Replace imports from sage.all (#123)

* Replace imports from sage.all

* python/snap/polished_reps.py: Use try..except for imports from Sage

* src/snappy/verify/upper_halfspace/finite_point.py: Use try..except for imports from Sage

* python/snap/polished_reps.py: Move try..except for imports to sage_helper

* python/number.py: Go through .sage_helper instead of sage.all

* python/verify/upper_halfspace/finite_point.py: Go through sage_helper instead of using try..except for imports

* python/sage_helper.py: Fix for is_RealIntervalFieldElement

* python/verify/upper_halfspace/ideal_point.py: Go through sage_helper

* python/number.py: If SR cannot be imported, just do not register a coercion

* python/verify/hyperbolicity.py: Go through sage_helper

* python/cusps/maximal_cusp_area_matrix.py: Go through sage_helper

* python/hyperboloid/distances.py: Go through sage_helper

* python/tiling/tile.py: Go through sage_helper

* python/verify/complex_volume/adjust_torsion.py: Go through sage_helper

* python/verify/maximal_cusp_area_matrix/cusp_tiling_engine.py: Go through sage_helper

* python/verify/upper_halfspace/finite_point.py: Go through sage_helper

* python/pari.py: Use try..except for import of PariError

* python/number.py: If SR cannot be imported, just do not register a coercion (fixup)

* python/verify/complex_volume/extended_bloch.py: Go through sage_helper

* python/verify/complex_volume/cusped.py: Go through sage_helper

* python/upper_halfspace/__init__.py: Go through sage_helper for arccosh

* python/database.py: Go through sage_helper

* Use 'from sage.symbolic.constants import pi'

* python/verify/complex_volume/closed.py: Go through sage_helper

* cython/core/fundamental_group.pyx: Use import

* python/testing.py: Use import

* cython/core/abelian_group.pyx: Use import

* cython/core/basic.pyx: Remove .all import

* python/sage_helper.py: Fix import of RealNumber

* python/sage_helper.py: Import Complex* later

* python/verify/upper_halfspace/extended_matrix.py: Use try..except for import

* python/verify/upper_halfspace/ideal_point.py: Use try...except for import

* python/sage_helper.py: Import CIF, RIF

* python/verify/upper_halfspace/extended_matrix.py: Import from sage_helper

* python/sage_helper.py: Add imports from python/snap/find_field.py

* python/sage_helper.py: Add imports from python/exterior_to_link/rational_linear_algebra*.py

* python/sage_helper.py: Import RealField_class

* More imports via sage_helper

* python/sage_helper.py: Import xgcd

* More imports via sage_helper

* Even more imports via sage_helper

* python/sage_helper.py: Import ComplexBallField, exp, sin, block_matrix, prime_range

* python/sage_helper.py: Move imports from nsagetools here

* python/sage_helper.py: Move remaining imports from slice_obs_HKL here

* python/snap/peripheral: Import ChainComplex via sage_helper

---------

Co-authored-by: Matthias Goerner <[email protected]>

cython/core/abelian_group.pyx

@@ -49,7 +49,8 @@ cdef class AbelianGroup():
                                  'as a sequence.')
         int_types = [int]
         if _within_sage:
-            int_types += [sage.rings.integer.Integer]
+            from sage.rings.integer import Integer
+            int_types += [Integer]
         for c in self.divisors:
             assert type(c) in int_types and c >= 0,\
                    'Elementary divisors must be non-negative integers.\n'

cython/core/basic.pyx

@@ -19,7 +19,6 @@ python_major_version = sys.version_info.major
 from .sage_helper import _within_sage, SageNotAvailable
 from .pari import pari as pari
 try:
-    import sage.all
     import sage.structure.sage_object
     from sage.groups.perm_gps.permgroup_element import is_PermutationGroupElement
     from sage.groups.perm_gps.permgroup import PermutationGroup

cython/core/fundamental_group.pyx

@@ -477,7 +477,8 @@ class FundamentalGroup(CFundamentalGroup):
 
 
 if _within_sage:
-    FundamentalGroup.__bases__ += (sage.structure.sage_object.SageObject,)
+    from sage.structure.sage_object import SageObject
+    FundamentalGroup.__bases__ += (SageObject,)
 
