Support sympy 1.11 to 1.14 by kwabenantim · Pull Request #306 · ModellingWebLab/chaste-codegen

kwabenantim · 2026-07-15T16:11:16Z

Description

Add support for newer versions of sympy

Use expr.replace() instead of expr.subs() where appropriate due to subs strictly requiring Sympy objects in 1.12+.
Made changes required for Float/Integer equality comparisons in sympy 1.13+.
Bumped minimum Python to 3.10 and upgraded dependencies to 3.10+ compatible ones.
Removed 33 legacy _alt and _python36 reference code variants.
Added 58 version dependent reference code variants:
- 19 sympy_1_11 variants due to coefficient folding in diff.
- 2 sympy_1_13 variants due to extracting negative Float exponents in Add.
- 32 sympy_1_14 variants due to disabling Float exponent extractions in Add.
- 5 python_3_11 variants due to a different ionic current sum ordering in Python3.10 + Pint 0.24, resulting from a Float(1.0) passing into coefficients e.g. 1.0 * HeartConfig::Instance()->GetCapacitance() in _get_ionic_vars. The 1.0 disappears in a different Python or Pint version.
Added helpers for version-referenced tests.
Added all supported sympy versions on CI.

Note

The added regenerate_reference(..) in conftest.py currently piggy-backs on the tests to generate reference files. It could possibly be moved into a separate "infra scripts" folder, but it might not be worth creating an infra section for just the one case. Also, it automatically labels variants with the sympy version used to generate them as this causes the majority of differences, so some manual renaming may be needed if e.g. the Python version is the cause of the difference.

Motivation and Context

Fixes #285

Types of changes

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to change)

Documentation checklist

I have updated all documentation in the code where necessary.
I have checked spelling in all (new) comments and documentation.
I have added a note to RELEASE.md if relevant (new feature, breaking change, or notable bug fix).
I have updated version & citation.txt & citation.cff version.

Testing

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Copilot

Pull request overview

This PR updates chaste_codegen to work with newer SymPy releases by broadening dependency constraints, adapting placeholder math-function substitution for SymPy’s stricter sympification behavior, and updating tests/reference outputs to support per-SymPy-version “golden” files.

Changes:

Updated setup.py dependency minimums/maximums (including SymPy, Pint, NetworkX, etc.) to target newer ecosystems.
Added SymPy-version-aware reference selection and updated Jacobian tests to use it, alongside new --sympy_X_Y reference variants.
Regenerated/adjusted stored reference models and removed legacy Python 3.6 reference artifacts.

