Merge pull request #39 from laurentheirendt/seminar

Adding keyword to optionally use the CT in PALM
opencobra · Oct 1, 2018 · 305456c · 305456c
2 parents 25e8357 + 13ac7ce
commit 305456c
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Showing 2 changed files with 16 additions and 13 deletions.
diff --git a/src/PALM.jl b/src/PALM.jl
@@ -238,7 +238,7 @@ See also: `loopModels()` and `shareLoad()`
 
 """
 
-function PALM(dir, scriptName, nMatlab::Int=2, outputFile::AbstractString="PALM_data.mat", varsCharact=[], cobraToolboxDir=ENV["HOME"]*Base.Filesystem.path_separator*"cobratoolbox", printLevel::Int=1)
+function PALM(dir, scriptName; nMatlab::Int=2, outputFile::AbstractString="PALM_data.mat", varsCharact=[], cobraToolboxDir=ENV["HOME"]*Base.Filesystem.path_separator*"cobratoolbox", printLevel::Int=1, useCOBRA::Bool=true)
 
     # read the content of the directory
     dirContent = readdir(dir)
@@ -269,11 +269,13 @@ function PALM(dir, scriptName, nMatlab::Int=2, outputFile::AbstractString="PALM_
     # declare an empty array for storing a summary of all data
     summaryData = Array{Union{Int,Float64,AbstractString}}(nModels + 1, nCharacteristics + 1)
 
-    for (p, pid) in enumerate(workers())
-        @spawnat (p + 1) begin
-            # clone a copy to a tmp folder as the cobtratoolbox is updated at runtime
-            if !isdir("/tmp/test-ct-$p")
-                run(`git clone $cobraToolboxDir /tmp/test-ct-$p`)
+    if useCOBRA
+        for (p, pid) in enumerate(workers())
+            @spawnat (p + 1) begin
+                # clone a copy to a tmp folder as the cobtratoolbox is updated at runtime
+                if !isdir("/tmp/test-ct-$p")
+                    run(`git clone $cobraToolboxDir /tmp/test-ct-$p`)
+                end
             end
         end
     end
@@ -285,13 +287,14 @@ function PALM(dir, scriptName, nMatlab::Int=2, outputFile::AbstractString="PALM_
             info("Launching MATLAB session on worker $(p+1).")
         end
 
-        # adding the model directory and eventual subdirectories to the MATLAB path
-        # Note: the fileseparator `/` also works on Windows systems if git Bash has been installed
-        @async R[p] = @spawnat (p+1) begin
-            eval(parse("mat\"addpath(genpath('/tmp/test-ct-$p'))\""))
-            eval(parse("mat\"run('/tmp/test-ct-$p/initCobraToolbox.m');\""))
+        if useCOBRA
+            # adding the model directory and eventual subdirectories to the MATLAB path
+            # Note: the fileseparator `/` also works on Windows systems if git Bash has been installed
+            @async R[p] = @spawnat (p+1) begin
+                eval(parse("mat\"addpath(genpath('/tmp/test-ct-$p'))\""))
+                eval(parse("mat\"run('/tmp/test-ct-$p/initCobraToolbox.m');\""))
+            end
         end
-
     end
 
     # print an informative message

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -89,7 +89,7 @@ if sizeof(Pkg.installed("MATLAB")) > 0
                    "nNz"]
 
     # launch PALM with the scriptFile on the 2 models
-    PALM(joinpath(TESTDIR, "testModels"), "scriptFile", 2, "modelCharacteristics.mat", varsCharact, "/tmp/cobratoolbox-cobrajl")
+    PALM(joinpath(TESTDIR, "testModels"), "scriptFile", nMatlab=2, outputFile="modelCharacteristics.mat", varsCharact=varsCharact, cobraToolboxDir="/tmp/cobratoolbox-cobrajl")
 
     # remove the directory with the test models
     rm(joinpath(TESTDIR, "testModels"), force=true, recursive=true)