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make the semantics cut #776

Merged
merged 19 commits into from
May 8, 2023
Merged

make the semantics cut #776

merged 19 commits into from
May 8, 2023

Commits on May 2, 2023

  1. the cut 

    (probably needs fixes at this point)
    @exaexa
    exaexa committed May 2, 2023
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  2. fixup: modelwrapper no longer knows about metabolites by default

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    exaexa committed May 2, 2023
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  3. fix optmodel object naming

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    exaexa committed May 2, 2023
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  4. type the defaults better

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    exaexa committed May 2, 2023
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  5. be slightly less brutal in the defaults

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    exaexa committed May 2, 2023
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  6. fixup: variable for solver names

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    exaexa committed May 2, 2023
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  7. fixup: same

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    exaexa committed May 2, 2023
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  8. todo: fix this later

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    exaexa committed May 2, 2023
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  9. fixup: format head^^

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    exaexa committed May 2, 2023
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  10. simplify the constraint labeling

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    exaexa committed May 2, 2023
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  11. fixup: format

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    exaexa committed May 2, 2023
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  12. fixup: do not inherit variable_count

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    exaexa committed May 2, 2023
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  13. at this point models now don't really need to have metabolites

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    exaexa committed May 2, 2023
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  14. turn the semantic matrices around 

    We'd get burned at stakes if we had stoichiometry with reactions in rows.
    @exaexa
    exaexa committed May 2, 2023
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Commits on May 8, 2023

  1. fix macro ident clash

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    exaexa committed May 8, 2023
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  2. add a note for the future

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    exaexa committed May 8, 2023
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  3. fix the parameter order

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    exaexa committed May 8, 2023
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  4. more notes

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    exaexa committed May 8, 2023
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  5. make models export the metabolite_variable mapping instead of stoichi… 

    …ometry by default
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    exaexa committed May 8, 2023
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