Add copy-base-classes command and rename package to chaste-sbml

[kwabenantim]

Summary

Supports #39

• Add a copy-base-classes subcommand and copy_base_classes() that copy the bundled C++ base classes out of the installed package; ship them as package data.
• Split the CLI into generate and copy-base-classes subcommands.
• Rename the console command to chaste-sbml and the import package to chaste_sbml (distribution chaste-sbml); update imports, coverage config, CI workflows and the SbmlRefModels infra scripts.
• Run main() under main so 'python -m chaste_sbml' works.
• Update the README and tests.

[Copilot]

Pull request overview

This PR renames the Python distribution/import package to chaste-sbml / chaste_sbml, adds a copy-base-classes CLI command to extract bundled C++ base/helper classes from an installed package, and expands the bundled SbmlRefModels C++ project + infra to support reference/case generation and CI.

Changes:

• Introduces a chaste-sbml CLI with generate and copy-base-classes subcommands, plus python -m chaste_sbml support.
• Bundles C++ base/helper classes as package data and adds Python APIs/tests to enumerate and copy them out (copy_base_classes()).
• Renames package/imports/config (coverage, CI workflows) from chaste_codegen_sbml to chaste_sbml and adds/updates SbmlRefModels sources, tests, and infra scripts.

Reviewed changes

Copilot reviewed 21 out of 119 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
README.md	Updates usage docs for new CLI/subcommands and venv setup.
pyproject.toml	Renames distribution + console script; adds package-data for bundled C++ files.
.coveragerc	Switches coverage source/omits to chaste_sbml.
.github/workflows/build_and_test.yml	Updates CI install/test steps and Chaste project symlink path.
.github/workflows/sbml_test_suite.yml	Updates SBML test-suite workflow path to new package location.
chaste_sbml/init.py	Exposes copy_base_classes in the public package API.
chaste_sbml/main.py	New CLI entrypoint with generate + copy-base-classes subcommands.
chaste_sbml/_base_classes.py	Implements discovery/copying of bundled C++ base/helper classes.
chaste_sbml/_config.py	New config/enums under renamed package.
chaste_sbml/_utils.py	New utility module under renamed package.
chaste_sbml/chaste_sbml_model.py	Updates Jinja PackageLoader to the new import package name.
chaste_sbml/.clang-format	Adds formatting config for C++ in SbmlRefModels.
chaste_sbml/.clang-format-ignore	Excludes Jinja templates from formatting.
chaste_sbml/templates/ode/ode.hpp	Adds ODE C++ generation template.
chaste_sbml/templates/srn/srn.hpp	Adds SRN model header generation template.
chaste_sbml/templates/srn/srn.cpp	Adds SRN model source generation template.
chaste_sbml/templates/cell_cycle/cell_cycle.hpp	Adds cell-cycle model header generation template.
chaste_sbml/templates/cell_cycle/cell_cycle.cpp	Adds cell-cycle model source generation template.
chaste_sbml/templates/cases/semantic.hpp	Adds semantic case test template.
chaste_sbml/tests/test_utils.py	Updates imports to chaste_sbml.
chaste_sbml/tests/test_generation.py	Updates imports to chaste_sbml.
chaste_sbml/tests/test_chaste_sbml_model.py	Updates imports to chaste_sbml.
chaste_sbml/tests/test_console.py	Adds tests for new chaste-sbml CLI behavior.
chaste_sbml/tests/test_base_classes.py	Adds tests for base-class discovery and copying.
chaste_sbml/SbmlRefModels/CMakeLists.txt	Adds Chaste project wiring for SbmlRefModels.
chaste_sbml/SbmlRefModels/README.md	Documents bundled C++ project purpose.
chaste_sbml/SbmlRefModels/generate_references.py	Updates generator to import chaste_sbml.
chaste_sbml/SbmlRefModels/generate_cases.py	Updates generator to import chaste_sbml.
chaste_sbml/SbmlRefModels/infra/.gitignore	Ignores build/output directories for infra scripts.
chaste_sbml/SbmlRefModels/infra/configure.sh	Adds helper script to configure a Chaste build for the project.
chaste_sbml/SbmlRefModels/infra/compile.sh	Adds helper script to build the project target.
chaste_sbml/SbmlRefModels/infra/test_references.sh	Adds helper script to run reference-model tests by label/name.
chaste_sbml/SbmlRefModels/infra/test_cases.sh	Adds helper script to run generated semantic tests based on status CSV/range.
chaste_sbml/SbmlRefModels/infra/reset_cases.sh	Updates paths to new package location for case reset flow.
chaste_sbml/SbmlRefModels/infra/generate_references.sh	Updates paths to new package location for reference generation flow.
chaste_sbml/SbmlRefModels/infra/generate_cases.sh	Updates paths to new package location for case generation flow.
chaste_sbml/SbmlRefModels/infra/filter_test_suite_cases.py	Adds utility to select cases + emit a ctest regex.
chaste_sbml/SbmlRefModels/infra/check_passing_cases_generated.py	Adds guard to ensure “pass” cases actually generate tests.
chaste_sbml/SbmlRefModels/test/CMakeLists.txt	Adds Chaste test-project definition for SbmlRefModels.
chaste_sbml/SbmlRefModels/test/.gitignore	Ignores WeeklyTestPack.txt in test directory.
chaste_sbml/SbmlRefModels/test/ContinuousTestPack.txt	Adds/updates the continuous test pack list.
chaste_sbml/SbmlRefModels/test/data/goldbeter_1991_srn_results.parameters	Adds reference test data file.
