Update mods to handle gecko model

[stelmo]

Update change_constraint and change_objective to include looking into genes for the objective or variable indices. This is important, because for GeckoModel genes are variables too...

[cylon-x]

🟥  Commit d779256 requires formatting!

Required formatting changes summary:

 src/analysis/modifications/generic.jl | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

[cylon-x]

🟢  Commit fe6d682 is formatted properly.

[codecov]

Codecov Report

Merging #612 (3cd91c2) into develop (581400d) will increase coverage by 0.17%.
The diff coverage is 83.33%.

@@             Coverage Diff             @@
##           develop     #612      +/-   ##
===========================================
+ Coverage    90.29%   90.46%   +0.17%     
===========================================
  Files           78       78              
  Lines         1876     1878       +2     
===========================================
+ Hits          1694     1699       +5     
+ Misses         182      179       -3     

Impacted Files	Coverage Δ
src/base/types/MetabolicModel.jl	89.39% <ø> (ø)
src/base/utils/enzymes.jl	33.33% <ø> (ø)
src/base/types/wrappers/GeckoModel.jl	91.66% <83.33%> (+6.37%)	⬆️
src/base/utils/gecko.jl	100.00% <0.00%> (+10.00%)	⬆️

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[cylon-x]

🟥  Commit c300e07 requires formatting!

Required formatting changes summary:

 src/analysis/modifications/generic.jl | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

[cylon-x]

🟥  Commit e861fcd requires formatting!

Required formatting changes summary:

 src/analysis/modifications/generic.jl |  6 ++----
 src/base/types/wrappers/GeckoModel.jl | 12 ++++++------
 src/base/utils/enzymes.jl             |  4 +++-
 test/analysis/gecko.jl                | 16 ++++++----------
 4 files changed, 17 insertions(+), 21 deletions(-)

[cylon-x]

🟢  Commit ceb6bfd is formatted properly.

[cylon-x]

🟢  Commit e70cb44 is formatted properly.

[cylon-x]

🟢  Commit 1e29e08 is formatted properly.

[cylon-x]

🟢  Commit ca95d97 is formatted properly.

[exaexa]

"mangeled", otherwise all ok

[cylon-x]

🟢  Commit 1fd4fd8 is formatted properly.

[cylon-x]

🟢  Commit 449fad1 is formatted properly.

[cylon-x]

🟢  Commit 449fad1 is formatted properly.

[cylon-x]

🟢  Commit ce5a8a5 is formatted properly.

[cylon-x]

🟢  Commit 8959378 is formatted properly.

[cylon-x]

🟢  Commit 3cd91c2 is formatted properly.