Support sympy 1.11 to 1.14

.flake8

@@ -7,9 +7,13 @@ ignore =
     # break before binary operator - allow either style
     W504,
     # break after binary operator - allow either style
-exclude=
-    .git,
+
+extend-exclude =
     .venv,
-    build,
-    dev-requirements,
     venv,
+    build,
+    dist,
+    *.egg-info,
+    .pytest_cache,
+    .mypy_cache,
+    .ipynb_checkpoints,

.github/workflows/pytest.yml

@@ -4,11 +4,22 @@ jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        include:
+          - python-version: "3.10"
+            sympy-version: "1.10"
+          - python-version: "3.11"
+            sympy-version: "1.11"
+          - python-version: "3.12"
+            sympy-version: "1.12"
+          - python-version: "3.13"
+            sympy-version: "1.13"
+          - python-version: "3.14"
+            sympy-version: "1.14"
     steps:
     - name: Checkout repository and submodules
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
       with:
         submodules: recursive
     - name: Set up Python ${{ matrix.python-version }}
@@ -20,12 +31,13 @@ jobs:
         python3 -m pip install --upgrade pip
         python3 -m pip install flake8 pytest
         python3 -m pip install .[test]
+        python3 -m pip install "sympy==${{ matrix.sympy-version }}"
     - name: Lint with flake8
       run: |
         python3 -m flake8
     - name: Test sorting with isort
       run: |
-        python3 -m isort --verbose --check-only --diff chaste_codegen tests setup.py
+        python3 -m isort --verbose --check-only --diff chaste_codegen setup.py
     - name: Test with pytest
       run: |
         python3 -m pytest --cov --cov-config=.coveragerc

CONTRIBUTING.md

@@ -53,7 +53,7 @@ $ flake8
 ```
 
 ## Python version
-Python 3.5+
+Python 3.10+
 
 ## Documentation
 

chaste_codegen/_chaste_printer.py

@@ -131,7 +131,7 @@ def _print_ordinary_pow(self, expr):
         """ Handles Pow(), handles just ordinary powers without division.
         For C++ printing we need to write ``x**y`` as ``pow(x, y)`` with lowercase ``p``."""
         p = precedence(expr)
-        if expr.exp == 0.5:
+        if (expr.exp - S.Half).is_zero:  # expr.exp == 0.5
             return 'sqrt(' + self._bracket(expr.base, p) + ')'
         return 'pow(' + self._bracket(expr.base, p) + ', ' + self._bracket(expr.exp, p) + ')'
 
@@ -185,7 +185,7 @@ def _print_Mul(self, expr):
         # Gather terms for numerator and denominator
         a, b = [], []
         for item in Mul.make_args(expr):
-            if item != 1.0:  # In multiplications remove 1.0 * ...
+            if not (item - S.One).is_zero:  # In multiplications remove 1.0 * ...
                 # Check if this is a negative power and it's not in a lookup table, so we can write it as a division
                 if (item.is_commutative and item.is_Pow and item.exp.is_Rational and item.exp.is_negative
                         and not self.lookup_table_function(item)):

chaste_codegen/_linearity_check.py

@@ -10,6 +10,7 @@
     Mul,
     Piecewise,
     Pow,
+    S,
     log,
 )
 from sympy.codegen.cfunctions import log2, log10
@@ -101,7 +102,7 @@ def max_kind(state_var, operands):
     elif isinstance(expr, Pow):
         if state_var not in expr.free_symbols:
             result = max_kind(state_var, operands)
-        elif len(expr.args) == 2 and expr.args[1] == -1:  # x/y divide is represented as x * pow(y, -1)
+        elif len(expr.args) == 2 and (expr.args[1] + S.One).is_zero:  # x/y divide is represented as x * pow(y, -1)
             # Linear iff only numerator linear
             result = _check_expr(expr.args[0], state_var, membrane_voltage_var, state_vars)
         else:

chaste_codegen/_lookup_tables.py

@@ -2,6 +2,7 @@
 from sympy import (
     Piecewise,
     Pow,
+    S,
     Symbol,
     acos,
     acosh,
@@ -132,7 +133,7 @@ def _set_lookup_table_if_appropriate(self, exp_func, vars_used, expr, in_pw):
 
         # Prevent putting expressions of the form 1 / A since the expressions might cause a singularity in the table
         # since expressions being analised might the bottom of a GHK equation os similar
-        if isinstance(expr, Pow) and expr.args[1] == -1.0:
+        if isinstance(expr, Pow) and (expr.args[1] + S.One).is_zero:  # ... and expr.args[1] == -1.0
             expr = expr.args[0]
 
         if exp_func and expr not in self._lookup_table_expr and \

chaste_codegen/_math_functions.py

@@ -76,7 +76,8 @@ def fdiff(self, argindex=1):
 
 
 # MATH_FUNC_SYMPY_MAPPING provides a mapping from our specified math functions back to sympy versions.
-# This can be used to put sympy function into an expression or evaluation. e.g. `expr.subs(MATH_FUNC_SYMPY_MAPPING)`.
+# Apply it via subs_math_func_placeholders(), which uses expr.replace(). Do not use expr.subs() with this
+# mapping as sympy >= 1.12 strictly sympifies the substitution values and rejects e.g. the sqrt function.
 MATH_FUNC_SYMPY_MAPPING = {abs_: Abs, acos_: acos, cos_: cos, exp_: exp, sin_: sin, sqrt_: sqrt}