fix and activate pycodestyle E221 and E225 (#95)

.github/workflows/lint.yml

@@ -19,7 +19,7 @@ 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,E21,E222,E227,E228,E262,E271,E272,E30,E401,E701,E702,E703,E704,E711,E713,E721,W2,W3,W6 python/
+        run: pycodestyle --select=E111,E21,E221,E222,E225,E227,E228,E262,E271,E272,E30,E401,E701,E702,E703,E704,E711,E713,E721,W2,W3,W6 python/
 
 env:
   MAKEFLAGS: -j2

python/app.py

@@ -190,7 +190,7 @@ def save_file_as(self, event=None):
             inputs = self.IP.history_manager.input_hist_raw
             results = self.IP.history_manager.output_hist
             for n in range(1,len(inputs)):
-                savefile.write('\n'+re.sub('\n+','\n',inputs[n]) +'\n')
+                savefile.write('\n'+re.sub('\n+','\n',inputs[n]) + '\n')
                 try:
                     output = repr(results[n]).split('\n')
                 except:

python/browser.py

@@ -273,7 +273,7 @@ def build_side_panel(self):
                 canvas.configure(background=self.style.groupBG)
             canvas.grid(row=0, column=0, sticky=Tk_.NSEW)
             filling_scrollbar.config(command=canvas.yview)
-        self.filling_vars=[]
+        self.filling_vars = []
 
         # Embedded windows in a canvas are clipped to their parent, not to
         # the canvas.
@@ -391,7 +391,7 @@ def build_invariants(self):
         ttk.Label(self.length_spectrum_frame, text='Cutoff:').grid(
             row=0, column=0, sticky=Tk_.E, pady=5)
         self.length_cutoff = 1.0
-        self.cutoff_var=Tk_.StringVar(self, self.length_cutoff)
+        self.cutoff_var = Tk_.StringVar(self, self.length_cutoff)
         self.cutoff_entry = cutoff_entry = ttk.Entry(
             self.length_spectrum_frame,
             takefocus=False,

python/database.py

@@ -267,7 +267,7 @@ def _manifold_factory(self, row, M=None):
         isosig = m.group(1)
         M._from_isosig(isosig)
 
-        fillings = eval( '[' + m.group(2).replace(')(', '),(')+ ']', {})
+        fillings = eval( '[' + m.group(2).replace(')(', '),(') + ']', {})
 
         if fillings:
             M.dehn_fill(fillings)

python/drilling/__init__.py

@@ -430,10 +430,10 @@ def drill_words_hp(*args, **kwargs):
 
 def _add_methods(mfld_class, high_precision = False):
     if high_precision:
-        mfld_class.drill_word  = drill_word_hp
+        mfld_class.drill_word = drill_word_hp
         mfld_class.drill_words = drill_words_hp
     else:
-        mfld_class.drill_word  = drill_word
+        mfld_class.drill_word = drill_word
         mfld_class.drill_words = drill_words
 
 

python/drilling/fixed_points.py

@@ -31,7 +31,7 @@ def r13_fixed_points_of_psl2c_matrix(m):
         if e0 > e1:
             return _r13_fixed_points_of_psl2c_matrix(m)
 
-    t    = matrix([[ 1, 0],[ 1, 1]], ring = m.base_ring())
+    t = matrix([[ 1, 0],[ 1, 1]], ring = m.base_ring())
     tinv = matrix([[ 1, 0],[-1, 1]], ring = m.base_ring())
 
     pts = _r13_fixed_points_of_psl2c_matrix(tinv * m * t)

python/drilling/moves.py

@@ -309,12 +309,12 @@ def two_three_move(given_pieces : Sequence[GeodesicPiece],
                 continue
 
             start_subsimplex = old_piece.endpoints[0].subsimplex
-            end_subsimplex   = old_piece.endpoints[1].subsimplex
+            end_subsimplex = old_piece.endpoints[1].subsimplex
 
             if (start_subsimplex | end_subsimplex) in simplex.OneSubsimplices:
                 for i, new_tet in enumerate(new_tets):
                     new_start_subsimplex = old_to_new_tets[j][i].image(start_subsimplex)
-                    new_end_subsimplex   = old_to_new_tets[j][i].image(end_subsimplex)
+                    new_end_subsimplex = old_to_new_tets[j][i].image(end_subsimplex)
 
                     if (new_start_subsimplex | new_end_subsimplex) == simplex.E23:
                         GeodesicPiece.replace_by(
@@ -345,7 +345,7 @@ def two_three_move(given_pieces : Sequence[GeodesicPiece],
                 end_j = j
 
