Regular merge of develop #1456

laurentheirendt · 2019-04-02T08:26:52Z

No description provided.

…fGenes for loading ref data

Bug fixes in Microbiome Modeling Toolbox functions

added visualization for epistasis

instructions for installing gfortran

Fix broken iMAT algorithm by renaming modelCom

This reverts commit f4a2000.

Fix for testAnalyzeGCdesign

This reverts commit 4923016.

Fix columnVector for correctly manipulating empty row and column vectors

codecov-io · 2019-04-02T09:02:41Z

Codecov Report

Merging #1456 into master will decrease coverage by 0.03%.
The diff coverage is 57.14%.

@@            Coverage Diff             @@
##           master    #1456      +/-   ##
==========================================
- Coverage   44.31%   44.27%   -0.04%     
==========================================
  Files         899      906       +7     
  Lines       64449    64711     +262     
==========================================
+ Hits        28562    28653      +91     
- Misses      35887    36058     +171

Impacted Files	Coverage Δ
src/base/solvers/getAvailableGAMSSolvers.m	`0% <ø> (ø)`	⬆️
src/base/solvers/setCplexParam.m	`100% <ø> (ø)`	⬆️
src/analysis/gMCS/buildGmatrix.m	`82.02% <ø> (-0.47%)`	⬇️
...ox/additionalAnalysis/calculateReactionAbundance.m	`0% <0%> (ø)`	⬆️
...ditionalAnalysis/correlateFluxWithTaxonAbundance.m	`0% <0%> (ø)`	⬆️
src/analysis/exploration/printFluxBounds.m	`0% <0%> (ø)`	⬆️
src/analysis/gMCS/calculateMCS.m	`0% <0%> (ø)`	⬆️
src/dataIntegration/transcriptomics/iMAT/iMAT.m	`0% <0%> (ø)`	⬆️
src/analysis/gMCS/GPR2models.m	`11.11% <0%> (ø)`	⬆️
...rwiseInteractionModeling/computeParetoOptimality.m	`0% <0%> (ø)`	⬆️
... and 46 more

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cjos238 and others added 30 commits January 14, 2019 04:33

added visualization for epistasis

f1161e5

moved testVisualizeEpistasis to verfiedTests from additionalTests

c14c56c

the input model is read using readCbModel rather than load function

a8c3409

Bug fixes in MMT functions, new tutorial

0e7cdd0

fixed the function headers of visualizeEpistasis

3398f62

changing file permissions from 755 to 644

711be6b

linting calculateReactionAbundance

6444b97

linting correlateFluxWithTaxonAbundance

abc8b64

linting of createPanModels

cc7b634

linting of createMultipleSpeciesModel

a3b1062

Adding index files for doc. of visualizeEpistasis

639db4c

minor changes for documentation generation

9fe2f9f

linting convertGene2PathwayInteractions

b828513

linting findSubsystemOfGenes

e9ae9f7

linting visualizePathwayInEpistasis

dfcbcb3

renaming test files

e921058

changes to test to fit overall structure

cc5cd4e

changes to testConvertGene2PathwayInteractions and testFindSubsystemO…

b292c81

…fGenes for loading ref data

Merge pull request #1417 from almut-heinken/MMTupdate

7d86cd1

Bug fixes in Microbiome Modeling Toolbox functions

Merge pull request #1415 from cjos238/add-epivis

6864f61

added visualization for epistasis

[documentation] adding instructions how to install gfortran

c69a2cc

Merge pull request #1418 from laurentheirendt/add-gfortran

23b4839

instructions for installing gfortran

Fix broken iMAT algorithm by renaming modelCom

c3ca200

Merge pull request #1420 from pablormier/patch-1

dc2abff

Fix broken iMAT algorithm by renaming modelCom

added rxns as input for printFluxBounds

83bd5c3

correction of little bugs

6573b02

possible old score

1c0b5a4

selection of KO list

45b5f9a

Also fixing modelCom in iMAT

1c65571

[documentation] update of citation

664d440

laurentheirendt and others added 18 commits March 27, 2019 06:37

[documentation] fix for documentation

f66ac05

Revert "debugging only"

7485dfc

This reverts commit f4a2000.

change of urls for certain images

9305b1d

fix urls of remaining images

f946c70

Merge branch 'update-badges' into develop

d45f9de

fix for test

9a362e0

Merge pull request #1454 from laurentheirendt/fix-testAnalyzeGCdesign

1da89b8

Fix for testAnalyzeGCdesign

[documentation] fix for local path of generated tutorials

63bc602

change location of deploy tutorials script

14bb14e

Update submodule

4923016

Revert "Update submodule"

de96506

This reverts commit 4923016.

Fix columnVector to handle empty vectors properly

442de47

debugging

504970b

fix for path of tutorial pdfs

1131bb9

update url of zip release

b9ee676

update tutorials submodule

7542c76

update url of submodule

3cecc85

Merge pull request #1455 from shjchan/fix_columnVector

a02a346

Fix columnVector for correctly manipulating empty row and column vectors

laurentheirendt added the do not merge label Apr 2, 2019

laurentheirendt assigned laurentheirendt and artenobot and unassigned laurentheirendt Apr 2, 2019

laurentheirendt requested a review from artenobot April 2, 2019 08:27

laurentheirendt closed this Apr 2, 2019

laurentheirendt reopened this Apr 2, 2019

laurentheirendt added ready to merge and removed do not merge labels Apr 2, 2019

artenobot approved these changes Apr 2, 2019

View reviewed changes

artenobot merged commit 2ed83d1 into master Apr 2, 2019

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Regular merge of develop #1456

Regular merge of develop #1456

laurentheirendt commented Apr 2, 2019

codecov-io commented Apr 2, 2019 •

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Regular merge of develop #1456

Regular merge of develop #1456

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