chaste_sbml/SbmlRefModels/test/reference/TestGoldbeter1991SbmlOdeSystem.hpp	Adds reference test for Goldbeter 1991 ODE system.
chaste_sbml/SbmlRefModels/test/reference/TestGardner1998SbmlCellCycleModel.hpp	Adds reference test for Gardner 1998 cell-cycle model.
chaste_sbml/SbmlRefModels/test/reference/TestChen2000SbmlCellCycleModel.hpp	Adds reference test for Chen 2000 cell-cycle model.
chaste_sbml/SbmlRefModels/test/reference/TestTan2014SbmlSrnModel.hpp	Adds reference test for Tan 2014 SRN model.
chaste_sbml/SbmlRefModels/test/reference/TestVanLeeuwen2007SbmlSrnModel.hpp	Adds reference test for van Leeuwen 2007 SRN model.
chaste_sbml/SbmlRefModels/test/reference/TestVanLeeuwen2007NonDimSbmlSrnModel.hpp	Adds reference test for non-dimensional van Leeuwen 2007 SRN model.
chaste_sbml/SbmlRefModels/src/SbmlEventType.hpp	Adds C++ event-type enum used by generated systems/models.
chaste_sbml/SbmlRefModels/src/SbmlMath.hpp	Adds SBML math helper declarations/inline templates.
chaste_sbml/SbmlRefModels/src/SbmlMath.cpp	Adds SBML math helper definitions.
chaste_sbml/SbmlRefModels/src/AbstractSbmlOdeSystem.hpp	Adds abstract ODE system base with event handling hooks.
chaste_sbml/SbmlRefModels/src/AbstractSbmlOdeSystem.cpp	Adds abstract ODE system base implementation.
chaste_sbml/SbmlRefModels/src/AbstractSbmlSrnModel.hpp	Adds SRN base model header.
chaste_sbml/SbmlRefModels/src/AbstractSbmlSrnModel.cpp	Adds SRN base model implementation.
chaste_sbml/SbmlRefModels/src/AbstractSbmlCellCycleModel.hpp	Adds cell-cycle base model header.
chaste_sbml/SbmlRefModels/src/AbstractSbmlCellCycleModel.cpp	Adds cell-cycle base model implementation.
chaste_sbml/SbmlRefModels/src/cases/README.md	Adds placeholder docs for SBML test-suite case sources.
chaste_sbml/SbmlRefModels/src/fortests/SbmlTestOdeSolution.hpp	Adds OdeSolution extension for per-step parameter recording.
chaste_sbml/SbmlRefModels/src/fortests/SbmlTestOdeSolution.cpp	Implements per-step parameter recording + derived-quantity evaluation.
chaste_sbml/SbmlRefModels/src/fortests/SbmlTestHelpers.hpp	Adds test helpers (CSV export, stats utilities).
chaste_sbml/SbmlRefModels/src/fortests/SbmlTestHelpers.cpp	Implements CSV export + formatting helper(s).
chaste_sbml/SbmlRefModels/src/reference/README.md	Adds reference-model index README.
chaste_sbml/SbmlRefModels/src/reference/Goldbeter1991/Goldbeter1991SbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Goldbeter1991/Goldbeter1991SbmlSrnModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Goldbeter1991/Goldbeter1991SbmlSrnModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/Gardner1998/Gardner1998SbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Gardner1998/Gardner1998SbmlCellCycleModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Gardner1998/Gardner1998SbmlCellCycleModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/Chen2000/Chen2000SbmlCellCycleModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Chen2000/Chen2000SbmlCellCycleModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/Chen2004/Chen2004SbmlCellCycleModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Chen2004/Chen2004SbmlCellCycleModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/Tan2014/Tan2014SbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Tan2014/Tan2014SbmlSrnModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/Tan2014/Tan2014SbmlSrnModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007SbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007SbmlSrnModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007SbmlSrnModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007NonDim/VanLeeuwen2007NonDimSbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007NonDim/VanLeeuwen2007NonDimSbmlSrnModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007NonDim/VanLeeuwen2007NonDimSbmlSrnModel.cpp	Adds reference model source implementation.
chaste_sbml/SbmlRefModels/src/reference/TysonNovak2001/TysonNovak2001SbmlOdeSystem.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/TysonNovak2001/TysonNovak2001SbmlCellCycleModel.hpp	Adds reference model source header.
chaste_sbml/SbmlRefModels/src/reference/TysonNovak2001/TysonNovak2001SbmlCellCycleModel.cpp	Adds reference model source implementation.
chaste_codegen_sbml/main.py	Removes old single-command CLI entrypoint.
chaste_codegen_sbml/tests/test_console.py	Removes old console-script tests for chaste_codegen_sbml.

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[codecov]

Codecov Report

❌ Patch coverage is 36.73469% with 31 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.19%. Comparing base (6c9f500) to head (9868042).
⚠️ Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
chaste_sbml/__main__.py	0.00%	31 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #40      +/-   ##
===========================================
- Coverage    89.27%   89.19%   -0.09%     
===========================================
  Files           48       49       +1     
  Lines         6320     6346      +26     
===========================================
+ Hits          5642     5660      +18     
- Misses         678      686       +8     

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