             r13_endpoints = [
-                O13_embeddings[j]     * old_pieces[ 0].endpoints[0].r13_point,
+                O13_embeddings[j] * old_pieces[ 0].endpoints[0].r13_point,
                 O13_embeddings[end_j] * old_pieces[-1].endpoints[1].r13_point
                 ]
 

python/exterior_to_link/barycentric_geometry.py

@@ -400,7 +400,7 @@ def barycentric_edge_embedding(arrow, north_pole=None):
     """
     if north_pole is None:
         north_pole = N
-    assert len(arrow.linking_cycle())==3
+    assert len(arrow.linking_cycle()) == 3
     arrow = arrow.copy()
     verts = [A, B, C, A]
     ans = []

python/exterior_to_link/link_projection.py

@@ -73,7 +73,7 @@ def straightenable_tri(points, extra_arcs=None):
     for i in range(n):
         indices = i, (i + 1) % n, (i + 2) % n
         tri = [points[k] for k in indices]
-        other_arcs = [(points[k], points[(k+1)% n])
+        other_arcs = [(points[k], points[(k+1) % n])
                       for k in range(n) if k not in indices[:2]]
         if pl_utils.colinear(*tri):
             return indices
@@ -87,7 +87,7 @@ def arcs_from_points(points_list):
     arcs = []
     for p in points_list:
         n = len(p)
-        arcs += [(p[k], p[(k+1)% n]) for k in range(n)]
+        arcs += [(p[k], p[(k+1) % n]) for k in range(n)]
     return arcs
 
 

python/exterior_to_link/main.py

@@ -152,7 +152,7 @@ def print_status(*args, **kwargs):
                  f'PL segments; max denom of coor is {M._curr_max_denom()}.')
     print_status('    Embedding in S3...', end='')
     link_in_R3 = put_in_S3.embed_link_in_S3(M)
-    link_in_R3  = link_projection.straighten_link(link_in_R3)
+    link_in_R3 = link_projection.straighten_link(link_in_R3)
     num_seg = sum(len(component) + 1 for component in link_in_R3)
     print_status('got PL link of', num_seg ,'segments.')
     print_status('    Projecting...', end='')

python/exterior_to_link/mcomplex_with_expansion.py

@@ -49,7 +49,7 @@ def _two_to_zero_base(self, arrow):
         implemented as a compound of four 2<->3 moves.
         """
         assert arrow.axis().valence() == 2
-        assert arrow.equator().valence()==2
+        assert arrow.equator().valence() == 2
         a = arrow.copy()
         a.opposite().next().reverse().opposite()
         if a.Tetrahedron == a.glued().Tetrahedron:

python/exterior_to_link/mcomplex_with_link.py

@@ -346,8 +346,8 @@ def safe_perturbation(self):
                         check = True
                         min_b, max_b = coor_min[b], coor_max[b]
                         for i in range(3):
-                            if (((min_a[i]-max_b[i])**2 >= min_distance_sq and (min_a[i]-max_b[i])>0)
-                            or ((min_b[i]-max_a[i])**2 >= min_distance_sq and (min_b[i]-max_a[i])>0)):
+                            if (((min_a[i]-max_b[i])**2 >= min_distance_sq and (min_a[i]-max_b[i]) > 0)
+                            or ((min_b[i]-max_a[i])**2 >= min_distance_sq and (min_b[i]-max_a[i]) > 0)):
                                 # arcs lie in different regions which are far apart so dont compare
                                 check = False
                                 break

python/horoviewer.py

@@ -77,7 +77,7 @@ def __init__(self, master, nbhd=None, which_cusp=0, cutoff=None,
             widget.set_background(1.0,1.0,1.0)
         widget.autospin_allowed = 0
         cyglSetStandardLighting()
-        option_frame= ttk.Frame(top_frame)
+        option_frame = ttk.Frame(top_frame)
         view_button = ttk.Menubutton(option_frame, text='View Options')
         self.view_menu = view_menu = Tk_.Menu(view_button, tearoff=0)
         view_menu.add_checkbutton(label='parallelogram', command=self.view_check,

python/infodialog.py

@@ -25,7 +25,7 @@ def body(self, master):
         if sys.platform == 'darwin':
             message = Tk_.Message(box, text=self.content)
         else:
-            bgColor=self.style.lookup('Button', 'background')
+            bgColor = self.style.lookup('Button', 'background')
             message = Tk_.Message(box, text=self.content, bg=bgColor)
         message.grid(row=0, column=1, padx=20, pady=10)
         box.pack()

python/numeric_output_checker.py

@@ -43,7 +43,7 @@ class NumericExample:
 # Store in dict precision : FLAG
 NUMERIC_DICT = {}
 # All or'ed together
-ALL_NUMERIC  = 0
+ALL_NUMERIC = 0
 
 
 def init_precisions(precisions):
@@ -93,7 +93,7 @@ def get_precision(optionflags):
 
