more cython-lint suggested fixes in cython/core

cython/core/abelian_group.pyx

@@ -141,7 +141,9 @@ cdef class PresentationMatrix():
     """
     A sparse representation of the presentation matrix of an abelian group.
     """
-    cdef rows, cols, _row_support, _col_support, _entries, _units, dead_columns
+    cdef int rows, cols
+    cdef dict _row_support, _col_support, _entries
+    cdef set _units, dead_columns
 
     def __init__(self, rows, cols):
         self.rows = rows
@@ -229,7 +231,7 @@ cdef class PresentationMatrix():
         Continue until no units remain.  When a generator is removed,
         remember its column index.
         """
-        cdef temp, m, i, j, k, l
+        cdef int temp, m, i, j, k, l
         while len(self._units) > 0:
             for i, j in self._units:
                 break

cython/core/basic.pyx

@@ -44,7 +44,7 @@ except ImportError:
 from .matrix import matrix, vector, SimpleMatrix
 from . import number
 
-## SnapPy components
+# SnapPy components
 import spherogram
 from .manifolds import __path__ as manifold_paths
 from . import database
@@ -322,7 +322,7 @@ def set_rand_seed(seed):
 # Ptolemy utility functions
 # convert and free an identification of variables structure
 cdef convert_and_free_identification_of_variables(
-    Identification_of_variables c_vars):
+        Identification_of_variables c_vars):
     var_list = []
 
     if c_vars.variables:
@@ -337,13 +337,13 @@ cdef convert_and_free_identification_of_variables(
 
 # convert and free an integer matrix from C
 cdef convert_and_free_integer_matrix(
-    Integer_matrix_with_explanations c_matrix):
+        Integer_matrix_with_explanations c_matrix):
     if not c_matrix.entries:
         return []
 
-    python_matrix = [
-        [ c_matrix.entries[i][j] for j in range(c_matrix.num_cols)]
-                                 for i in range(c_matrix.num_rows)]
+    python_matrix = [[c_matrix.entries[i][j]
+                      for j in range(c_matrix.num_cols)]
+                     for i in range(c_matrix.num_rows)]
 
     explain_row = []
 
@@ -452,7 +452,7 @@ cdef Real2gen_direct(Real R):
     divisible by 32.
 
     """
-    IF HIGH_PRECISION: # Real = qd_real
+    IF HIGH_PRECISION:  # Real = qd_real
         cdef double* qd = <double*>&R
         cdef int i
         # The value of a qd_real is the sum of the values of its four doubles.
@@ -476,7 +476,7 @@ ctypedef object (*func_real_to_obj)(Real)
 # Convert Real to gen in an appropriate manner for this environment
 cdef func_real_to_obj Real2gen
 
-if hasattr(pari, '_real_coerced_to_bits_prec'): # Cypari
+if hasattr(pari, '_real_coerced_to_bits_prec'):  # Cypari
     Real2gen = Real2gen_direct
 else:
     Real2gen = Real2gen_string
@@ -557,31 +557,31 @@ cdef double Real2double(Real R):
 
 cdef Complex gen2Complex(g):
     cdef Complex result
-    IF HIGH_PRECISION: # Real = qd_real; 212 bits of precision
+    IF HIGH_PRECISION:  # Real = qd_real; 212 bits of precision
         cdef py_string
         cdef char* c_string
         cdef Real real_part, imag_part
         old_precision = pari.set_real_precision(64)
 
-        py_string = to_byte_str(str(g.real()).replace(' E','E')) # save a reference
+        py_string = to_byte_str(str(g.real()).replace(' E','E'))  # save a reference
         c_string = py_string
         real_part = <Real>c_string
-        py_string = to_byte_str(str(g.imag()).replace(' E','E')) # save a reference
+        py_string = to_byte_str(str(g.imag()).replace(' E','E'))  # save a reference
         c_string = py_string
         imag_part = <Real>c_string
         result.real, result.imag = real_part, imag_part
 
         pari.set_real_precision(old_precision)
-    ELSE: # Real = double
+    ELSE:  # Real = double
         result.real, result.imag = g.real(), g.imag()
     return result
 
