make the semantics cut

[exaexa]

I have this specially separated from the rest of the (RELATIVELY HARMLESS) semantics-are-everywhere change because it's gonna be the most breaking part, and the reviews should be kinda clear.

In this state it's not looking good (tests will fail until I fix them) but most of the errors I see seem fixable.

As the main points:

• stoichiometry is now just a nice name for metabolite_variables_matrix
• balance is gone, instead of that the metabolites have the balance bounds
• stoichiometry is no more matrixy "by default", the dictionary-ish metabolite_variables is the master form now as with other semantics..
  • pros: resizing variables or reactions doesn't kill stoichiometry and you don't need to care about that much
  • cons: reconstructing the stoichiometry from dicts isn't that nicely efficient, we'll need a bit of extra annotations to be able to pipe the matrixy form through wrappers easily

I'll fix the rest, at this points any comments welcome.

[exaexa]

@stelmo I guess this is ready for merging into the bigger PR now (at least the tests pass). It might be necessary to redo the logic of the community models a bit. Matrix passthrough still doesn't really work but that's patchable later (it's mostly a minor performance issue)

[codecov[bot]]

Codecov Report

Patch coverage: 89.76% and project coverage change: -0.07 :warning:

Comparison is base (6272230) 89.03% compared to head (9173d69) 88.97%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## mk-finalize-semantics #776 +/- ## ========================================================= - Coverage 89.03% 88.97% -0.07% ========================================================= Files 92 92 Lines 2444 2403 -41 ========================================================= - Hits 2176 2138 -38 + Misses 268 265 -3 ``` | [Impacted Files](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | Coverage Δ | | |---|---|---| | [src/analysis/sampling/affine\_hit\_and\_run.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3NhbXBsaW5nL2FmZmluZV9oaXRfYW5kX3J1bi5qbA==) | `94.11% <ø> (ø)` | | | [src/analysis/variability\_analysis.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3ZhcmlhYmlsaXR5X2FuYWx5c2lzLmps) | `97.29% <ø> (ø)` | | | [src/io/show/AbstractMetabolicModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2lvL3Nob3cvQWJzdHJhY3RNZXRhYm9saWNNb2RlbC5qbA==) | `100.00% <ø> (ø)` | | | [src/reconstruction/MatrixCoupling.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL01hdHJpeENvdXBsaW5nLmps) | `96.05% <ø> (ø)` | | | [src/utils/looks\_like.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3V0aWxzL2xvb2tzX2xpa2Uuamw=) | `44.44% <0.00%> (ø)` | | | [src/wrappers/SimplifiedEnzymeConstrainedModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3dyYXBwZXJzL1NpbXBsaWZpZWRFbnp5bWVDb25zdHJhaW5lZE1vZGVsLmps) | `92.59% <ø> (ø)` | | | [src/wrappers/misc/mmdf.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3dyYXBwZXJzL21pc2MvbW1kZi5qbA==) | `100.00% <ø> (ø)` | | | [src/types/wrappers/EqualGrowthCommunityModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL3dyYXBwZXJzL0VxdWFsR3Jvd3RoQ29tbXVuaXR5TW9kZWwuamw=) | `84.21% <33.33%> (ø)` | | | [src/types/accessors/AbstractMetabolicModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9BYnN0cmFjdE1ldGFib2xpY01vZGVsLmps) | `74.57% <50.00%> (-3.04%)` | :arrow_down: | | [src/solver.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3NvbHZlci5qbA==) | `85.00% <77.77%> (+8.72%)` | :arrow_up: | | ... and [17 more](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/776?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | |

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[stelmo]

@stelmo I guess this is ready for merging into the bigger PR now (at least the tests pass). It might be necessary to redo the logic of the community models a bit. Matrix passthrough still doesn't really work but that's patchable later (it's mostly a minor performance issue)

🚀 let's figure out the problems as they come up

[exaexa]

ok :boom: