change codes for julia 1.0+

.artenolis.yml

@@ -19,24 +19,35 @@ script:
     # rename the cloned folder
     - cd .. && cp -r $NODE_LABELS COBRA && cd COBRA
 
+    # change the test dependencies on Linux and macOS (ARTENOLIS)
+    - if [ "$ARCH" == "Linux" ] || [ "$ARCH" == "macOS" ]; then
+          perl -i -pe's/test = \["GLPKMathProgInterface", "GLPK", "Test"\]/test = \["GLPKMathProgInterface", "GLPK", "Test", "MAT", "MATLAB", "Gurobi", "CPLEX"\]/g' Project.toml;
+      fi
+
     # launch the tests
     - bash .artenolis/runtests.sh
 
-    # clean up the build directory
-    - cd .. && rm -rf COBRA
-
     # clean up the tmp folder
     - rm -rf ~/tmp
 
 after_success:
-    - if [ "$ARCH" == "Linux" ]; then $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'cd(Pkg.dir("COBRA")); using Coverage; tmp=process_folder(); Codecov.submit(tmp, verbose=false); Coveralls.submit(tmp);'; fi
+
+    # submit coverage report
+    - if [ "$ARCH" == "Linux" && "$JULIA_VER" = "v1.2.0" ]; then
+        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())';
+      fi
 
     # set environment variables for documentation deployment
     - if [[ "$ARCH" == "Linux" && "$JENKINS_PULL_REQUEST" != "True" ]]; then
         export TRAVIS_BRANCH=$GIT_BRANCH;
         export TRAVIS_PULL_REQUEST=false;
         var=$GIT_URL; export TRAVIS_REPO_SLUG=${var:7:${#var}};
-        export TRAVIS_OS_NAME="linux";
+        export TRAVIS_OS_NAME=$label;
         export TRAVIS_JULIA_VERSION=$JULIA_VER;
-        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'cd(Pkg.dir("COBRA")); include(joinpath("docs", "makeDoc.jl"))';
+        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()';
+        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --project=docs/ docs/make.jl;
       fi
+
+after_script:
+    # clean up the build directory
+    - cd .. && rm -rf COBRA

.artenolis/runtests.sh

@@ -5,39 +5,21 @@ echo "MATLAB_VER = $MATLAB_VER"
 
 # launch the test script
 if [ "$ARCH" == "Linux" ]; then
-    if [ "$JULIA_VER" == "v0.6.4" ]; then
-        # remove th julia directory to clean the installation directory
-        rm -rf $JULIA_PKGDIR/v0.6/COBRA
-
-        # add the COBRA module
-        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'Pkg.clone(pwd()); cd(Pkg.dir("COBRA")); Pkg.test(pwd(), coverage=true);'
-
-    elif [ "$JULIA_VER" == "v0.7.0" ]; then
-        # add the COBRA module
-        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'using Pkg; Pkg.clone(pwd())'
-    fi
+    $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("COBRA", coverage=true); Pkg.rm("COBRA");'
 
 elif [ "$ARCH" == "macOS" ]; then
-    # remove th julia directory to clean the installation directory
-    rm -rf ~/.julia/v0.6/COBRA
-
     caffeinate -u &
-    /Applications/Julia-$JULIA_VER.app/Contents/Resources/julia/bin/julia --color=yes -e 'Pkg.clone(pwd()); cd(Pkg.dir("COBRA")); Pkg.test(pwd());'
+    /Applications/Julia-$JULIA_VER.app/Contents/Resources/julia/bin/julia --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("COBRA"); Pkg.rm("COBRA");'
 
 elif [ "$ARCH" == "windows" ]; then
-    if [ "$JULIA_VER" == "v0.6.4" ]; then
-        # remove th julia directory to clean the installation directory
-        rm -rf ~/.julia/v0.6/COBRA
-
-        unset Path
-        nohup "$ARTENOLIS_SOFT_PATH\\julia\\$JULIA_VER\\\bin\\julia.exe" --color=yes -e 'import Base; ENV["MATLAB_HOME"]="D:\\MATLAB\\$(ENV["MATLAB_VER"])"; Pkg.clone(pwd()); cd(Pkg.dir("COBRA")); Pkg.test(pwd());' > output.log & PID=$!
+    unset Path
+    nohup "$ARTENOLIS_SOFT_PATH\\julia\\$JULIA_VER\\\bin\\julia.exe" --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("COBRA"); Pkg.rm("COBRA");' > output.log & PID=$!
 