 
 # Holonomy Groups
@@ -594,4 +595,5 @@ class HolonomyGroup(CHolonomyGroup):
 
 
 if _within_sage:
-    HolonomyGroup.__bases__ += (sage.structure.sage_object.SageObject,)
+    from sage.structure.sage_object import SageObject
+    HolonomyGroup.__bases__ += (SageObject,)

dev/drilling/smoke_test.py

@@ -5,7 +5,7 @@
 from snappy.drilling import exceptions
 from snappy.drilling import perturb
 
-from sage.all import pi
+from sage.symbolic.constants import pi
 
 # perturb._tube_developing_radius = 1
 

dev/drilling/smoke_test2.py

@@ -5,7 +5,7 @@
 from snappy.drilling import exceptions
 from snappy.drilling import perturb
 
-from sage.all import pi
+from sage.symbolic.constants import pi
 
 # perturb._tube_developing_radius = 1
 

python/cusps/maximal_cusp_area_matrix.py

@@ -9,7 +9,7 @@
 from ..hyperboloid.distances import distance_r13_horoballs
 
 if _within_sage:
-    import sage.all
+    from ..sage_helper import Infinity
 
 def maximal_cusp_area_matrix(manifold, bits_prec, verified):
     """
@@ -63,7 +63,7 @@ def _diagonal_scale(mcomplex, i):
             return e ** 2
 
     if mcomplex.verified:
-        d = mcomplex.RF(sage.all.Infinity)
+        d = mcomplex.RF(Infinity)
     else:
         d = mcomplex.RF(1e20)
 
@@ -93,7 +93,7 @@ def _non_diagonal_scale(mcomplex, i, j):
             return e ** 2
 
     if mcomplex.verified:
-        d = mcomplex.RF(sage.all.Infinity)
+        d = mcomplex.RF(Infinity)
     else:
         d = mcomplex.RF(1e20)
 

python/database.py

@@ -22,17 +22,17 @@
 import collections
 
 if _within_sage:
-    import sage.all
+    from .sage_helper import Integer, RealDoubleElement, RealNumber
 
     def is_int(slice):
-        return isinstance(slice, (sage.all.Integer, int))
+        return isinstance(slice, (Integer, int))
 
     def is_int_or_none(slice):
-        return isinstance(slice, (sage.all.Integer, int, type(None)))
+        return isinstance(slice, (Integer, int, type(None)))
 
     def is_float_or_none(slice):
-        return isinstance(slice, (float, sage.all.RealDoubleElement,
-                                  sage.rings.real_mpfr.RealNumber, type(None)))
+        return isinstance(slice, (float, RealDoubleElement,
+                                  RealNumber, type(None)))
 else:
     def is_int(slice):
         return isinstance(slice, int)

python/exterior_to_link/rational_linear_algebra.py

@@ -17,7 +17,7 @@
 from .. import sage_helper
 
 if sage_helper._within_sage and not use_pari_even_inside_sage:
-    from sage.all import QQ, RR, vector, matrix, VectorSpace
+    from ..sage_helper import QQ, RR, vector, matrix, VectorSpace
 
     def rational_sqrt(x):
         """

python/exterior_to_link/rational_linear_algebra_wrapped.py

@@ -16,7 +16,7 @@
 This file is not currently used by SnapPy, but is kept for possible
 future reference.
 """
-from sage.all import QQ, vector, matrix, VectorSpace
+from ..sage_helper import QQ, vector, matrix, VectorSpace
 
 
 class Vector:

python/geometric_structure/cusp_neighborhood/complex_cusp_cross_section.py

@@ -384,7 +384,8 @@ def _add_one_cusp_vertex_positions(self, cusp : t3m.Vertex):
                     visited.add((tet1.Index, vert1))
 
     def _debug_show_horotriangles(self, cusp : int =0):
-        from sage.all import line, real, imag
+        from sage.plot.line import line
+        from sage.functions.other import real, imag
 
         self.add_vertex_positions_to_horotriangles()
 