-#IF HIGH_PRECISION:
+# IF HIGH_PRECISION:
 cdef Real2Number(Real R):
     return Number(Real2gen(R))
 cdef Complex2Number(Complex C):
     return Number(Complex2gen(C))
-#ELSE:
+# ELSE:
 #    cdef Real2Number(Real R):
 #        return Number(R)
 #    cdef Complex2Number(Complex C):

cython/core/dirichlet.pyx

@@ -1,10 +1,11 @@
 # Dirichlet Domains
 
-cdef (WEPolyhedron*, int) get_generators_from_bytes(
-    data_bytes, double vertex_epsilon,
-    displacement, centroid_at_origin,
-    maximize_injectivity_radius,
-    include_words)except*:
+cdef (WEPolyhedron*, int) get_generators_from_bytes(data_bytes,
+                                                    double vertex_epsilon,
+                                                    displacement,
+                                                    centroid_at_origin,
+                                                    maximize_injectivity_radius,
+                                                    include_words) except *:
 
     cdef int num_gens
 
@@ -25,7 +26,7 @@ cdef (WEPolyhedron*, int) get_generators_from_bytes(
         for i in range(num_gens):
             for j in range(4):
                 for k in range(4):
-                    num_string = nums.pop(0) # save a reference
+                    num_string = nums.pop(0)  # save a reference
                     generators[i][j][k] = <Real_struct>Real_from_string(
                         <char*>num_string)
     elif len(nums) == 8*num_gens:
@@ -36,10 +37,10 @@ cdef (WEPolyhedron*, int) get_generators_from_bytes(
             temp_gens[i].parity = orientation_preserving
             for j in range(2):
                 for k in range(2):
-                    num_string = nums.pop(0) # save a reference
+                    num_string = nums.pop(0)  # save a reference
                     temp_gens[i].matrix[j][k].real = Real_from_string(
                         <char*>num_string)
-                    num_string = nums.pop(0) # save a reference
+                    num_string = nums.pop(0)  # save a reference
                     temp_gens[i].matrix[j][k].imag = Real_from_string(
                         <char*>num_string)
         Moebius_array_to_O31_array(temp_gens, generators, num_gens)
@@ -63,12 +64,12 @@ cdef (WEPolyhedron*, int) get_generators_from_bytes(
     free(generators)
     return dirichlet_domain, num_gens
 
-cdef WEPolyhedron* dirichlet_from_O31_matrix_list(
-    matrices,
-    double vertex_epsilon,
-    displacement, centroid_at_origin,
-    maximize_injectivity_radius,
-    include_words)except*:
+cdef WEPolyhedron* dirichlet_from_O31_matrix_list(matrices,
+                                                  double vertex_epsilon,
+                                                  displacement,
+                                                  centroid_at_origin,
+                                                  maximize_injectivity_radius,
+                                                  include_words) except *:
 
     cdef WEPolyhedron* c_dirichlet_domain
     cdef O31Matrix* generators
@@ -81,7 +82,7 @@ cdef WEPolyhedron* dirichlet_from_O31_matrix_list(
                 generators[i][j][k] = <Real_struct>Object2Real(A[j,k])
     if not O31_determinants_OK(generators, num_gens, det_error_epsilon):
         raise ValueError('The data given do not have the '
-                            'right determinants.')
+                         'right determinants.')
     cdef double c_displacement[3]
     for n from 0 <= n < 3:
         c_displacement[n] = <double>displacement[n]
@@ -105,7 +106,7 @@ cdef class CDirichletDomain():
     def __cinit__(self,
                   Manifold manifold=None,
                   vertex_epsilon=default_vertex_epsilon,
-                  displacement=[0.0, 0.0, 0.0],
+                  displacement=None,
                   centroid_at_origin=True,
                   maximize_injectivity_radius=True,
                   include_words = False,
@@ -114,6 +115,8 @@ cdef class CDirichletDomain():
                   O31_generators=None,
                   str manifold_name='unnamed'):
         cdef double c_displacement[3]
+        if displacement is None:
+            displacement = [0.0, 0.0, 0.0]
         self.c_dirichlet_domain = NULL
         if generator_file != '':
             with open(generator_file, mode='rb') as input_file:
@@ -231,10 +234,10 @@ cdef class CDirichletDomain():
         return self._number_(radius)
 
