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Develop #2212

Merged
merged 75 commits into from
Jan 10, 2024
Merged

Develop #2212

merged 75 commits into from
Jan 10, 2024

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rmtfleming
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Please include a short description of enhancement here

I hereby confirm that I have:

  • Tested my code on my own machine
  • Followed the guidelines in the Contributing Guide
  • Selected develop as a target branch (top left drop-down menu)

(Note: You may replace [ ] with [X] to check the box)

silvtal and others added 30 commits September 5, 2023 17:41
@silvtal
typo at addCOBRAVariables.m
6856b00
@silvtal
MMT bug: createMultipleSpeciesModel.m ignored the biomasses argument …
182c2af 
…from joinModelsPairwiseFromList.m
@rosieluo2021
Fixing bug for xomicsTomodelm
c881bd7
@rosieluo2021
fixing bug
0b1316a
@bramnap
Fix file location path
0655842
@CodeGeasrb
Update modelExtraction.m
e217468
@ithiele
recent edits
1eed7f6
@rmtfleming
Merge pull request #2182 from CodeGeasrb/master
23ea87f 
Update ModelExtraction.m
@rmtfleming
Merge pull request #2183 from ithiele/it_10_10_2023
3532645 
recent edits
@rmtfleming
Merge pull request #2179 from bramnap/updateMexFastFVA
fade501 
Fix file location path in generateMexFastFva
@rmtfleming
Merge pull request #2177 from rosieluo2021/metaPD
59ce33b 
Fixing bug for xomicsTomodelm
@rmtfleming
Merge pull request #2175 from silvtal/master
b9cc060 
Small bug fix for Microbiome Modelling Toolbox
@annasheehy
Update individualised lab report
deea412
@farid-zare
Update createNewMetaboliteStructure.m
238c584
@farid-zare
Update testFluxShifts.m
527e73a
@farid-zare
Update calculateFluxShifts.m
4d3bace
@farid-zare
Update filterNonFluxReactions.m
02b8c62
@farid-zare
Update testNonFluxReactions.m
0ac5440
@farid-zare
Update testRateLimittingReactions.m
62bf2f2
@farid-zare
Update filterRateLimittingReactions.m
8ff55a5
@trjhensen
updated paths in tutorials and added VMH reaction data
56b6f1b
@farid-zare
Update testCheckModelPreFBA.m
a610c82
@farid-zare
Update testPrintFluxVector.m
dafa69e
@farid-zare
Update printFluxVector.m
2471695
@farid-zare
Update refData_printFluxVectorFormula.txt
2d540a0
@ithiele
Merge pull request #2188 from trjhensen/develop
24d1f0d 
updated paths in tutorials and added VMH reaction data
@ithiele
Merge pull request #2186 from FaridZare17/MetabAnnotaor1
d5ff360 
Update createNewMetaboliteStructure.m
@ithiele
Merge pull request #2185 from annasheehy/indLabReport-fix
a8dcaee 
Update individualisedLabReport
@ithiele
changes to reportTemplate
cb58328
@ithiele
Merge pull request #2189 from ithiele/it_21_11_2023
805e7f8 
changes to reportTemplate
Sami990 and others added 29 commits November 30, 2023 13:30
@Sami990
Update getFormulaAndChargeFromInChI.m
ed841b7
@Sami990
Update testFindRxnsFromGenes.m
4b3f392
@Yanjun2021
testPrintConstraintm
b8800fd
@Yanjun2021
debug testPrintConstraintsm
f123e88
@hadjar11
Debug testBiomassPrecursorCheck function
864db3b
@rmtfleming
Merge pull request #2199 from Yanjun2021/newFunc_escherMap
fea7522 
new function for eshcer map
@rmtfleming
Merge pull request #2201 from Yanjun2021/testPrintConstraint
72f5834 
Test print constraint
@rmtfleming
Merge pull request #2202 from hadjar11/231129
a9f7b2b 
Debug testBiomassPrecursorCheck function
@farid-zare
Update testPrintFluxVector.m
9317682
@farid-zare
Update refData_printFluxVectorFormula.txt
a95bb4a
@farid-zare
Update printFluxVector.m
9068ce7
@farid-zare
Update testCheckModelPreFBA.m
b1a1277
@Yanjun2021
update function in XomicsToModel
b3cad97
adding MatGPT to CobraToolbox
6d64af1
test
0c2646a
remove folders
a862a58
remove unwanted files
196f8e6
test
a30f813
remove test
c8db84c
@Yanjun2021
FastLeakTest modification
50be405
@rmtfleming
Merge pull request #2208 from Yanjun2021/FastLeakTest-modification
a0d8a88 
FastLeakTest modification
@rmtfleming
Merge pull request #2207 from farid-zare/MatGPT
f8e9ef7 
Mat gpt
@farid-zare
Add MatGPT
46f9a63
@rmtfleming
Merge pull request #2211 from farid-zare/MatGPT_submodule
a98bdee 
Add MatGPT
@rmtfleming
Merge pull request #2205 from Yanjun2021/update-function-in-XomicsToM…
c102c2a 
…odel

update function in XomicsToModel
@rmtfleming
Merge pull request #2196 from almut-heinken/addPlotOption
fddd334 
Add plot option
@rmtfleming
Merge pull request #2200 from Sami990/Debug-testAll-function
23f477a 
Debug test all function
@rmtfleming
Merge pull request #2204 from farid-zare/update-testAll-function2
8c0dc17 
Update test all function2
@rmtfleming
Merge branch 'master' into develop
20467cf
@rmtfleming rmtfleming merged commit 2fc8332 into master Jan 10, 2024
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