Fix deprecated syntax for Pkg.dir in docs and tests

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()
 ```
 

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.

src/distributedFBA.jl

@@ -343,7 +343,7 @@ See also: `distributeFBA()`, `MathProgBase.HighLevelInterface`
 """
 
 function loopFBA(m, rxnsList, nRxns::Int, rxnsOptMode=2 .+ zeros(Int, length(rxnsList)), iRound::Int=0, pid::Int=1,
-                 resultsDir::String="$(Pkg.dir("COBRA"))/results", logFiles::Bool=false, onlyFluxes::Bool=false, printLevel::Int=1)
+                 resultsDir::String=joinpath(dirname(pathof(COBRA)), "..")*"/results", logFiles::Bool=false, onlyFluxes::Bool=false, printLevel::Int=1)
 
     # initialize vectors and counters
     retObj = zeros(nRxns)
@@ -524,7 +524,7 @@ See also: `preFBA!()`, `splitRange()`, `buildCobraLP()`, `loopFBA()`, or `fetch(
 
 function distributedFBA(model, solver; nWorkers::Int=1, optPercentage::Union{Float64, Int64}=0.0, objective::String="max",
                         rxnsList=1:length(model.rxns), strategy::Int=0, rxnsOptMode=2 .+ zeros(Int, length(model.rxns)),
-                        preFBA::Bool=false, saveChunks::Bool=false, resultsDir::String="$(Pkg.dir("COBRA"))/results",
+                        preFBA::Bool=false, saveChunks::Bool=false, resultsDir::String=joinpath(dirname(pathof(COBRA)), "..")*"/results",
                         logFiles::Bool=false, onlyFluxes::Bool=false, printLevel::Int=1)
 
     # convert type of optPercentage

test/p_all.jl

@@ -12,7 +12,7 @@ if !@isdefined includeCOBRA
     includeCOBRA = true
 end
 
-pkgDir = joinpath(dirname(pathof(COBRA)))
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
 
 # output information
 testFile = @__FILE__
@@ -25,7 +25,7 @@ if includeCOBRA
     # define the name of the default solver
     solverName = :GLPKMathProgInterface
     connectSSHWorkers = false
-    include(pkgDir*"/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -336,24 +336,24 @@ printSolSummary(testFile, optSol, maxFlux, minFlux, solTime, nWorkers, solverNam
 
 # remove the results folder to clean up
 try
-    rm("$(Pkg.dir("COBRA"))/results", recursive=true, force=true)
+    rm(pkgDir*"/results", recursive=true, force=true)
 catch
     @info "The directory $(Pkg.dir("COBRA"))/results cannot be removed. Please check permissions.\n"
 end
 
 # create folders if they are not present
-if !isdir("$(Pkg.dir("COBRA"))/results")
-    mkdir("$(Pkg.dir("COBRA"))/results")
+if !isdir(pkgDir*"/results")
+    mkdir(pkgDir*"/results")
     printstyled("Directory `results` created.\n\n"; color=:green)
 
     # create a folder for storing the chunks of the fluxes of each minimization
-    if !isdir("$(Pkg.dir("COBRA"))/results/fvamin")
-        mkdir("$(Pkg.dir("COBRA"))/results/fvamin")
+    if !isdir(pkgDir*"/results/fvamin")
+        mkdir(pkgDir*"/results/fvamin")
     end
 
     # create a folder for storing the chunks of the fluxes of each maximization
-    if !isdir("$(Pkg.dir("COBRA"))/results/fvamax")
-        mkdir("$(Pkg.dir("COBRA"))/results/fvamax")
+    if !isdir(pkgDir*"/results/fvamax")
+        mkdir(pkgDir*"/results/fvamax")
     end
 else
     printstyled("Directory `results` already exists.\n\n", color=:green)
@@ -391,13 +391,13 @@ run(`rm testFile.mat`)
 
 # remove the results folder to clean up
 try
-    rm("$(Pkg.dir("COBRA"))/results", recursive=true, force=true)
+    rm(pkgDir*"/results", recursive=true, force=true)
 catch
     @info "The directory $(Pkg.dir("COBRA"))/results cannot be removed. Please check permissions.\n"
 end
 
-# create the logs folder
-resultsDir = "$(Pkg.dir("COBRA"))/results"
+# create the pkgDir*"/
+resultsDir = pkgDir*"/results"
 
 if isdir("$resultsDir/logs")
     try
@@ -416,7 +416,7 @@ minFlux, maxFlux, optSol, fbaSol, fvamin, fvamax, statussolmin, statussolmax = d
 
 # remove the results folder to clean up
 try
-    rm("$(Pkg.dir("COBRA"))/results", recursive=true, force=true)
+    rm(pkgDir*"/results", recursive=true, force=true)
 catch
     @info "The directory $(Pkg.dir("COBRA"))/results cannot be removed. Please check permissions.\n"
 end
@@ -430,12 +430,12 @@ minFlux, maxFlux, optSol, fbaSol, fvamin, fvamax, statussolmin, statussolmax = d
 # call to write logFiles with onlyFluxes
 minFlux, maxFlux, optSol, fbaSol, fvamin, fvamax, statussolmin, statussolmax = distributedFBA(model, solver, nWorkers=nWorkers, onlyFluxes=true, rxnsList=1:10, logFiles=true)
 
-# test if the /logs folder has been created
-@test isdir("$(Pkg.dir("COBRA"))/results/logs")
+# test if thpkgDir*"/en created
+@test isdir(pkgDir*"/results/logs")
 
 # remove the results folder to clean up
-try
-    rm("$(Pkg.dir("COBRA"))/results", recursive=true, force=true)
+trypkgDir*"/
+    rm(pkgDir*"/results", recursive=true, force=true)
 catch
     @info "The directory $(Pkg.dir("COBRA"))/results cannot be removed. Please check permissions.\n"
 end

test/p_distinct.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 4
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -37,13 +39,13 @@ end
 getTestModel()
 
 # include the solver configuration file
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # define an optPercentage value
 optPercentage = 90.0

test/p_range.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 4
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -37,13 +39,13 @@ end
 getTestModel()
 
 # include a common deck for running tests
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # select the number of reactions
 rxnsList = 1:30

test/runtests.jl

@@ -9,18 +9,18 @@
 
 using Pkg, Distributed, LinearAlgebra, COBRA
 
-pkgDir = joinpath(dirname(pathof(COBRA)))
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
 
 # retrieve all packages that are installed on the system
-include(pkgDir*"/checkSetup.jl")
+include(pkgDir*"/src/checkSetup.jl")
 packages = checkSysConfig()
 
 # configure for runnint the tests in batch
 solverName = :GLPKMathProgInterface
 nWorkers = 4
 connectSSHWorkers = false
-include(pkgDir*"/connect.jl")
-TESTDIR = pkgDir*"/../test"
+include(pkgDir*"/src/connect.jl")
+TESTDIR = pkgDir*"/test"
 
 # create a parallel pool and determine its size
 if (@isdefined nWorkers) && (@isdefined connectSSHWorkers)

test/s_all.jl

@@ -12,7 +12,7 @@ if !@isdefined includeCOBRA
     includeCOBRA = true
 end
 
-pkgDir = joinpath(dirname(pathof(COBRA)))
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
 
 # output information
 testFile = @__FILE__
@@ -23,7 +23,7 @@ nWorkers = 1
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include(pkgDir*"/connect.jl")
+    include(pkgDir*"/src//connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -39,13 +39,13 @@ end
 getTestModel()
 
 # include a common deck for running tests
-include(pkgDir*"/../config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel(pkgDir*"/../test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # select the number of reactions
 rxnsList = 1:length(model.rxns)

test/s_core.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 1
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -37,13 +39,13 @@ end
 getTestModel()
 
 # include a common deck for running tests
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # select the number of reactions
 rxnsList = 1:length(model.rxns)

test/s_distinct.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 1
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -37,13 +39,13 @@ end
 getTestModel()
 
 # include a common deck for running tests
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # define an optPercentage value
 optPercentage = 90.0

test/s_fba.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 1
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -37,13 +39,13 @@ end
 getTestModel()
 
 # include a common deck for running tests
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 modelOrig = model
 

test/s_tools.jl

@@ -18,10 +18,12 @@ testFile = @__FILE__
 # number of workers
 nWorkers = 1
 
+pkgDir = joinpath(dirname(pathof(COBRA)), "..")
+
 # create a pool and use the COBRA module if the testfile is run in a loop
 if includeCOBRA
     connectSSHWorkers = false
-    include("$(Pkg.dir("COBRA"))/src/connect.jl")
+    include(pkgDir*"/src/connect.jl")
 
     # create a parallel pool and determine its size
     if isdefined(:nWorkers) && isdefined(:connectSSHWorkers)
@@ -32,13 +34,13 @@ if includeCOBRA
 end
 
 # include a common deck for running tests
-include("$(Pkg.dir("COBRA"))/config/solverCfg.jl")
+include(pkgDir*"/config/solverCfg.jl")
 
 # change the COBRA solver
 solver = changeCobraSolver(solverName, solParams)
 
 # load an external mat file
-model = loadModel("$(Pkg.dir("COBRA"))/test/ecoli_core_model.mat", "S", "model")
+model = loadModel(pkgDir*"/test/ecoli_core_model.mat", "S", "model")
 
 # find the reaction ID of one reaction
 rxnIDs, rxnIDsNE = findRxnIDS(model, ["PPC"])