     def length_spectrum_dicts(self, cutoff_length=1.0,
-                        full_rigor=True,
-                        multiplicities=True,
-                        user_radius=0.0,
-                        grouped=True):
+                              full_rigor=True,
+                              multiplicities=True,
+                              user_radius=0.0,
+                              grouped=True):
         """
         Return a list of info objects describing the short
         geodesics up to the specified cutoff length.  The keys are
@@ -280,7 +283,7 @@ cdef class CDirichletDomain():
         for n from 0 <= n < num_lengths:
             length = Complex2Number(geodesics[n].length)
             its_matrix = matrix([[self._number_(Real2Number(<Real>geodesics[n].matrix[i][j]))
-                                      for j in range(4)] for i in range(4)] )
+                                  for j in range(4)] for i in range(4)] )
             d = {
                 "length" : self._number_(length),
                 "parity" : MatrixParity[geodesics[n].parity],
@@ -338,8 +341,8 @@ cdef class CDirichletDomain():
                 {'position': ( self._number_(Real2Number(<Real>vertex.x[1])),
                                self._number_(Real2Number(<Real>vertex.x[2])),
                                self._number_(Real2Number(<Real>vertex.x[3])) ),
-                  'ideal': bool(vertex.ideal),
-                  'vertex_class' : vertex.v_class.index
+                 'ideal': bool(vertex.ideal),
+                 'vertex_class' : vertex.v_class.index
                  })
             vertex = vertex.next
         return vertices
@@ -480,18 +483,17 @@ cdef class CDirichletDomain():
         """
 
         cdef WEEdge *edge = &self.c_dirichlet_domain.edge_list_begin
-        edges = []
+        cdef list edges = []
 
         vertex_to_index = self._vertex_to_index_dict()
 
         edge = edge.next
         while edge != &self.c_dirichlet_domain.edge_list_end:
 
             edges.append(
-                { 'tail_vertex_index' : vertex_to_index[<size_t>(edge.v[0])],
-                  'tip_vertex_index'  : vertex_to_index[<size_t>(edge.v[1])],
-                  'edge_class' : edge.e_class.index
-                })
+                {'tail_vertex_index': vertex_to_index[<size_t>(edge.v[0])],
+                 'tip_vertex_index': vertex_to_index[<size_t>(edge.v[1])],
+                 'edge_class': edge.e_class.index})
 
             edge = edge.next
 
@@ -500,10 +502,9 @@ cdef class CDirichletDomain():
     def view(self):
         if PolyhedronViewer:
             return ViewerWindow(PolyhedronViewer, facedicts=self.face_list(),
-                title='Dirichlet Domain of %s' % self.manifold_name)
-        else:
-            raise RuntimeError('The PolyhedronViewer class '
-                               'was not imported.')
+                                title=f'Dirichlet Domain of {self.manifold_name}')
+        raise RuntimeError('The PolyhedronViewer class '
+                           'was not imported.')
 
     def manifold(self):
         """

cython/core/fundamental_group.pyx

@@ -5,9 +5,11 @@ Alphabet = '$abcdefghijklmnopqrstuvwxyzZYXWVUTSRQPONMLKJIHGFEDCBA'
 
 # Helper functions for manipulating fg. words
 
+
 def inverse_list_word(word):
     return [ -x for x in word[::-1] ]
 
+
 def reduce_list_word(word):
     """
     Cancels inverse generators.
@@ -20,6 +22,7 @@ def reduce_list_word(word):
             result.append(letter)
     return result
 
