Replace Yield with StoichSpecies

[boulderdaze]

This PR:

• Replaces Yield with StoichSpecies
  • I went with StoichSpecies over Stoichiometry since it more clearly represents a pairing of a species with its stoichiometric coefficient, while Stoichiometry feels more like the general concept. I’m open to renaming it to Stoichiometry if the team feels that’s a better fit.
• Updates the fedora and ubuntu version used in docker images and github actions
• Removes the libc++ compiler flag for Ubuntu. libstdc++ is the default for Ubuntu even when using clang
• Adds the --ignore-errors mismatch flag to the lcov commands, to treat the mismatch as a warning rather than a fatal error
• Fixes null pointer dereference in State copy constructor and copy assignment
• Removes the dead code (Dockerfile.llvm)

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.91%. Comparing base (d02f4ec) to head (8351468).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #905      +/-   ##
==========================================
+ Coverage   94.76%   94.91%   +0.15%     
==========================================
  Files          65       64       -1     
  Lines        3226     3027     -199     
==========================================
- Hits         3057     2873     -184     
+ Misses        169      154      -15     

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[Copilot]

Pull request overview

This PR replaces the old Yield type with a new StoichSpecies type across the API, tests, and docs, and updates CI/build tooling (CMake, Docker, GitHub Actions, lcov). It also removes now-unnecessary libc++ flags on Ubuntu/Clang and adds an .lcovrc to smooth coverage runs with GoogleTest.

Changes:

• Introduces micm::StoichSpecies as the product-species representation and wires it through ChemicalReaction, ChemicalReactionBuilder, and all tests/tutorials/docs, removing the legacy Yield type.
• Updates build/CI environment: raises the CMake minimum to 3.24, switches GitHub Ubuntu runners to ubuntu-latest, and changes several Docker and devcontainer base images from fedora:37 to fedora:latest.
• Adds .lcovrc to ignore certain lcov mismatch/inconsistent errors, improving robustness of coverage runs.

