=True)
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
-        m = self.build_mdt_from_sequence(mlib, [attyp1, attyp2, bsep],
-                        'ARNDCQEHFWY', residue_span_range=(0,0,0,0))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
+        m = self.build_mdt_from_sequence(
+            mlib, [attyp1, attyp2, bsep], 'ARNDCQEHFWY',
+            residue_span_range=(0, 0, 0, 0))
         atom_types = {}
         for n, b in enumerate(m.features[0].bins):
             atom_types[b.symbol] = n
@@ -179,10 +183,11 @@ def test_external(self):
         mlib = self.get_all_libraries()
         attyp1 = mdt.features.AtomType(mlib)
         attyp2 = mdt.features.AtomType(mlib, pos2=True)
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
-        m = self.build_mdt_from_sequence(mlib, [attyp1, attyp2, bsep],
-                        'ARN', residue_span_range=(-999,-1,1,999))
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
+        m = self.build_mdt_from_sequence(
+            mlib, [attyp1, attyp2, bsep], 'ARN',
+            residue_span_range=(-999, -1, 1, 999))
         atom_types = {}
         for n, b in enumerate(m.features[0].bins):
             atom_types[b.symbol] = n
@@ -204,11 +209,10 @@ def assertBondSep(at1, at2, numbond, sep):
     def test_disulfide(self):
         """Test handling of disulfide bonds"""
         mlib = self.get_all_libraries()
-        bsep = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0))
-        bsep_ss = mdt.features.AtomBondSeparation(mlib,
-                                        bins=mdt.uniform_bins(20, 0, 1.0),
-                                        disulfide=True)
+        bsep = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0))
+        bsep_ss = mdt.features.AtomBondSeparation(
+            mlib, bins=mdt.uniform_bins(20, 0, 1.0), disulfide=True)
         env = self.get_environ()
         mdl = modeller.model(env)
         mdl.build_sequence('CC')
@@ -224,11 +228,12 @@ def test_disulfide(self):
             a = modeller.alignment(env)
             a.append_model(mdl, atom_files='test', align_codes='test')
             m = mdt.Table(mlib, features=bsep)
-            m.add_alignment(a, residue_span_range=(-999,0,0,999))
+            m.add_alignment(a, residue_span_range=(-999, 0, 0, 999))
             self.assertEqual(m[1], 11.0)
             m2 = mdt.Table(mlib, features=bsep_ss)
-            m2.add_alignment(a, residue_span_range=(-999,0,0,999))
+            m2.add_alignment(a, residue_span_range=(-999, 0, 0, 999))
             self.assertEqual(m2[1], num)
 
+
 if __name__ == '__main__':
     unittest.main()