fix and activate pycodestyle E225 in dev/ (#52)

.github/workflows/lint.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Run pycodestyle
         shell: bash -l {0}
         # We currently only check for some warnings. We should enable & fix more of them.
-        run: pycodestyle --select=E111,E302,E306,E401,E701,E702,E703,E704,W391,W605,E711,E713,E721 spherogram_src/
+        run: pycodestyle --select=E111,E225,E302,E306,E401,E701,E702,E703,E704,W391,W605,E711,E713,E721 spherogram_src/
       - name: Run cython-lint
         shell: bash -l {0}
         run: cython-lint .

dev/DTcodes.py

@@ -101,21 +101,20 @@ def entry_slot(self, N):
     def exit_slot(self, N):
         if N == self[0]:
             return North
-        elif N == self[1]:
+        if N == self[1]:
             return West
-        else:
-            raise ValueError('%d is not a label of %s'% (N, self))
+        raise ValueError('%d is not a label of %s' % (N, self))
 
     def first_under(self):
         first, second, even_over = self
         if even_over:
-            return first-1 if first%2 == 1 else second-1
+            return first-1 if first % 2 == 1 else second-1
         else:
-            return first-1 if first%2 == 0 else second-1
+            return first-1 if first % 2 == 0 else second-1
 
     def upper_pair(self):
         first, second, even_over = self
-        return (0,2) if bool(first%2) ^ even_over else (1,3)
+        return (0,2) if bool(first % 2) ^ even_over else (1,3)
 
 
 class DTPath():
@@ -471,7 +470,7 @@ def sign(self, vertex):
         See the documentation for Spherogram.link.
         """
         flipped = self.flipped(vertex)
-        even_first = bool(vertex[0] %2 == 0)
+        even_first = bool(vertex[0] % 2 == 0)
         return -1 if (flipped ^ vertex[2] ^ even_first) else 1
 
     def KLP_strand(self, vertex, edge):
@@ -481,7 +480,7 @@ def KLP_strand(self, vertex, edge):
         """
         W = edge(vertex)
         slot = edge.slot(W)
-        return 'X' if (slot==0 or slot==2) ^ self.flipped(W) else 'Y'
+        return 'X' if (slot == 0 or slot == 2) ^ self.flipped(W) else 'Y'
 
     def KLP_dict(self, vertex, indices):
         """

dev/dev_jennet/spanning_trees.py

@@ -21,6 +21,7 @@ def spanning_trees(G):
     else:
         return []
 
+
 def rec(part_G,G):
     """
     Recursive function 'rec' from Read paper
@@ -31,7 +32,7 @@ def rec(part_G,G):
         return []
 
     if len(G.edges()) == len(part_G.edges()):
-        trees +=[part_G.copy()]
+        trees += [part_G.copy()]
     else:
 
         # let e be an edge not in part_G

dev/dev_jennet/test_links.py

@@ -25,10 +25,10 @@ def setUp(self):
         # Hopf Link
         a = spherogram.Crossing('a')
         b = spherogram.Crossing('b')
-        a[0]=b[1]
-        a[1]=b[0]
-        a[2]=b[3]
-        a[3]=b[2]
+        a[0] = b[1]
+        a[1] = b[0]
+        a[2] = b[3]
+        a[3] = b[2]
         self.L2a1 = spherogram.Link([a,b])
 
         #Borromean Link (3)
@@ -142,7 +142,7 @@ def testConnectedSum(self):
             self.assertEqual(Sum.alexander_poly(), k1.alexander_poly()*k2.alexander_poly())
             self.assertEqual(Sum.signature(),      k1.signature()+k2.signature())
             self.assertEqual(Sum.determinant(),    k1.determinant()*k2.determinant())
-            repeat -=1
+            repeat -= 1
 
     def testSignature(self):
         self.assertEqual(abs(self.Tref.signature()),       2)
@@ -165,7 +165,7 @@ def testCopy(self):
             self.assertEqual(k1.writhe(),         k1_prime.writhe())
             self.assertEqual(k1.signature(),      k1_prime.signature())
             self.assertEqual(k1.alexander_poly(), k1_prime.alexander_poly())
-            repeat-=1
+            repeat -= 1
 