Reviewed changes

Copilot reviewed 20 out of 72 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
setup.py	Bumps runtime dependency constraints to support newer SymPy and related packages.
docs/index.rst	Updates contributor instructions for dependency bumps and versioned reference files.
dev-requirements/dev.txt	Updates pinned dev dependency versions (notably Pint).
chaste_codegen/tests/test_jacobian.py	Switches Jacobian tests to SymPy-versioned reference reading.
chaste_codegen/tests/conftest.py	Adds SymPy-versioned reference selection and optional reference regeneration mode.
chaste_codegen/model_with_conversions.py	Uses `subs_math_func_placeholders` to avoid SymPy `subs` sympification issues.
chaste_codegen/_math_functions.py	Documents correct placeholder substitution approach for SymPy >= 1.12.
chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36	Removes legacy Python 3.6-specific expected output.
chaste_codegen/data/tests/test_jacobian_matrix_2.txt_alt	Removes alternate legacy expected output format.
chaste_codegen/data/tests/test_jacobian_matrix_2--sympy_1_13.txt	Adds SymPy 1.13-specific Jacobian matrix expected output.
chaste_codegen/data/tests/test_jacobian_matrix_2--sympy_1_11.txt	Adds SymPy 1.11-specific Jacobian matrix expected output.
chaste_codegen/data/tests/test_jacobian_matrix_1.txt_python36	Removes legacy Python 3.6-specific expected output.
chaste_codegen/data/tests/test_jacobian_matrix_1.txt_alt	Removes alternate legacy expected output format.
chaste_codegen/data/tests/test_jacobian_matrix_1--sympy_1_11.txt	Adds SymPy 1.11-specific Jacobian matrix expected output.
chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36	Removes legacy Python 3.6-specific expected output.
chaste_codegen/data/tests/test_jacobian_equations_2.txt_alt	Removes alternate legacy expected output format.
chaste_codegen/data/tests/test_jacobian_equations_2.txt	Updates baseline expected output to match newer SymPy behavior.
chaste_codegen/data/tests/test_jacobian_equations_1.txt_python36	Removes legacy Python 3.6-specific expected output.
chaste_codegen/data/tests/test_jacobian_equations_1.txt_alt	Removes alternate legacy expected output format.
chaste_codegen/data/tests/test_jacobian_equations_1.txt	Updates baseline expected output to match newer SymPy behavior.
chaste_codegen/data/tests/chaste_reference_models/RLopt/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.
chaste_codegen/data/tests/chaste_reference_models/RL/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Adds generated reference output for SymPy 1.13 (RL model type).
chaste_codegen/data/tests/chaste_reference_models/Opt/test_luo_rudy_1991_with_range_cap_dimensionless.cpp_python36	Removes legacy Python 3.6 generated reference output.
chaste_codegen/data/tests/chaste_reference_models/Opt/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.
chaste_codegen/data/tests/chaste_reference_models/Opt/beeler_reuter_model_1977_lookup_tables.cpp_python36	Removes legacy Python 3.6 generated reference output.
chaste_codegen/data/tests/chaste_reference_models/GRL2Opt/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.
chaste_codegen/data/tests/chaste_reference_models/GRL2/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.
chaste_codegen/data/tests/chaste_reference_models/GRL1Opt/beeler_reuter_model_1977--sympy_1_11.cpp	Updates generated reference output for SymPy 1.11 behavior.
chaste_codegen/data/tests/chaste_reference_models/GRL1/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.
chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Adds generated reference output for SymPy 1.13 (Cvode + Jacobian).
chaste_codegen/data/tests/chaste_reference_models/Cvode_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_11.cpp	Updates generated reference output for SymPy 1.11 behavior.
chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Adds generated reference output for SymPy 1.13 (Cvode opt + Jacobian).
chaste_codegen/data/tests/chaste_reference_models/Cvode_opt_with_jacobian/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_11.cpp	Updates generated reference output for SymPy 1.11 behavior.
chaste_codegen/data/tests/chaste_reference_models/CVODE_DATA_CLAMP_OPT/hodgkin_huxley_squid_axon_model_1952_modified--sympy_1_13.cpp	Updates generated reference output for SymPy 1.13 behavior.

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…rsion

…erences

…fected variants

…kup-table and linearity analysis

Copilot

Pull request overview

Copilot reviewed 26 out of 86 changed files in this pull request and generated 2 comments.

codecov · 2026-07-20T15:11:06Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (7878bf3) to head (f0d6978).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##            master      #306   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           30        30           
  Lines         1789      1789           
=========================================
  Hits          1789      1789

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…variants for ionic term ordering

…ts to python_3_11

Copilot

Pull request overview

Copilot reviewed 32 out of 102 changed files in this pull request and generated 4 comments.

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

MichaelClerx

Quick look at the first model files shows what looks like big differences in code.

Are these significant? And is this the best way to test if we have to manually review 100 files?

