Merge pull request #56 from opencobra/develop

Regular merge of develop

.artenolis.yml

@@ -10,38 +10,45 @@ script:
 
     # add MATLAB to the path
     - if [ "$ARCH" == "Linux" ]; then
-         export PATH="/mnt/prince-data/MATLAB/$MATLAB_VER/bin:$PATH";
+          export PATH="$PATH:$ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin";
       fi
 
-    # clone the COBRA Toolbox
-    - rm -rf /tmp/cobratoolbox-cobrajl
-    - git clone https://github.com/opencobra/cobratoolbox.git /tmp/cobratoolbox-cobrajl --depth=1
-    - cd /tmp/cobratoolbox-cobrajl
-    - git submodule update --init --remote --no-fetch --depth=1
-
     # change to the current directory
     - cd $CURRENT_DIR
 
     # 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
+          CURRENT_DIR=`pwd`;
+          cd ~/tmp/cobratoolbox-cobrajl;
+          git pull origin master;
+          cd $CURRENT_DIR;
+          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
-
 after_success:
-    - if [ "$ARCH" == "Linux" ]; then /mnt/prince-data/JULIA/$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 [ "$ARCH" == "Linux" ]; then
+    - if [[ "$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:${#var}};
         export TRAVIS_OS_NAME=$label;
         export TRAVIS_JULIA_VERSION=$JULIA_VER;
+        $ARTENOLIS_SOFT_PATH/julia/$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
 
-    # deploy documentation
-    - if [ "$ARCH" == "Linux" ]; then /mnt/prince-data/JULIA/$JULIA_VER/bin/julia --color=yes -e 'cd(Pkg.dir("COBRA")); include(joinpath("docs", "makeDoc.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/v0.6/COBRA
-
-        # add the COBRA module
-        /mnt/prince-data/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
-        /mnt/prince-data/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 "D:\\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"]

README.md

@@ -50,8 +50,9 @@ Shall no solvers be detected on your system, error messages may be thrown when t
 
 The code has been benchmarked against the `fastFVA` implementation [[3](#References-1)]. A test model `ecoli_core_model.mat` [[4](#References-1)] can be used to pre-compile the code and can be downloaded using
 ```Julia
-julia> using Requests
-julia> include("$(Pkg.dir("COBRA"))/test/getTestModel.jl")
+julia> using HTTP, COBRA
+julia> pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+julia> include(pkgDir*"/test/getTestModel.jl")
 julia> getTestModel()
 ```
 

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",

docs/makeDoc.jl → docs/make.jl

@@ -7,24 +7,9 @@
 
 #-------------------------------------------------------------------------------------------
 
+import Pkg
 using Documenter
-
-if !isdefined(:includeCOBRA) includeCOBRA = true end
-
-if includeCOBRA
-    include("../src/COBRA.jl")
-    include("../src/load.jl")
-    include("../src/solve.jl")
-    include("../src/distributedFBA.jl")
-    include("../src/connect.jl")
-    include("../src/checkSetup.jl")
-    include("../src/tools.jl")
-
-    # only include PALM.jl if MATLAB is present
-    if sizeof(Pkg.installed("MATLAB")) > 0
-        include("../src/PALM.jl")
-    end
-end
+using COBRA
 
 # special concatenation of tutorials until issue 701 is fixed:
 # https://github.com/JuliaDocs/Documenter.jl/issues/701
@@ -34,20 +19,22 @@ end
 currentDir = pwd()
 
 # concatenate tutorial files
-cd("$(Pkg.dir("COBRA"))/tutorials")
+pkgDir = joinpath(dirname(pathof(COBRA)))
+cd(pkgDir*"/../tutorials")
 
 # define list of tutorials to be concatenated
 tutorials = ["tutorial-COBRA.jl.md", "tutorial-distributedFBA.jl.md", "tutorial-PALM.jl.md"]
 
 # concatenate the tutorials properly speaking
 cat = ""
 for tut in tutorials
+    global cat
     tmp = read(tut, String)
     cat = cat * tmp
 end
 