         repeat = 3
         while repeat > 0:
@@ -175,24 +175,24 @@ def testCopy(self):
             self.assertEqual(k2.writhe(),         k2_prime.writhe())
             self.assertEqual(k2.signature(),      k2_prime.signature())
             self.assertEqual(k2.alexander_poly(), k2_prime.alexander_poly())
-            repeat-=1
+            repeat -= 1
 
     def testMirror(self):
         repeat = 3
         while repeat > 0:
             k1 = self.random_knot()
             k1_prime = k1.mirror()
-            self.assert_(k1.signature() == -1*k1_prime.signature(), msg="knot signature failed for "+ repr(k1))
-            self.assert_(k1.writhe() == -1*k1_prime.writhe(), msg="knot writhe failed for "+repr(k1))
-            repeat-=1
+            self.assert_(k1.signature() == -1*k1_prime.signature(), msg="knot signature failed for " + repr(k1))
+            self.assert_(k1.writhe() == -1*k1_prime.writhe(), msg="knot writhe failed for " + repr(k1))
+            repeat -= 1
 
         repeat = 3
         while repeat > 0:
             k2 = self.random_link()
             k2_prime = k2.mirror()
             self.assert_(k2.signature() == -1*k2_prime.signature(), msg="link signature failed for " + repr(k2))
             self.assert_(k2.writhe() == -1*k2_prime.writhe(), msg="link writhe failed for " + repr(k2))
-            repeat-=1
+            repeat -= 1
 
     def testDet(self):
         self.assertEqual(self.K3_1.determinant(),                 3)
@@ -240,13 +240,13 @@ def testBlackGraph(self):
         while repeat > 0:
             k1 = self.random_knot()
             self.assert_(k1.black_graph().is_planar())
-            repeat-=1
+            repeat -= 1
 
         repeat = 3
         while repeat > 0:
             k2 = self.random_link()
             self.assert_(k2.black_graph().is_planar())
-            repeat-=1
+            repeat -= 1
 
 
 suite = unittest.TestLoader().loadTestsFromTestCase(TestLinkFunctions)

dev/dev_malik/fast_jones_patch.py

@@ -80,14 +80,15 @@ def simplify_jones_expression(poly):
 #        print(poly)
     return poly
 
+
 def simplify_monomial(monomial):
     monomial = remove_squares(monomial)
     monomial = remove_loops(monomial)
     A = sympy.Symbol('A')
     strand_vars = monomial.free_symbols - set(sympy.symbols('A,B'))
     strand_labels = all_labels(strand_vars)
 
-    while len(set(strand_labels))<len(strand_labels):
+    while len(set(strand_labels)) < len(strand_labels):
 #        collections.Counter
 #        print(monomial)
         for l in strand_labels:

dev/dev_malik/knots/random_knots.py

@@ -12,9 +12,10 @@ def random_knot(n):
     connect_loose_strands(crossings, loose_cs, final_cs)
     return Link(crossings)
 
+
 def random_open_string(n):
     crossings = [Crossing('0')]
-    crossings[0][2]=crossings[0][3]
+    crossings[0][2] = crossings[0][3]
     final_cs = crossings[0].crossing_strands()[0]
     loose_cs = crossings[0].crossing_strands()[1]
     for i in range(n):
@@ -39,10 +40,12 @@ def random_open_string(n):
 
     return crossings, loose_cs, final_cs
 
+
 def flip_crossings(crossings, loose_cs, final_cs):
     for c in crossings:
         if c != loose_cs.crossing and c != final_cs.crossing:
-            c.rotate(randint(0,1))
+            c.rotate(randint(0, 1))
+
 
 def cross_strand(crossings, loose_cs, strand_to_cross, new_label):
     opposite = strand_to_cross.opposite()

dev/dev_malik/mutation/link_planar_isotopy.py

@@ -25,9 +25,9 @@ def isosig(self, root=None, over_or_under=False):
 isosig_to_link = {}
 for i in range(num_samples):
     print(i)
-    K, root = random_rooted_link(size,edge_conn)
-    isosig = K.isosig(root,over_or_under=True)
-    isosig_to_link[isosig]=(K,root)
+    K, root = random_rooted_link(size, edge_conn)
+    isosig = K.isosig(root, over_or_under=True)
+    isosig_to_link[isosig] = (K, root)
     isosigs.append(isosig)
 
 C = Counter(isosigs)