Add competitive inhibition and uncompetitive inhibition

[AntoniaBerger]

This PR fixes #386 and fixes #388.

To-do

• Update residual
• Update Jacobian
• Test for simulation (comparison with micro kinetic)
• Test for Jacobian (comparison with AD-jacobian)
• Add Test do Cadet-Verification
• Update documentation
• Update parameter documentation

[Copilot]

Pull Request Overview

This PR aims to update and refactor Michaelis–Menten test cases in reaction model simulations to reflect new distinctions between substrates and inhibitors. Key changes include:

• Renaming test cases from inhibitor-related to substrate/non-inhibitor nomenclature.
• Adding an extra tag "[testHere]" to test case identifiers.
• Removing the inhibition-specific test function from ReactionModelTests.cpp.

Reviewed Changes

Copilot reviewed 7 out of 14 changed files in this pull request and generated no comments.

File	Description
test/ReactionModels.cpp	Test case names updated to reflect substrates/non-inhibitor behavior and extra tags added.
test/ReactionModelTests.cpp	Inhibition-specific test function removed to align with new test case focus.

Files not reviewed (7)

• doc/interface/reaction/michaelis_menten_kinetics.rst: Language not supported
• doc/interface/reaction/michaelis_menten_kinetics_with_inhibition.rst: Language not supported
• doc/modelling/reaction/michaelis_menten_kinetics.rst: Language not supported
• test/data/configuration_CSTR_MichaelisMenten_benchmark1.json: Language not supported
• test/data/configuration_CSTR_MichaelisMenten_benchmark2.json: Language not supported
• test/data/configuration_CSTR_MichaelisMenten_twoInhib_benchmark1.json: Language not supported
• test/data/configuration_CSTR_MicroKineticsSMA_benchmark1.json: Language not supported

Comments suppressed due to low confidence (2)

test/ReactionModelTests.cpp:322

• The removal of the inhibition-specific test function could reduce test coverage for inhibition behavior. Ensure that inhibition scenarios are adequately covered by the new tests or update the documentation accordingly.

// Removed testMichaelisMentenToSMAInhibitionMicroKinetic function

test/ReactionModels.cpp:92

• Test case names now reference 'substrates' rather than 'inhibitors', which seems inconsistent with the PR title mentioning inhibition. Verify that the test descriptions, configuration files, and overall PR purpose are aligned.

TEST_CASE("MichaelisMenten kinetic with two substrates and specific mass action law micro-kinetics yield same result", "[MichaelisMenten],[ReactionModel],[Simulation],[Reference],[CI],[testHere]")

[schmoelder]

Excellent work @AntoniaBerger, really looking forward to this feature in CADET :)

Just some small comments, mostly regarding typos.

[lieres]

In general, rates are defined per unit volume and time, whereas fluxes are defined per unit area and time. However, the terminology can be confusing, as the term flux is sometimes used interchangeably with rate, for instance, in metabolic flux analysis. For clarity and consistency with SI units, let's use the term rate here.

[jbreue16]

what does the commit "Enable backward compatibility with previous Michaelis Menten interface" do exactly?
Does this include multiple interfaces now or am I missing something?

[AntoniaBerger]

what does the commit "Enable backward compatibility with previous Michaelis Menten interface" do exactly? Does this include multiple interfaces now or am I missing something?

It deletes the old version, which had an additional module for the competitive version, and integrates these features into the standard Meachelis Menten implementation. However, doing so also makes it possible to use the 'ki' parameter, which was present in the old version.

Edit: This is already the squashes version of this branch, so the commits are not 100% clean anymore.

[jbreue16]

It deletes the old version, which had an additional module for the competitive version, and integrates these features into the standard Meachelis Menten implementation. However, doing so also makes it possible to use the 'ki' parameter, which was present in the old version.

ok i understand this as no multiple interfaces, which is great

[jbreue16]

looks good, so cool !
we should remove the USER_SOLUTION_TIMES from the config files in the future to not have multiple thousands lines of code just for this, I thought that before in my PR's, Ive opened an issue for this

I believe all requested changes were addressed.