opencobra/cobratoolbox — pull request #10 by rmtfleming (2013-07-31 08:52:59+00:00)
Title: merge of cobra-devel with git/master

Dear All,

some time ago, it was unilaterally decided that the matlab code on svn for the cobratoolbox be split into two. Now, one version has unilaterally been moved such that it is being hosted by github, leaving the other using a separate version control software. Due to the clear benefits of git/github, I have MANUALLY merged as much as possible of the master version of https://github.com/opencobra/cobratoolbox with http://sourceforge.net/projects/opencobra/cobra-devel.

As the unilaterally chosen development model for the opencobra toolbox hosted on github is for contributors to create a fork of the repository in github, and then submit a pull request to have those changes merged into the master version, the merged version is available from my fork https://github.com/rmtfleming/cobratoolbox, pending its merger with the master version.

During the effort to merge the two versions, there were some functions that were by now so different, I did not dare to try to merge them. Even if the output of testAll is positive for the respective tests, this does not necessiarily mean that the merged code is perfect. What is needed now are some volunteers, with expert knowledge of the following functions, to do the merge.

More generally, my position is that we should aim that the master version on github is truly the collaborative and collegial effort between the community and therefore reduce the amount of major unilateral decisions made concerning the project. Only this way will the community more fully engage. The planning of the opencobra project is something we should engage in together over the coming months so that the direction of the project is decided democratically, with voting proportional to the previous effort on the code.

Here are the problem files that I have not tried to merge:

convertCobraToSBML
convertSBMLToCobra
writeCbToSBML
fluxVariability

Here are merged files, but not sure that the merge is perfect, thought they pass the test:
drawText
drawCbMap
drawFlux
setMapOptions
createTissueSpecificModel

Experts on these functions, please take a look, especially if you have made your commits to cobra-devel in the past. Within 2 weeks, the cobra-devel version will be depreciated. It was nice to overview all of the improvements from the 384 commits, made by many dfferent people over the past couple of years. Hopefully with the hosting on github, the different forks of the cobratoolbox do not grow to be too different from eachother. We are a relatively small development community and should stick together.

By the way, this is a beautiful tool for manually merging two sets of code: http://meldmerge.org/

Regards,

Ronan Fleming

Output of testAll:
Tests passed:
testBuildMPS
testDeletionStudy
testElementalBalance
testFBA
testFVA
testMOMA
testMaps
testModelManipulation
testOptKnock
testRobustnessAnalysis
testSampleCbModel
testgpSampler
testTissueModel
testpFBA
testDifferentLPSolvers

Tests not passed: - understandable as no NLP setup & no SBML
testC13Fitting
testGDLS
testGrowthExpMatch
testSBML
testSolvers