@@ -398,7 +399,8 @@ def _debug_show_horotriangles(self, cusp : int =0):
               if tet.Class[V].Index == cusp ])
 
     def _debug_show_lifted_horotriangles(self, cusp : int =0):
-        from sage.all import line, real, imag
+        from sage.plot.line import line
+        from sage.functions.other import real, imag
 
         self.add_vertex_positions_to_horotriangles()
 

python/hyperboloid/distances.py

@@ -8,7 +8,7 @@
 from ..sage_helper import _within_sage # type: ignore
 
 if _within_sage:
-    import sage.all # type: ignore
+    from ..sage_helper import Infinity
 
 __all__ = ['distance_r13_lines',
            'lower_bound_distance_r13_line_triangle']
@@ -183,7 +183,7 @@ def _safe_sqrt(p):
 
     if is_RealIntervalFieldElement(p):
         RIF = p.parent()
-        p = p.intersection(RIF(0, sage.all.Infinity))
+        p = p.intersection(RIF(0, Infinity))
     else:
         if p < 0:
             RF = p.parent()
@@ -193,7 +193,7 @@ def _safe_sqrt(p):
 def _safe_log(p):
     if is_RealIntervalFieldElement(p):
         RIF = p.parent()
-        p = p.intersection(RIF(0, sage.all.Infinity))
+        p = p.intersection(RIF(0, Infinity))
     else:
         if p <= 0:
             RF = p.parent()
@@ -207,7 +207,7 @@ def _safe_log_non_neg(p):
     if p == 0:
         if is_RealIntervalFieldElement(p):
             RIF = p.parent()
-            return RIF(-sage.all.Infinity)
+            return RIF(-Infinity)
         else:
             RF = p.parent()
             return RF(-1e20)
@@ -217,7 +217,7 @@ def _safe_log_non_neg(p):
 def _safe_arccosh(p):
     if is_RealIntervalFieldElement(p):
         RIF = p.parent()
-        p = p.intersection(RIF(1, sage.all.Infinity))
+        p = p.intersection(RIF(1, Infinity))
     else:
         if p < 1:
             RF = p.parent()
@@ -233,9 +233,9 @@ def _safe_div(a, b):
     if is_RealIntervalFieldElement(b):
         RIF = b.parent()
         if b == 0:
-            return RIF(sage.all.Infinity)
+            return RIF(Infinity)
         else:
-            return a / b.intersection(RIF(0, sage.all.Infinity))
+            return a / b.intersection(RIF(0, Infinity))
     else:
         if b <= 0:
             RIF = b.parent()

python/math_basics.py

@@ -21,7 +21,8 @@ def is_Interval(x):
     return is_RealIntervalFieldElement(x) or is_ComplexIntervalFieldElement(x)
 
 if _within_sage:
-    from sage.all import prod, xgcd
+    from .sage_helper import prod, xgcd
+
     from sage.rings.real_mpfi import RealIntervalFieldElement
     from sage.rings.complex_interval import ComplexIntervalFieldElement
 

python/number.py

@@ -11,7 +11,7 @@
 precision_of_exact_GEN = pari(0).precision()
 
 if _within_sage:
-    from sage.all import RealField, Integer, Rational, ZZ, QQ, RR, CC, SR
+    from .sage_helper import RealField, Integer, Rational, ZZ, QQ, RR, CC
     from sage.structure.parent import Parent
     from sage.structure.unique_representation import UniqueRepresentation
     from sage.categories.homset import Hom
@@ -66,8 +66,13 @@ def __init__(self, precision):
             self._precision = precision
             self.register_coercion(MorphismToSPN(ZZ, self, self._precision))
             self.register_coercion(MorphismToSPN(QQ, self, self._precision))
-            to_SR = Hom(self, SR, Sets())(lambda x: SR(x.sage()))
-            SR.register_coercion(to_SR)
+            try:
+                from sage.symbolic.ring import SR
+            except ImportError:
+                pass
+            else:
+                to_SR = Hom(self, SR, Sets())(lambda x: SR(x.sage()))
+                SR.register_coercion(to_SR)
 