MichaelClerx · 2026-07-22T13:11:09Z

        const double var_background_currents__E_Ca = 0.5 * var_membrane__R * var_membrane__T * log(mParameters[1] / var_chaste_interface__intracellular_ion_concentrations__Ca_i) / var_membrane__F; // millivolt
-        const double var_Ca_independent_transient_outward_K_current__i_sus = (((var_environment__CT == 1) && (var_environment__PM == 0)) ? (0.098000000000000004 + 0.0014 * var_chaste_interface__membrane__V) : (((var_environment__CT == 0) && (var_environment__PM == 1)) ? (0.16799999999999998 + 0.0023999999999999998 * var_chaste_interface__membrane__V) : (0.070000000000000007 + 0.001 * var_chaste_interface__membrane__V))); // picoA
-        const double var_Ca_independent_transient_outward_K_current__i_to = (((var_environment__CT == 1) && (var_environment__PM == 0)) ? (0.20000000000000001 * (0.40000000000000002 + 0.59999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s3_gate__s3, 6)) * (-var_Ca_independent_transient_outward_K_current__E_K + var_chaste_interface__membrane__V) * (0.58999999999999997 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s1_gate__s1, 3) + 0.40999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s2_gate__s2, 3)) * var_Ca_independent_transient_outward_K_current__g_to * var_chaste_interface__Ca_independent_transient_outward_K_current_r_gate__r) : (((var_environment__CT == 0) && (var_environment__PM == 1)) ? (0.34999999999999998 * (0.40000000000000002 + 0.59999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s3_gate__s3, 6)) * (-var_Ca_independent_transient_outward_K_current__E_K + var_chaste_interface__membrane__V) * (0.58999999999999997 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s1_gate__s1, 3) + 0.40999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s2_gate__s2, 3)) * var_Ca_independent_transient_outward_K_current__g_to * var_chaste_interface__Ca_independent_transient_outward_K_current_r_gate__r) : ((0.40000000000000002 + 0.59999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s3_gate__s3, 6)) * (-var_Ca_independent_transient_outward_K_current__E_K + var_chaste_interface__membrane__V) * (0.58999999999999997 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s1_gate__s1, 3) + 0.40999999999999998 * pow(var_chaste_interface__Ca_independent_transient_outward_K_current_s2_gate__s2, 3)) * var_Ca_independent_transient_outward_K_current__g_to * var_chaste_interface__Ca_independent_transient_outward_K_current_r_gate__r))); // picoA
+        const double var_Ca_independent_transient_outward_K_current__i_sus = (((var_environment__CT == 1) && (var_environment__PM == 0)) ? (0.098000000000000004 + 0.0014 * var_chaste_interface__membrane__V) : (((var_environment__PM == 1) && (var_environment__CT == 0)) ? (0.16799999999999998 + 0.0023999999999999998 * var_chaste_interface__membrane__V) : (0.070000000000000007 + 0.001 * var_chaste_interface__membrane__V))); // picoA


Is this just pseudo-random differences? Or were we e.g. sorting before but not now? Would be nice to avoid reviewing a 100 models 😅

Good point! Sorry about the number of new reference files. In this particular one, it looks like I've managed to confuse git into thinking an old python 3.6 alternative reference (which has been deleted) was renamed to a newly added alternative reference generated with sympy 1.14.

It might be worth adding in some numerical tests to check things.

This ordering is pre-existing between the python 3.6 variant and the original reference as well.

MichaelClerx · 2026-07-22T13:12:18Z

-        const double var_x10 = 1 / (1.3999999999999999 + var_x9 + 0.80000000000000004 * var_chaste_interface__Ca_handling_by_the_SR__Ca_up);
-        const double var_x11 = (var_x9 - 0.32000000000000006 * var_chaste_interface__Ca_handling_by_the_SR__Ca_up) / pow((0.00041999999999999996 + 0.00023999999999999998 * var_chaste_interface__Ca_handling_by_the_SR__Ca_up + var_chaste_interface__intracellular_ion_concentrations__Ca_i), 2);
-        const double var_x12 = 0.23999999999999999 * exp(-1.6000000000000001 + 0.080000000000000002 * var_chaste_interface__membrane__V);
+        const double var_x8 = 1.3999999999999999 + 0.80000000000000004 * var_chaste_interface__Ca_handling_by_the_SR__Ca_up + 3333.3333333333335 * var_chaste_interface__intracellular_ion_concentrations__Ca_i;


These look like real differences. What's going on?

