compute propagator for each block of block-diagonal system matrix

.github/workflows/ode-toolbox-build.yml

@@ -43,7 +43,7 @@ jobs:
       fail-fast: false
       matrix:
         with_gsl: ["0", "1"]
-        sympy_version: ["==1.4", "!=1.5,!=1.5.*,!=1.6rc1,!=1.6rc2,!=1.6,!=1.6.*,!=1.10,!=1.10.*,!=1.13,!=1.13.*"]
+        sympy_version: ["==1.4", ""]  # empty string for "latest"
 
     steps:
       - name: Checkout ODE-toolbox code

odetoolbox/system_of_shapes.py

@@ -203,7 +203,6 @@ def _generate_propagator_matrix(self, A):
         XXX: the default custom simplification expression does not work well with sympy 1.4 here. Consider replacing sympy.simplify() with _custom_simplify_expr() if sympy 1.4 support is dropped.
         """
 
-
         # naive: calculate propagators in one step
         # P_naive = sympy.simplify(sympy.exp(A * sympy.Symbol(Config().output_timestep_symbol)))
 

requirements.txt

@@ -1,4 +1,4 @@
-sympy!=1.5,!=1.5.*,!=1.6rc1,!=1.6rc2,!=1.6,!=1.6.*,!=1.10,!=1.10.*,!=1.13,!=1.13.*
+sympy>=1.13
 scipy
 numpy>=1.8.2
 pytest

tests/test_system_matrix_construction.py

@@ -34,9 +34,9 @@ def test_system_matrix_construction(self):
         shapes, parameters = _from_json_to_shapes(indict)
         sigma, beta = sympy.symbols("sigma beta")
         shape_sys = SystemOfShapes.from_shapes(shapes, parameters=parameters)
-        assert shape_sys.A_ == sympy.Matrix([[-sigma, sigma, 0.0],
-                                             [0.0, 0.0, 0.0],
-                                             [0.0, 0.0, -beta]])
+        assert shape_sys.A_ == sympy.Matrix([[-sigma, sigma, 0],
+                                              [0, 0, 0],
+                                              [0, 0, -beta]])
         x, y, z = sympy.symbols("x y z")
         assert shape_sys.c_ == sympy.Matrix([[0],
                                              [3 * z * x**2 - x * y],
@@ -63,10 +63,10 @@ def test_morris_lecar(self):
         shape_sys = SystemOfShapes.from_shapes(shapes, parameters=parameters)
         C_m, g_Ca, g_K, g_L, E_Ca, E_K, E_L, I_ext = sympy.symbols("C_m g_Ca g_K g_L E_Ca E_K E_L I_ext")
         assert shape_sys.A_ == sympy.Matrix([[sympy.parsing.sympy_parser.parse_expr("-500.0 * g_Ca / C_m - 1000.0 * g_L / C_m"), sympy.parsing.sympy_parser.parse_expr("1000.0 * E_K * g_K / C_m")],
-                                            [sympy.parsing.sympy_parser.parse_expr("0.0"), sympy.parsing.sympy_parser.parse_expr("0.0")]])
+                                            [sympy.parsing.sympy_parser.parse_expr("0"), sympy.parsing.sympy_parser.parse_expr("0")]])
 
         V, W = sympy.symbols("V W")
         assert shape_sys.b_ == sympy.Matrix([[sympy.parsing.sympy_parser.parse_expr("500.0 * E_Ca * g_Ca / C_m + 1000.0 * E_L * g_L / C_m + 1000.0 * I_ext / C_m")],
-                                             [sympy.parsing.sympy_parser.parse_expr("0.0")]])
+                                             [sympy.parsing.sympy_parser.parse_expr("0")]])
         assert shape_sys.c_ == sympy.Matrix([[sympy.parsing.sympy_parser.parse_expr("500.0 * E_Ca * g_Ca * tanh(V / 15 + 1 / 15) / C_m - 1000.0 * V * W * g_K / C_m - 500.0 * V * g_Ca * tanh(V / 15 + 1 / 15) / C_m")],
                                              [sympy.parsing.sympy_parser.parse_expr("-200.0 * W * cosh(V / 60) + 100.0 * cosh(V / 60) * tanh(V / 30) + 100.0 * cosh(V / 60)")]])