ModellingWebLab · kwabenantim · Jul 15, 2026 · Jul 15, 2026 · Jul 15, 2026 · Jul 15, 2026
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -5,10 +5,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
     steps:
     - name: Checkout repository and submodules
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
       with:
         submodules: recursive
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -53,7 +53,7 @@ $ flake8
 ```
 
 ## Python version
-Python 3.5+
+Python 3.10+
 
 ## Documentation
 

diff --git a/chaste_codegen/_math_functions.py b/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}
 
 

diff --git a/...E/aslanidi_atrial_model_2009.cpp_python36 → ...slanidi_atrial_model_2009--sympy_1_11.cpp b/...E/aslanidi_atrial_model_2009.cpp_python36 → ...slanidi_atrial_model_2009--sympy_1_11.cpp
diff --git a/..._codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009--sympy_1_13.cpp b/..._codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009--sympy_1_13.cpp
diff --git a/..._codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009--sympy_1_14.cpp b/..._codegen/data/tests/chaste_reference_models/BE/aslanidi_atrial_model_2009--sympy_1_14.cpp
diff --git a/...tt_kim_rasmusson_2004_apical.cpp_python36 → ...kim_rasmusson_2004_apical--sympy_1_11.cpp b/...tt_kim_rasmusson_2004_apical.cpp_python36 → ...kim_rasmusson_2004_apical--sympy_1_11.cpp
diff --git a/...ste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_13.cpp b/...ste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_13.cpp
diff --git a/...ste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_14.cpp b/...ste_reference_models/BE/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_14.cpp
diff --git a/...temanche_ramirez_nattel_1998.cpp_python36 → ...anche_ramirez_nattel_1998--sympy_1_11.cpp b/...temanche_ramirez_nattel_1998.cpp_python36 → ...anche_ramirez_nattel_1998--sympy_1_11.cpp
diff --git a/...tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_13.cpp b/...tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_13.cpp
diff --git a/...tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_14.cpp b/...tests/chaste_reference_models/BE/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_14.cpp
diff --git a/...ni_bers_2010_ssBackwardEuler.cpp_python36 → ...bers_2010_ssBackwardEuler--sympy_1_11.cpp b/...ni_bers_2010_ssBackwardEuler.cpp_python36 → ...bers_2010_ssBackwardEuler--sympy_1_11.cpp
diff --git a/...ts/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler--sympy_1_13.cpp b/...ts/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler--sympy_1_13.cpp
diff --git a/...ts/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler--sympy_1_14.cpp b/...ts/chaste_reference_models/BE/grandi_pasqualini_bers_2010_ssBackwardEuler--sympy_1_14.cpp
diff --git a/...ence_models/BE/li_mouse_2010.cpp_python36 → ...e_models/BE/li_mouse_2010--sympy_1_11.cpp b/...ence_models/BE/li_mouse_2010.cpp_python36 → ...e_models/BE/li_mouse_2010--sympy_1_11.cpp
diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010--sympy_1_13.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010--sympy_1_13.cpp
diff --git a/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010--sympy_1_14.cpp b/chaste_codegen/data/tests/chaste_reference_models/BE/li_mouse_2010--sympy_1_14.cpp
diff --git a/...tt_kim_rasmusson_2004_apical.cpp_python36 → ...kim_rasmusson_2004_apical--sympy_1_11.cpp b/...tt_kim_rasmusson_2004_apical.cpp_python36 → ...kim_rasmusson_2004_apical--sympy_1_11.cpp
diff --git a/..._reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_13.cpp b/..._reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_13.cpp
diff --git a/..._reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_14.cpp b/..._reference_models/BEopt/bondarenko_szigeti_bett_kim_rasmusson_2004_apical--sympy_1_14.cpp
diff --git a/...nce_models/BEopt/decker_2009.cpp_python36 → ..._models/BEopt/decker_2009--sympy_1_11.cpp b/...nce_models/BEopt/decker_2009.cpp_python36 → ..._models/BEopt/decker_2009--sympy_1_11.cpp
diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009--sympy_1_13.cpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009--sympy_1_13.cpp
diff --git a/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009--sympy_1_14.cpp b/chaste_codegen/data/tests/chaste_reference_models/BEopt/decker_2009--sympy_1_14.cpp
diff --git a/...temanche_ramirez_nattel_1998.cpp_python36 → ...anche_ramirez_nattel_1998--sympy_1_11.cpp b/...temanche_ramirez_nattel_1998.cpp_python36 → ...anche_ramirez_nattel_1998--sympy_1_11.cpp
diff --git a/...ts/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_13.cpp b/...ts/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_13.cpp
diff --git a/...ts/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_14.cpp b/...ts/chaste_reference_models/BEopt/dynamic_courtemanche_ramirez_nattel_1998--sympy_1_14.cpp
diff --git a/...tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers--sympy_1_13.cpp b/...tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers--sympy_1_13.cpp
diff --git a/...tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers--sympy_1_14.cpp b/...tests/chaste_reference_models/CVODE_DATA_CLAMP/Shannon2004_with_modifiers--sympy_1_14.cpp
diff --git a/...egen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996--sympy_1_13.cpp b/...egen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996--sympy_1_13.cpp
diff --git a/...egen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996--sympy_1_14.cpp b/...egen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dokos_model_1996--sympy_1_14.cpp
diff --git a/...n/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004--sympy_1_13.cpp b/...n/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004--sympy_1_13.cpp
diff --git a/...n/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004--sympy_1_14.cpp b/...n/data/tests/chaste_reference_models/CVODE_DATA_CLAMP/dynamic_Shannon2004--sympy_1_14.cpp
diff --git a/...ence_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp--sympy_1_13.cpp b/...ence_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp--sympy_1_13.cpp
diff --git a/...ence_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp--sympy_1_14.cpp b/...ence_models/CVODE_DATA_CLAMP/grandi_pasqualini_bers_2010_ssCvodeDataClamp--sympy_1_14.cpp
diff --git a/...dels/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt--sympy_1_13.cpp b/...dels/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt--sympy_1_13.cpp
diff --git a/...dels/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt--sympy_1_14.cpp b/...dels/CVODE_DATA_CLAMP_OPT/grandi_pasqualini_bers_2010_ssCvodeDataClampOpt--sympy_1_14.cpp
diff --git a/...uid_axon_model_1952_modified.cpp_python36 → ..._axon_model_1952_modified--sympy_1_13.cpp b/...uid_axon_model_1952_modified.cpp_python36 → ..._axon_model_1952_modified--sympy_1_13.cpp