This is also pre-existing between Python 3.6 and the main reference, although it's a bit different there as well with:

const double var_x8 = 1 / (1.3999999999999999 + 0.80000000000000004 * var_chaste_interface__Ca_handling_by_the_SR__Ca_up + 3333.3333333333335 * var_chaste_interface__intracellular_ion_concentrations__Ca_i);

Probably needs numerical testing.

Might just be re-organising the temporary variables to represent different bits of calculation for some reason. I think the numerical tests are done within Chaste, so could try and run it with this branch if that's possible?

https://github.com/Chaste/Chaste/tree/develop/heart/test/ionicmodels/TestCodegenLong

MichaelClerx · 2026-07-22T13:12:34Z

        rJacobian[1][13] = 0.0;
        rJacobian[2][0] = 0.0;
        rJacobian[2][1] = 0.0;
-        rJacobian[2][2] = 1.0 - (mDt * (-var_x12 - var_x17));


What's happening here?

This also seems to be pre-existing between the Python 3.6 version and the main reference, although the original main reference has something slightly different:

rJacobian[2][2] = 1.0 - (mDt * (-var_x16));

I think these may be due to a stale Python 3.6 alternative version, but definitely worth putting in some numerical testing!

kwabenantim · 2026-07-22T15:20:42Z

Quick look at the first model files shows what looks like big differences in code.

Are these significant? And is this the best way to test if we have to manually review 100 files?

Thanks @MichaelClerx . These particular changes are pre-existing and don't appear to be significant. I am getting all the generated reference models to run through numerical testing, so we probably don't need to review all of those manually.

kwabenantim added 7 commits July 15, 2026 12:36

#285 Bump up to Python 3.10-compatible dependencies

81bed7a

#285 Pin Pint to 0.25.3 in the dev requirements

e944ead

#285 Fix model loading on sympy 1.12 and later

615b4b6

#285 Select test reference files per sympy version

008108f

#285 Add per-sympy-version variants of the generated code references

dfc6adf

#285 Version jacobian references and remove version-specific excludes

7af23b3

#285 Document the versioned reference scheme

ffad5e3

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kwabenantim added 10 commits July 15, 2026 21:46

#285 Bump minimum Python to 3.10

2032a4d

#285 Fix docs grammar and formatting

81bb1b7

#285 Declare Python 3.10-3.14 support in metadata and docs

1533699

#285 Version linearity-check and lookup-table references per sympy ve…

fb5ce1d

…rsion

#285 Add per-sympy-version console-script and string reference variants

732fce4

#285 Version the partial-eval reference per sympy version

46736ff

#285 Fix printer 1.0 comparison

6dc6ae7

#285 Regenerate per-sympy reference variants and version jacobian ref…

2064cd2

…erences

#285 Use structural is_zero for sqrt exponent check and regenerate af…

c3e2e61

…fected variants

#285 Use structural is_zero for reciprocal and division checks in loo…

a478d52

…kup-table and linearity analysis

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kwabenantim added 4 commits July 17, 2026 16:16

#285 Fix release.txt references

23e1151

#285 Parse sympy version with a regex to tolerate pre-release formats

f5deb05

#285 Pair each Python version with a specific sympy version in CI

ee63b09

#285 Require cellmlmanip >= 0.3.8

dd1b001

kwabenantim added 2 commits July 20, 2026 19:22

#285 Rebase base references to Python 3.10 output and add sympy_1_11 …

966a244

…variants for ionic term ordering

#285 Use flake extend-exclude

cd2034c

#285 Accept any matching reference variant and rename ordering varian…

af4051f

…ts to python_3_11

kwabenantim marked this pull request as ready for review July 21, 2026 16:58

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mirams and others added 5 commits July 21, 2026 20:51

Potential fix for pull request finding

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#285 Remove stale tests path from isort step

95e5859

#285 Refactor and document test reference-comparison helpers

88941af

#285 Move reference-comparison harness tests into test_conftest.py

004db77

kwabenantim requested review from MichaelClerx and mirams July 22, 2026 12:59

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