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[Feature] Equality of metabolites and reactions

4

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Problem I want to be able to detect if metabolites or reactions are equal...

In 1.11 something changed i guess with inlining, constant-propagation and/or unrolling. And now `inds = ntuple(d -> d == dims ? p : (:), N)` doesn't infer. It used to...

Fix type inference failure in norm on structural matrix

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This fixes the 1.11 failures on CI. Not sure its the best way, but it basically boils down to Julia 1.11 introduced a minor regression in inference of: `zero.(Diagonal(Float64[;])) .*...

code in a few places e.g. `norm.jl` uses a helper function called `withsomezeros` that handles making Triangular and Diagonal (etc) matrixes back into the correct types. This seems very similar...

cf https://github.com/JuliaTesting/ExprTools.jl/pull/41

No-Op solver

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### Checklist - [x] There are [no similar issues or pull requests](https://github.com/opencobra/optlang/issues) for this yet. ### Is your feature related to a problem? Please describe it. When using cobrapy, sometimes...

When something is dict-like, and defined `getindex` like `Node` does to access attributes, I expect it to also provide `get` to do that with a default. ``` julia> n =...

Stop vendoring imports so precompile times remain sensible?

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On CI i have seen ExplictImports taking over 2 minutes to precompile. Which is completely unreasonable) Locally, @KristofferC saw it take 10s (which still rather high). A likely candidate is...

[BUG] build_reaction_from_string wipes reaction's bounds

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### Is there an existing issue for this? - [x] I have searched the existing issues ### Problem description I thought i would set up a reaction 1. First by...

Adding a reaction that is already part of a model to another model creates an alias (not a copy)

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Consider: ``` model1 = cobra.Model("M1") model1.add_reactions([cobra.Reaction("R1")]) model2 = cobra.Model("M2") model2.add_reactions(model1.reactions) print(model1.reactions.R1.bounds) model2.reactions.R1.bounds = (500,600) print(model1.reactions.R1.bounds) ``` which prints: ``` (0.0, 1000.0) (500, 600) ``` We would have expected that changing...