         def _repr_(self):
             return "SnapPy Numbers with %s bits precision" % self._precision

python/pari.py

@@ -17,7 +17,11 @@
     from cypari2.pari_instance import (prec_words_to_bits,
                                        prec_bits_to_dec,
                                        prec_dec_to_bits)
-    from sage.all import PariError
+    try:
+        from sage.all import PariError
+    except ImportError:
+        from sage.libs.pari.all import PariError
+
     shut_up = lambda: None
     speak_up = lambda: None
 

python/sage_helper.py

@@ -9,7 +9,7 @@
 """
 
 try:
-    import sage.all
+    import sage.structure.sage_object
     _within_sage = True
 except ImportError:
     _within_sage = False
@@ -22,11 +22,73 @@ def sage_method(function):
         function._sage_method = True
         return function
 
+    try:
+        # Monolithic Sage library
+        from sage.all import RealField, RealDoubleElement, gcd, xgcd, prod, powerset
+        from sage.all import MatrixSpace, matrix, vector, ZZ
+        from sage.all import Integer, Rational, QQ, RR, CC
+        from sage.all import sqrt
+        from sage.all import I, Infinity
+        from sage.all import arccosh
+        from sage.all import RIF, CIF
+        from sage.all import (cached_method, real_part, imag_part, round, ceil, floor, log,
+                              CDF, ComplexDoubleField, ComplexField, CyclotomicField, NumberField, PolynomialRing, identity_matrix)
+        from sage.all import FiniteField as GF
+        from sage.all import VectorSpace, ChainComplex
+        from sage.all import ComplexBallField, exp, sin, block_matrix, prime_range, det
+        from sage.all import LaurentPolynomialRing, AbelianGroup, GroupAlgebra
+    except ImportError:
+        # Modularized Sage library
+        from sage.algebras.group_algebra import GroupAlgebra
+        from sage.arith.misc import gcd, xgcd
+        from sage.combinat.subset import powerset
+        from sage.functions.hyperbolic import arccosh
+        from sage.functions.log import exp
+        from sage.functions.other import (real as real_part,
+                                          imag as imag_part,
+                                          ceil,
+                                          floor)
+        from sage.functions.trig import sin
+        from sage.groups.abelian_gps.abelian_group import AbelianGroup
+        from sage.homology.chain_complex import ChainComplex
+        from sage.matrix.constructor import Matrix as matrix
+        from sage.matrix.matrix_space import MatrixSpace
+        from sage.matrix.special import block_matrix, identity_matrix
+        from sage.misc.cachefunc import cached_method
+        from sage.misc.functional import det, log, round, sqrt
+        from sage.misc.misc_c import prod
+        from sage.modules.free_module import VectorSpace
+        from sage.modules.free_module_element import free_module_element as vector
+        from sage.rings.cc import CC
+        from sage.rings.cif import CIF
+        from sage.rings.complex_arb import ComplexBallField
+        from sage.rings.complex_double import CDF, ComplexDoubleField
+        from sage.rings.complex_mpfr import ComplexField
+        from sage.rings.fast_arith import prime_range
+        from sage.rings.finite_rings.finite_field_constructor import FiniteField as GF
+        from sage.rings.imaginary_unit import I
+        from sage.rings.infinity import Infinity
+        from sage.rings.integer import Integer
+        from sage.rings.integer_ring import ZZ
+        from sage.rings.polynomial.laurent_polynomial_ring import LaurentPolynomialRing
+        from sage.rings.number_field.number_field import CyclotomicField, NumberField
+        from sage.rings.polynomial.polynomial_ring_constructor import PolynomialRing
+        from sage.rings.rational import Rational
+        from sage.rings.rational_field import QQ
+        from sage.rings.real_double import RealDoubleElement
+        from sage.rings.real_mpfi import RIF
+        from sage.rings.real_mpfr import RealField, RealNumber, RR
+
+    from sage.rings.complex_interval_field import ComplexIntervalField
+    from sage.rings.real_mpfi import is_RealIntervalFieldElement, RealIntervalField
+    from sage.rings.real_mpfr import RealNumber, RealField_class
+    from sage.structure.sage_object import SageObject
+
     try:  # Sage >= 9.3, see https://trac.sagemath.org/ticket/24483
         from sage.rings.complex_mpfr import (ComplexField,
                                              ComplexField_class,
                                              create_ComplexNumber)
-    except ModuleNotFoundError:
+    except ImportError:
         from sage.rings.complex_field import ComplexField, ComplexField_class
         from sage.rings.complex_number import create_ComplexNumber
 