 # set all headers one level lower
-cat = replace(cat, "\n#", "\n##")
+cat = replace(cat, "\n#" => "\n##")
 
 # write out the tutorial to new file
 open("tutorials.md", "w") do f
@@ -56,12 +43,12 @@ open("tutorials.md", "w") do f
 end
 
 # move the tutorials.md file to the docs folder
-mv("tutorials.md", "$(Pkg.dir("COBRA"))/docs/src/tutorials.md", remove_destination=true)
+mv("tutorials.md", pkgDir*"/../docs/src/tutorials.md", force=true)
 
 # change back to the old directory
 cd(currentDir)
 
-makedocs(format = :html,
+makedocs(format = Documenter.HTML(),
          sitename = "COBRA.jl",
          pages = Any[ # Compat: `Any` for 0.4 compat
                  "index.md",
@@ -76,9 +63,8 @@ makedocs(format = :html,
         )
 
 deploydocs(repo = "github.com/opencobra/COBRA.jl.git",
-           julia  = get(ENV, "JULIA_VER", ""),
            target = "build",
-           make = nothing,
-           deps = nothing,
-           latest = get(ENV, "GIT_BRANCH", "")
+           branch = "gh-pages",
+           devbranch = "origin/develop",
+           versions = ["stable" => "v^", "v#.#"]
           )

docs/src/beginnerGuide.md

@@ -3,7 +3,8 @@
 What is Julia?
 --------------
 
-"*Julia is a high-level, high-performance dynamic programming language […]*". You may read more about Julia [here](http://julialang.org).
+"*Julia is a high-level, high-performance dynamic programming language […]*".
+You may read more about Julia [here](http://julialang.org).
 
 How do I get Julia?
 -------------------
@@ -36,7 +37,7 @@ If you need help, you can always type a `?`at the Julia REPL. For instance, if y
 ? abs
 ```
 
-You may also find the [FAQ section](faq.html) of this documentation interesting, especially if you are running into issues.
+You may also find the [FAQ](@ref) of this documentation interesting, especially if you are running into issues.
 
 How do I install a solver?
 --------------------------
@@ -72,11 +73,6 @@ Pkg.add("GLPKMathProgInterface")
 
 Other supported solvers, such as `CPLEX`, `Clp`, `Gurobi`, or `Mosek`, may be installed in a similar way. Their respective interfaces are described [here](https://github.com/JuliaOpt). If you want to use `CPLEX`, you must follow the installation instructions [here](https://github.com/JuliaOpt/CPLEX.jl). Most importantly, make sure that you set the `LD_LIBRARY_PATH` environment variable.
 
-Now I have a solver, and I have Julia. What is next?
-------------------------------------------------------
-
-You are now all set to install `COBRA.jl`. Follow the installation instructions [here](index.html). You may then also follow this [tutorial](cobratutorial.html) to get you started.
-
 There is a tutorial, but I cannot open it. What should I do?
 ------------------------------------------------------------
 

docs/src/configuration.md

@@ -4,7 +4,8 @@
 
 In order to load currently defined solver parameters, the following file may be included in the script, which defines the `solParams` array:
 ```julia
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+include(pkgDir*"/config/solverCfg.jl")
 ```
 Then, the `COBRA` solver can be set with:
 ```julia
@@ -49,7 +50,8 @@ solParams = [
 
 A parallel pool with workers on SSH nodes can be created using:
 ```julia
-include("$(Pkg.dir("COBRA"))/src/connect.jl")
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+include(pkgDir*"/src/connect.jl")
 workersPool, nWorkers = createPool(12, true, "mySSHCfg.jl")
 ```
 which will connect 12 local workers, and all workers defined in `mySSHCfg.jl`. An example connection file is provided in the `config/` folder of the `COBRA` package installation folder.

docs/src/faq.md

@@ -1,4 +1,4 @@
-# Frequently Asked Questions (FAQ)
+# [Frequently Asked Questions (FAQ)](@id FAQ)
 
 Why can't I build packages in Julia?
 ------------------------------------
@@ -64,4 +64,4 @@ How can I get the latest version of `COBRA.jl`
 If you want to enjoy the latest untagged (but eventually unstable) features of `COBRA.jl`, do the following from within `Julia`:
 ```Julia
 julia> Pkg.checkout("COBRA", "develop")
-```
+```