.gitignore

# Windows default autosave extension
*.asv
Thumbs.db

# OSX / *nix default autosave extension
*.*~

# Compiled MEX binaries (all platforms)
*.mex*

# Simulink Code Generation
slprj/

# Session info
octave-workspace

# hidden extensions
.DS_Store

# specific extensions
*.pyc
*.mps

# logfiles
*.log
*.zip

# coverage
coverage.json
coverage_html

# omit DB settings from rBionet
src/reconstruction/rBioNet/rBioNetSettingsDB.mat

# specific folders
src/dataIntegration/fluxomics/c13solver/IsotopomerModel.txt
src/dataIntegration/fluxomics/c13solver/convertCarbonInput.m
src/dataIntegration/fluxomics/c13solver/slvrCumomer.m
src/dataIntegration/fluxomics/c13solver/slvrCumomer_fast.m
src/dataIntegration/fluxomics/c13solver/slvrEMU.m
src/dataIntegration/fluxomics/c13solver/slvrEMU_fast.m

# model files for testing
test/models/*.xml
test/models/*.mat
!test/models/Recon2.0model.mat

# tests
test/testGrowthExpMatch/GEMLog.txt
test/testGrowthExpMatch/GEMLog_solution_1.mat
test/testMaps/target.svg

# verified tests
test/verifiedTests/testSampling/ACHRParallelError.txt
test/verifiedTests/testSampling/ACHR_last_point.mat
test/verifiedTests/testSampling/ACHRerror.txt
test/verifiedTests/testSampling/EcoliModelSamples_1.mat
test/verifiedTests/testSampling/EcoliModelSamples_2.mat
test/verifiedTests/testSampling/EcoliModelSamples_3.mat
test/verifiedTests/testSampling/EcoliModelSamples_4.mat
test/verifiedTests/testSampling/modelRedTmp.mat
test/verifiedTests/testSampling/sampleCbModelTmp.mat
test/verifiedTests/testSampling/sampleStructTmp.mat
test/verifiedTests/testMultiSpeciesModelling/*.mat
test/verifiedTests/testSBML/*.sbml.xml
test/verifiedTests/testFastGapFill/KEGGMatrix.mat
test/verifiedTests/testTools/testPrintMatrix.txt
test/verifiedTests/testMassChargeBalance/*.txt
test/verifiedTests/testFastGapFill/*.mat
test/verifiedTests/testTools/testData_printLabeledData.txt
test/verifiedTests/testSolvers/MILPProblem.mat
test/verifiedTests/testOutputNetworkCytoscape/data*
test/verifiedTests/testPrint/printConstraints.txt

# shared libraries
*.so

# Windows executable files
*.exe
*.exe.*

# Windows dynamic library files
*.dll

# dump files
sh.exe.stackdump

# autogenerated documentation
docs/build
docs/source/list_contributors.rst

# examples folder in gapFilling
src/reconstruction/fastGapFill/examples/

# generated .mat files in tutorials
tutorials/fastGapFill/results_*.mat
tutorials/fastGapFill/KEGGMatrix.mat
tutorials/fastGapFill/prepareFGFResultsDefault.mat
tutorials/IO/Abiotrophia_defectiva_ATCC_49176.xml
tutorials/IO/ecoli_core_model.mat
PPP120.mat
E.mat

# generated tutorial documentation
docs/source/_static/tutorials/*.html
docs/source/tutorials/tutorial*.rst

# hidden folders
.vscode/

# temporary folder
.tmp/
output/