Reviewed changes

Copilot reviewed 45 out of 45 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
test/unit/solver/test_solver_builder.cpp	Switches reaction products in solver builder unit tests from Yield to StoichSpecies.
test/unit/solver/test_rosenbrock_solver_policy.hpp	Updates Rosenbrock solver policy tests to use StoichSpecies for products.
test/unit/solver/test_rosenbrock.cpp	Uses StoichSpecies instead of Yield in a Rosenbrock solver tolerance test reaction.
test/unit/solver/test_backward_euler.cpp	Replaces Yield with StoichSpecies for backward Euler solver test reactions.
test/unit/process/test_process_set_policy.hpp	Migrates process-set policy tests to StoichSpecies, including random-system product vectors.
test/unit/process/test_process_configuration.cpp	Updates configuration/scoping tests to include stoich_species.hpp and use StoichSpecies in builder calls.
test/unit/process/test_process.cpp	Uses StoichSpecies for chemical reaction products in process construction tests.
test/unit/openmp/test_openmp.cpp	Replaces Yield with StoichSpecies in OpenMP unit tests’ toy mechanisms.
test/unit/cuda/solver/test_cuda_solver_builder.cpp	Updates CUDA solver builder tests to use micm::StoichSpecies for products.
test/tutorial/test_vectorized_matrix_solver.cpp	Tutorial test updated to construct reactions with StoichSpecies products.
test/tutorial/test_solver_results.cpp	Uses StoichSpecies in solver results tutorial test reactions.
test/tutorial/test_solver_configuration.cpp	Replaces Yield with StoichSpecies in solver configuration tutorial tests.
test/tutorial/test_rate_constants_user_defined_by_hand.cpp	Converts the user-defined rate constant tutorial test to StoichSpecies for all products.
test/tutorial/test_rate_constants_no_user_defined_by_hand.cpp	Same as above for the non-user-defined variant tutorial.
test/tutorial/test_openmp.cpp	Updates tutorial OpenMP example to use micm::StoichSpecies instead of micm::Yield.
test/tutorial/test_multiple_grid_cells.cpp	Multiple-grid-cells tutorial now uses micm::StoichSpecies for products.
test/tutorial/test_README_example.cpp	README example test switched from Yield to StoichSpecies for consistency with the new API.
test/regression/regression_policy.hpp	Regression policy test updated to use micm::StoichSpecies for SOA products.
test/regression/RosenbrockChapman/util.hpp	Rosenbrock–Chapman regression utilities now construct processes with micm::StoichSpecies products.
test/integration/test_integrated_reaction_rates.cpp	Integration tests for reaction rates now use micm::StoichSpecies for product definitions.
test/integration/test_chapman_integration.cpp	Chapman integration tests updated to micm::StoichSpecies in all product lists.
test/integration/terminator.hpp	Terminator integration test toy mechanism updated to micm::StoichSpecies.
test/integration/analytical_surface_rxn_policy.hpp	Analytical surface reaction policy tests now use micm::StoichSpecies products.
test/integration/analytical_policy.hpp	Analytical integration tests (various rate laws and stiff systems) migrated from Yield to StoichSpecies.
include/micm/system/yield.hpp	Removes the legacy Yield struct, deprecating it in favor of StoichSpecies.
include/micm/system/stoich_species.hpp	Introduces the StoichSpecies struct as the new representation of species plus stoichiometric coefficient.
include/micm/process/process.hpp	Switches process headers to include stoich_species.hpp instead of yield.hpp.
include/micm/process/phase_transfer_process_builder.hpp	Updates includes to stoich_species.hpp for phase-transfer process builder.
include/micm/process/phase_transfer_process.hpp	Likewise, uses stoich_species.hpp in the phase transfer process interface.
include/micm/process/chemical_reaction_builder.hpp	Changes SetProducts to accept std::vector<StoichSpecies> and stores StoichSpecies products internally.
include/micm/process/chemical_reaction.hpp	Updates ChemicalReaction to store products as std::vector<StoichSpecies>.
include/micm/System.hpp	System umbrella header now includes stoich_species.hpp instead of yield.hpp.
docs/source/user_guide/user_defined_rate_constant_tutorial.rst	Documentation sample code switched to StoichSpecies and updated reaction list to include new user-defined processes.
docker/Dockerfile.publish	Changes base image from fedora:37 to fedora:latest for the publish image.
docker/Dockerfile.openmp	Same Fedora base image change for the OpenMP Dockerfile.
docker/Dockerfile.mpi	Same Fedora base image change for the MPI Dockerfile.
docker/Dockerfile.memcheck	Same Fedora base image change for the memcheck Dockerfile.
docker/Dockerfile.docs	Same Fedora base image change for the docs Dockerfile.
docker/Dockerfile.coverage	Same Fedora base image change for the coverage Dockerfile.
docker/Dockerfile	Same Fedora base image change for the main Dockerfile.
README.md	README example code updated to use StoichSpecies in product lists.
CMakeLists.txt	Bumps cmake_minimum_required to 3.24 and removes duplicated/obsolete libc++ configuration for Linux/Clang.
.lcovrc	New lcov configuration to ignore mismatch/inconsistent errors from GoogleTest macros.
.github/workflows/ubuntu.yml	Aligns Ubuntu CI jobs to run on ubuntu-latest for both gcc and clang.
.devcontainer/Dockerfile.codespace	Devcontainer/Codespaces base image updated from fedora:37 to fedora:latest.

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[Copilot]

Pull request overview

Copilot reviewed 46 out of 46 changed files in this pull request and generated 9 comments.

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[K20shores]

It's all fine with me. An alternative is to just use a std::pair and then we don't have a named type. Not sure if it's better, but throwing it out there

[K20shores]

Oh that's neat. I wasn't aware of deprecataeds existence

[boulderdaze]

Yeah I also learned the deprecated warning from the copilot. Apparently it goes back to C++14.
About using std::pair, since this is used in SetProducts() (and probably SetReactants() too), I think making it a struct would help make things clearer.

[dwfncar]

Approved, all OK