Support sympy 1.11 to 1.14

[kwabenantim]

Description

Add support for newer versions of sympy

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

• Testing is done automatically and codecov shows test coverage
• This cannot be tested automatically

[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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