 # 4.5?e-3 would split into groups ('4.5?e-3', '4.5', '?", 'e-3').
 number_re = re.compile('(' + mantissa_pat + interval_pat + exponent_pat + ')')
-number_group_count  = 4
+number_group_count = 4
 number_split_stride = number_group_count + 1
 
 # Use whitespace normalization for text pieces
@@ -182,13 +182,13 @@ def compare_numeric(self, want, got, optionflags):
 
         # "[4.5e-9]" yields ('[', '4.5e-9', '4.5', None, 'e-9', ']')
         split_want = re.split(number_re, want)
-        split_got  = re.split(number_re, got)
+        split_got = re.split(number_re, got)
 
         # Check same number of numbers
         if len(split_want) != len(split_got):
             return ('COUNT',
                     (len(split_want) // number_split_stride,
-                     len(split_got)  // number_split_stride))
+                     len(split_got) // number_split_stride))
 
         # Compare text pieces between numbers
         flags = optionflags | NUMERIC_DEFAULT_OPTIONFLAGS

python/polyviewer.py

@@ -23,8 +23,8 @@ def __init__(self, parent, facedicts=[], **kwargs):
         self.main_window = kwargs.get('main_window', None)
         self.topframe = topframe = ttk.Frame(self)
         self.bottomframe = bottomframe = ttk.Frame(self)
-        self.model_var=Tk_.StringVar(self, value='Klein')
-        self.sphere_var=Tk_.IntVar(self, value=1)
+        self.model_var = Tk_.StringVar(self, value='Klein')
+        self.sphere_var = Tk_.IntVar(self, value=1)
         self.klein = ttk.Radiobutton(topframe, text='Klein',
                                      variable = self.model_var,
                                      value='Klein',

python/ptolemy/coordinates.py

@@ -1198,8 +1198,8 @@ def complex_volume(self, with_modulo = False):
                 if key[:2] == 'z_' ])
 
         cvol = sum_L_functions / pari('I')
-        vol  = cvol.real()
-        cs   = cvol.imag() % m
+        vol = cvol.real()
+        cs = cvol.imag() % m
 
         if cs > m/2 + pari('1e-12'):
             cs = cs - m
@@ -2030,8 +2030,8 @@ def get_obstruction_variable(face):
             s1 = get_obstruction_variable(1)
             s2 = get_obstruction_variable(2)
             s3 = get_obstruction_variable(3)
-            z   = s0 * s1 * z
-            zp  = s0 * s2 * zp
+            z = s0 * s1 * z
+            zp = s0 * s2 * zp
             zpp = s0 * s3 * zpp
 
         variable_end = '_%d%d%d%d' % tuple(index) + '_%d' % tet
@@ -2049,14 +2049,14 @@ def make_triple(w, z):
                                     branch_factor, evenN)
 
             return [
-                ('z'   + variable_end, make_triple(w  ,z  )),
-                ('zp'  + variable_end, make_triple(wp ,zp )),
+                ('z' + variable_end, make_triple(w  ,z  )),
+                ('zp' + variable_end, make_triple(wp ,zp )),
                 ('zpp' + variable_end, make_triple(wpp,zpp)) ]
 
         else:
             return [
-                ('z'   + variable_end, z),
-                ('zp'  + variable_end, zp),
+                ('z' + variable_end, z),
+                ('zp' + variable_end, zp),
                 ('zpp' + variable_end, zpp) ]
 
     return dict(
@@ -2153,12 +2153,12 @@ def evaluate_key_for_root(key, value):
             v = _evaluate_at_root(value, root)
 
             if key[:2] == 'z_':
-                z   = v
-                zp  = 1 / (1 - z)
+                z = v
+                zp = 1 / (1 - z)
                 zpp = 1 - 1 / z
 
                 return [(key,              z),
-                        ('zp_'  + key[2:], zp),
+                        ('zp_' + key[2:], zp),
                         ('zpp_' + key[2:], zpp)]
             elif key[:3] == 'zp_' or key[:4] == 'zpp_':
                 return []

python/ptolemy/matrix.py

@@ -16,7 +16,7 @@ def col_is_zero(m, col):
     if col < 0:
         return True
     for row in m:
-        if not row[col]==0:
+        if not row[col] == 0:
             return False
     return True
 

python/ptolemy/processMagmaFile.py

@@ -234,7 +234,7 @@ def run_magma(content,
     else:
         resolved_dir = tempfile.mkdtemp() + '/'
 
