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Change set_bound to change_bound to fit in with CoreModel functions #346

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merged 29 commits into from
Jul 10, 2021

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@stelmo stelmo commented Jun 18, 2021

This closes #329

@exaexa, should I also change with_set_bound to with_change_bound?

@stelmo stelmo added the quality improves maintainability and code clarity label Jun 18, 2021
@stelmo stelmo added this to the Release - v1.0.3 milestone Jun 18, 2021
@stelmo stelmo requested a review from exaexa June 18, 2021 08:22
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codecov bot commented Jun 18, 2021

Codecov Report

Merging #346 (a67eaec) into master (018e476) will increase coverage by 1.00%.
The diff coverage is 93.54%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #346      +/-   ##
==========================================
+ Coverage   87.51%   88.52%   +1.00%     
==========================================
  Files          58       59       +1     
  Lines        1426     1446      +20     
==========================================
+ Hits         1248     1280      +32     
+ Misses        178      166      -12     
Impacted Files Coverage Δ
src/COBREXA.jl 0.00% <ø> (ø)
src/base/utils/Reaction.jl 58.33% <0.00%> (ø)
src/io/show/FluxVariabilitySummary.jl 0.00% <0.00%> (ø)
src/reconstruction/modifications/generic.jl 0.00% <0.00%> (ø)
src/base/macros/change_bounds.jl 100.00% <100.00%> (ø)
src/base/types/Reaction.jl 100.00% <100.00%> (ø)
src/reconstruction/CoreModel.jl 96.61% <100.00%> (+0.02%) ⬆️
src/reconstruction/CoreModelCoupled.jl 98.68% <100.00%> (+0.24%) ⬆️
src/reconstruction/Reaction.jl 97.43% <100.00%> (ø)
src/reconstruction/StandardModel.jl 100.00% <100.00%> (+19.29%) ⬆️
... and 4 more

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cylon-x commented Jul 9, 2021

🟥  Commit 3882c6a requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         | 78 ++++++++++++++++++----------
 src/reconstruction/CoreModelCoupled.jl  | 90 ++++++++++++++++++++++++---------
 src/reconstruction/StandardModel.jl     | 26 +++++++---
 test/reconstruction/CoreModel.jl        | 29 +++++++----
 test/reconstruction/CoreModelCoupled.jl | 31 ++++++++----
 test/reconstruction/StandardModel.jl    | 24 ++++++---
 7 files changed, 196 insertions(+), 88 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit 0a94f77 requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         | 106 +++++++++++++++++++++-------
 src/reconstruction/CoreModelCoupled.jl  | 118 +++++++++++++++++++++++++-------
 src/reconstruction/StandardModel.jl     |  40 ++++++++---
 test/reconstruction/CoreModel.jl        |  29 +++++---
 test/reconstruction/CoreModelCoupled.jl |  31 ++++++---
 test/reconstruction/StandardModel.jl    |  24 +++++--
 7 files changed, 266 insertions(+), 88 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit b7b8df6 requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         | 102 +++++++++++++++++++++-------
 src/reconstruction/CoreModelCoupled.jl  | 116 +++++++++++++++++++++++++-------
 src/reconstruction/StandardModel.jl     |  40 ++++++++---
 test/reconstruction/CoreModel.jl        |  29 +++++---
 test/reconstruction/CoreModelCoupled.jl |  31 ++++++---
 test/reconstruction/StandardModel.jl    |  24 +++++--
 7 files changed, 263 insertions(+), 85 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit 7205fd1 requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         | 46 ++++++++++++++++++++++++++-------
 src/reconstruction/CoreModelCoupled.jl  | 36 ++++++++++++++++++++------
 test/reconstruction/CoreModel.jl        | 29 ++++++++++++++-------
 test/reconstruction/CoreModelCoupled.jl | 31 +++++++++++++++-------
 test/reconstruction/StandardModel.jl    | 24 ++++++++++++-----
 6 files changed, 133 insertions(+), 48 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit 8972842 requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         |  95 +++++++++++++++++++++-------
 src/reconstruction/CoreModelCoupled.jl  | 109 +++++++++++++++++++++++++-------
 src/reconstruction/StandardModel.jl     |  40 +++++++++---
 test/reconstruction/CoreModel.jl        |  29 ++++++---
 test/reconstruction/CoreModelCoupled.jl |  31 ++++++---
 test/reconstruction/StandardModel.jl    |  24 +++++--
 7 files changed, 257 insertions(+), 86 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit 14e4374 requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl         |  95 +++++++++++++++++++++-------
 src/reconstruction/CoreModelCoupled.jl  | 109 +++++++++++++++++++++++++-------
 src/reconstruction/StandardModel.jl     |  40 +++++++++---
 test/reconstruction/CoreModel.jl        |  43 +++++++++----
 test/reconstruction/CoreModelCoupled.jl |  31 ++++++---
 test/reconstruction/StandardModel.jl    |  37 +++++++----
 7 files changed, 278 insertions(+), 92 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit 1f6b229 requires formatting!

Required formatting changes summary:

 1 file changed, 11 insertions(+), 4 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit ab6ac9a requires formatting!

Required formatting changes summary:

 src/reconstruction/CoreModel.jl        |  9 +++------
 src/reconstruction/CoreModelCoupled.jl |  3 +--
 3 files changed, 15 insertions(+), 12 deletions(-)

@stelmo stelmo requested a review from exaexa July 9, 2021 12:29
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cylon-x commented Jul 9, 2021

🟥  Commit dd521c7 requires formatting!

Required formatting changes summary:

 1 file changed, 11 insertions(+), 4 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit dd521c7 requires formatting!

Required formatting changes summary:

 1 file changed, 11 insertions(+), 4 deletions(-)

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stelmo commented Jul 9, 2021

Hmm, no idea what is wrong with the format... @exaexa?

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cylon-x commented Jul 9, 2021

🟥  Commit a4761a5 requires formatting!

Required formatting changes summary:

 1 file changed, 11 insertions(+), 4 deletions(-)

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cylon-x commented Jul 9, 2021

🟥  Commit a4761a5 requires formatting!

Required formatting changes summary:

src/base/docstrings/docstrings.jl | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

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cylon-x commented Jul 9, 2021

🟢  Commit 9357e09 is formatted properly.

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cylon-x commented Jul 9, 2021

🟢  Commit 9357e09 is formatted properly.

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cylon-x commented Jul 9, 2021

🟢  Commit a67eaec is formatted properly.

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Teeeeeeeeeeeeests are great!

@exaexa exaexa merged commit fcaedc5 into master Jul 10, 2021
@exaexa exaexa deleted the mo-homo-set-change-bound branch July 10, 2021 08:52
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🪓 Homogenize set_bound and change_bounds! and make them generic
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