finalize the semantics

[exaexa]

This will add the constraints to semantics. Basically, everything except plain variables (reactions, metabolites, coupling, enzymes, ...........) will become semantics.

still to-do:

• [ ] enzymatic constraints get out of coupling into enzyme semantics
• [ ] the "good old" coupling gets its own semantics (if ever required; we might just kill it as well)
• [ ] there's an user-accessible way to discover all the semantics
• [ ] semantics are saved in the H5 model (somehow)
• [ ] there's a way to declare that model doesn't touch variables and/or changes only given semantics, giving an automated way to pull the matrix representations of the semantics by default.

[codecov[bot]]

Codecov Report

Patch coverage: 88.33% and project coverage change: -0.38 :warning:

Comparison is base (3e7ea04) 89.34% compared to head (74ab0d0) 88.97%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## next #775 +/- ## ========================================== - Coverage 89.34% 88.97% -0.38% ========================================== Files 92 92 Lines 2422 2403 -19 ========================================== - Hits 2164 2138 -26 - Misses 258 265 +7 ``` | [Impacted Files](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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/envelopes.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL2VudmVsb3Blcy5qbA==) | `100.00% <ø> (ø)` | | | [src/analysis/minimize\_metabolic\_adjustment.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21pbmltaXplX21ldGFib2xpY19hZGp1c3RtZW50Lmps) | `100.00% <ø> (ø)` | | | [src/analysis/modifications/loopless.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21vZGlmaWNhdGlvbnMvbG9vcGxlc3Muamw=) | `100.00% <ø> (ø)` | | | [src/io/show/AbstractMetabolicModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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/types/misc/ObjectModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21pc2MvT2JqZWN0TW9kZWwuamw=) | `83.33% <ø> (ø)` | | | [src/wrappers/misc/enzyme\_constrained.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3dyYXBwZXJzL21pc2MvZW56eW1lX2NvbnN0cmFpbmVkLmps) | `100.00% <ø> (ø)` | | | [src/wrappers/misc/mmdf.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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/utils/looks\_like.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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% <16.66%> (ø)` | | | [src/wrappers/MatrixCoupling.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3dyYXBwZXJzL01hdHJpeENvdXBsaW5nLmps) | `89.47% <50.00%> (ø)` | | | [src/types/wrappers/EqualGrowthCommunityModel.jl](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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% <64.70%> (ø)` | | | ... and [30 more](https://app.codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/775?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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[exaexa]

By popular decision the plans for COBREXA2 shifted a bit towards a different system. I'll base that upon next branch. This should not get lost (as a warning for future generations I guess) so I'm merging it