-        # follow the log file
-        tail -n0 -F --pid=$! output.log 2>/dev/null
+    # follow the log file
+    tail -n0 -F --pid=$! output.log 2>/dev/null
 
-        # wait until the background process is done
-        wait $PID
-    fi
+    # wait until the background process is done
+    wait $PID
 fi
 
 CODE=$?

.gitignore

@@ -17,5 +17,5 @@ docs/build/
 docs/tutorial/results.mat
 results/*
 test/testModels
-
-docs/src/tutorials.md
+Manifest.toml
+docs/src/tutorials.md

.travis.yml

@@ -4,13 +4,11 @@ os:
     - linux
 
 julia:
-    - 0.6
-    - 0.7
+    - 1.0
     - nightly
 
 matrix:
   allow_failures:
-    - julia: 0.7
     - julia: nightly
 
 notifications:
@@ -25,18 +23,3 @@ addons:
         - libgmp-dev
         - libglpk-dev
 
-git:
-    depth: 99999
-
-before_install:
-    - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-
-script:
-    # update all packages
-    - julia --color=yes -e 'Pkg.update();'
-
-    # temporary addition for julia 0.6 until new version of MAT tagged
-    - julia --color=yes -e 'Pkg.add("MAT"); Pkg.checkout("MAT")'
-
-    # add and test the COBRA module
-    - julia --color=yes -e 'Pkg.clone(pwd()); Pkg.test("COBRA")'

Project.toml

@@ -0,0 +1,32 @@
+name = "COBRA"
+uuid = "58298e0b-d05c-52ec-a210-0694647ebfc7"
+version = "0.3.0"
+
+[deps]
+CPLEX = "a076750e-1247-5638-91d2-ce28b192dca0"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
+GLPKMathProgInterface = "3c7084bd-78ad-589a-b5bb-dbd673274bea"
+HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+MathProgBase = "fdba3010-5040-5b88-9595-932c9decdf73"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[compat]
+HTTP = ">= 0.8.0"
+MAT = ">= 0.5.0"
+julia = "1"
+
+[extras]
+CPLEX = "a076750e-1247-5638-91d2-ce28b192dca0"
+GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
+GLPKMathProgInterface = "3c7084bd-78ad-589a-b5bb-dbd673274bea"
+Gurobi = "2e9cd046-0924-5485-92f1-d5272153d98b"
+MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+MATLAB = "10e44e05-a98a-55b3-a45b-ba969058deb6"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["GLPKMathProgInterface", "GLPK", "Test"]

config/sshCfg.jl

@@ -7,21 +7,21 @@
 
 #-------------------------------------------------------------------------------------------
 
-sshWorkers = Array{Dict{Any, Any}}(3)
+sshWorkers = Array{Dict{Any, Any}}(undef, 3)
 
-sshWorkers[1,:] = Dict( "usernode"   => "[email protected]",
+sshWorkers[1] = Dict( "usernode"   => "[email protected]",
                         "procs"  => 8,
                         "dir"    => `"~"/COBRA.jl/`,
                         "flags"  => `-6 -p8022`,
                         "exename"=> "/usr/bin/julia/bin/./julia")
 
-sshWorkers[2,:] = Dict( "usernode"   => "[email protected]",
+sshWorkers[2] = Dict( "usernode"   => "[email protected]",
                         "procs"  => 16,
                         "dir"    => `"~"/COBRA.jl/`,
                         "flags"  => "-p22",
                         "exename"=> "/usr/bin/julia/bin/./julia")
 
-sshWorkers[3,:] = Dict( "usernode"   => "[email protected]",
+sshWorkers[3] = Dict( "usernode"   => "[email protected]",
                         "procs"  => 32,
                         "dir"    => `"~"/COBRA.jl/`,
                         "flags"  => "-4 -p9997",

src/COBRA.jl

@@ -17,9 +17,10 @@ The documentation is here: http://opencobra.github.io/COBRA.jl
 module COBRA
 
     # include the load file to load a model of .mat format
-    using MAT
-    using MathProgBase
-    if sizeof(Pkg.installed("MATLAB")) > 0
+    import Pkg
+    using SparseArrays, Distributed, LinearAlgebra
+    using MAT, MathProgBase
+    if "MATLAB" in keys(Pkg.installed())
         using MATLAB
     end
 
@@ -30,7 +31,7 @@ module COBRA
     include("solve.jl")
     include("distributedFBA.jl")
     include("tools.jl")
-    if sizeof(Pkg.installed("MATLAB")) > 0
+    if "MATLAB" in keys(Pkg.installed())
         include("PALM.jl")
     end