+
 cdef c_word_as_int_list(int *word):
     cdef int n = 0
     word_list = []
@@ -125,7 +128,6 @@ cdef class CFundamentalGroup():
             ','.join(self.generators()),
             '\n   '.join(self.relators()))
 
-
     def num_generators(self):
         """
         Return the number of generators for the presentation.
@@ -197,7 +199,7 @@ cdef class CFundamentalGroup():
 
         while len(moves) > 0:
             a = moves.pop(0)
-            if a >= len(words): # new generator added
+            if a >= len(words):  # new generator added
                 n = moves.index(a)  # end symbol location
                 # word is the expression of the new generator in terms
                 # of the old ones
@@ -210,9 +212,9 @@ cdef class CFundamentalGroup():
                 if a == b:  # generator removed
                     words[a] = words[-1]
                     words = words[:-1]
-                elif a == -b: # invert generator
+                elif a == -b:  # invert generator
                     words[a] = inverse_list_word(words[a])
-                else: #handle slide
+                else:  # handle slide
                     A, B = words[abs(a)], words[abs(b)]
                     if a*b < 0:
                         B = inverse_list_word(B)
@@ -473,9 +475,11 @@ class FundamentalGroup(CFundamentalGroup):
         longitude(n)     --> word representing the longitude on cusp #n
     """
 
+
 if _within_sage:
     FundamentalGroup.__bases__ += (sage.structure.sage_object.SageObject,)
 
+
 # Holonomy Groups
 cdef class CHolonomyGroup(CFundamentalGroup):
     def _matrices(self, word):
@@ -527,6 +531,7 @@ cdef class CHolonomyGroup(CFundamentalGroup):
         """
         return self._matrices(word)[2]
 
+
 class HolonomyGroup(CHolonomyGroup):
     """
     A FundamentalGroup represents a presentation of the fundamental
@@ -585,5 +590,6 @@ class HolonomyGroup(CHolonomyGroup):
     def _number_(n):
         return number.number_to_native_number(n)
 
+
 if _within_sage:
     HolonomyGroup.__bases__ += (sage.structure.sage_object.SageObject,)

cython/core/manifold.pyx

@@ -412,10 +412,10 @@ cdef class Manifold(Triangulation):
         return filled
 
     def fundamental_group(self,
-                   simplify_presentation = True,
-                   fillings_may_affect_generators = True,
-                   minimize_number_of_generators = True,
-                   try_hard_to_shorten_relators = True):
+                          simplify_presentation = True,
+                          fillings_may_affect_generators = True,
+                          minimize_number_of_generators = True,
+                          try_hard_to_shorten_relators = True):
         """
         Return a HolonomyGroup representing the fundamental group of
         the manifold, together with its holonomy representation.  If

cython/core/pickle.pyx

@@ -248,8 +248,8 @@ cdef c_Triangulation* unpickle_triangulation(bytes pickle) except *:
     free(cusps)
     return tri
 
-cdef int unpickle_tetrahedron_data(
-    c_TetrahedronData *data, bytes pickle, int start, int flag) except *:
+cdef int unpickle_tetrahedron_data(c_TetrahedronData *data, bytes pickle,
+                                   int start, int flag) except *:
     cdef int i, j, v, f
     cdef int n = start
     cdef unsigned char perm
@@ -324,9 +324,11 @@ cdef c_Triangulation* listlike_to_triangulation(listlike,
     if num_tets == 0:
         raise ValueError('No tetrahedra data provided')
 
-    first = listlike[0]
-    if (len(first) != 2 or len(first[0]) != 4 or
-        not [len(x) for x in first[1]] == [4, 4, 4, 4]):
+    try:
+        first0, first1 = listlike[0]
+    except ValueError:
+        raise ValueError('Tetrahedra data appears invalid')
+    if len(first0) != 4 or [len(x) for x in first1] != [4, 4, 4, 4]:
         raise ValueError('Tetrahedra data appears invalid')
 
     py_name = b'from_data'