-    in_file  = resolved_dir + filename_base + '.magma'
+    in_file = resolved_dir + filename_base + '.magma'
     out_file = resolved_dir + filename_base + '.magma_out'
 
     if verbose:

python/ptolemy/ptolemyVariety.py

@@ -811,7 +811,7 @@ def merge_two_dicts(sign, power, var1, var2, dict1, dict2):
         sign1, power1 = dict1[var1]
         sign2, power2 = dict2[var2]
 
-        new_sign  = sign1  * sign  * sign2
+        new_sign = sign1 * sign * sign2
         new_power = power1 - power - power2
 
         for v2, (s2, p2) in dict2.items():

python/ptolemy/reginaWrapper.py

@@ -611,7 +611,7 @@ def _ptolemy_equations_identified_coordinates(self, N,
                     power = 0
 
                 # Get the two corresponding Ptolemy coordinates
-                ptolemy       = ('c_%d%d%d%d' % ptolemy_index +
+                ptolemy = ('c_%d%d%d%d' % ptolemy_index +
                                  '_%d' % tet_index)
                 other_ptolemy = ('c_%d%d%d%d' % other_ptolemy_index +
                                  '_%d' % other_tet_index)

python/ptolemy/test.py

@@ -302,7 +302,7 @@ def is_close(cvol1, cvol2, epsilon):
 
     from snappy import OrientableCuspedCensus
 
-    for M in (list(OrientableCuspedCensus()[0:10])+
+    for M in (list(OrientableCuspedCensus()[0:10]) +
               list(OrientableCuspedCensus()[10000:10010])):
 
         flattening = Flattenings.from_tetrahedra_shapes_of_manifold(M)

python/raytracing/finite_viewer.py

@@ -367,7 +367,7 @@ def create_navigation_frame(self, parent):
         label = ttk.Label(frame, text = u"Keys: \u2190\u2191\u2192\u2193xz")
         label.grid(row = row, column = 3, sticky = tkinter.NSEW)
 
-        row +=1
+        row += 1
         label = ttk.Label(frame, text = _mouse_gestures_text())
         label.grid(row = row, column = 0, columnspan = 4)
 

python/raytracing/gui_utilities.py

@@ -252,10 +252,10 @@ def set_widths(self):
     def set_scrollbar(self, low, high):
         if float(low) <= 0.0 and float(high) >= 1.0:
             self.scrollbar.pack_forget()
-            self.scrollbar.is_visible=False
+            self.scrollbar.is_visible = False
         else:
             self.scrollbar.pack(side="right", fill="y", anchor="nw", pady=10)
-            self.scrollbar.is_visible=True
+            self.scrollbar.is_visible = True
         self.scrollbar.set(low, high)
 
     def resize(self, event=None):

python/raytracing/hyperboloid_navigation.py

@@ -68,10 +68,10 @@ def _turn_ccw(rot_amount, trans_amount): # z
 
 
 def _add_cursor_keys(d):
-    d['left']  = _turn_left
+    d['left'] = _turn_left
     d['right'] = _turn_right
-    d['up']    = _turn_up
-    d['down']  = _turn_down
+    d['up'] = _turn_up
+    d['down'] = _turn_down
     return d
 
 

python/raytracing/ideal_raytracing_data.py

@@ -427,7 +427,7 @@ def _o13_matrix_for_face(tet, F):
 
 def _compute_cusp_triangle_vertex_positions(tet, V, i):
 
-    z  = tet.ShapeParameters[t3m.E01]
+    z = tet.ShapeParameters[t3m.E01]
     CF = z.parent()
 
     triangle = tet.horotriangles[V]
@@ -463,7 +463,7 @@ def _compute_cusp_to_tet_and_inverse_matrices(tet, vertex, i):
 
     otherVerts = [ t3m.ZeroSubsimplices[(i + j) % 4] for j in range(1, 4) ]
 
-    tet_vertices  = [ tet.complex_vertices[v] for v in otherVerts ]
+    tet_vertices = [ tet.complex_vertices[v] for v in otherVerts ]
 
     cusp_vertices = [ trig.vertex_positions[vertex | v]
                       for v in otherVerts ]