python/snap/character_varieties.py

@@ -359,7 +359,7 @@ def character_variety_ideal(gens, rels=None):
     2
     """
     presentation = character_variety(gens, rels)
-    from sage.all import PolynomialRing, QQ
+    from ..sage_helper import PolynomialRing, QQ
     R = PolynomialRing(QQ, [repr(v) for v in presentation.gens])
     return R.ideal([R(p) for p in presentation.rels])
 

python/snap/find_field.py

@@ -1,8 +1,9 @@
-from sage.all import (cached_method, real_part, imag_part, round, ceil, floor, log,
-                      ZZ, QQ, CDF, ComplexField, NumberField, PolynomialRing,
-                      matrix, identity_matrix)
 import itertools
 
+from ..sage_helper import (cached_method, real_part, imag_part, round, ceil, floor, log,
+                           ZZ, QQ, CDF, ComplexField, NumberField, PolynomialRing,
+                           matrix, identity_matrix)
+
 
 def error(poly, z, a=ZZ(0)):
     """

python/snap/fundamental_polyhedron.py

@@ -11,7 +11,7 @@
 
 from ..sage_helper import _within_sage
 if _within_sage:
-    from sage.all import matrix
+    from ..sage_helper import matrix
 else:
     from .utilities import Matrix2x2 as matrix
 

python/snap/nsagetools.py

@@ -5,11 +5,9 @@
 from ..sage_helper import _within_sage, sage_method
 
 if _within_sage:
-    import sage
-    from sage.all import (ZZ, vector, matrix, block_matrix, identity_matrix,
-                          gcd, prod, det, MatrixSpace, AbelianGroup, GroupAlgebra,
-                          SageObject, PolynomialRing, LaurentPolynomialRing)
-
+    from ..sage_helper import ZZ, vector, matrix, block_matrix, identity_matrix, gcd, prod, det
+    from ..sage_helper import MatrixSpace, PolynomialRing, LaurentPolynomialRing
+    from ..sage_helper import SageObject, AbelianGroup, GroupAlgebra
     from .polished_reps import polished_holonomy, MatrixRepresentation
     Id2 = MatrixSpace(ZZ, 2)(1)
 else:

python/snap/peripheral/dual_cellulation.py

@@ -6,7 +6,8 @@
 from .. import t3mlite as t3m
 
 if sage_helper._within_sage:
-    from sage.all import (ZZ, matrix, vector, ChainComplex, Graph)
+    from ...sage_helper import ZZ, matrix, vector, ChainComplex
+    from sage.graphs.graph import Graph
 
 
 class DualCell():

python/snap/peripheral/peripheral.py

@@ -3,7 +3,7 @@
 from . import link, dual_cellulation
 
 if sage_helper._within_sage:
-    from sage.all import matrix, vector, ZZ
+    from ...sage_helper import matrix, vector, ZZ
 
 
 def peripheral_curve_from_snappy(dual_cell, snappy_data):