From f74280a410bf5b4cd50f36f29e8e56e0e35b0e21 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Thu, 1 Apr 2021 11:20:21 +0200
Subject: [PATCH] use pkg relativity in test

---
 test/analysis/fba.jl                 | 10 +++++-----
 test/analysis/fva.jl                 |  2 +-
 test/analysis/pfba.jl                |  2 +-
 test/base/solver.jl                  |  4 ++--
 test/runtests.jl                     |  3 +--
 test/sampling/sampling_tools_test.jl |  2 +-
 6 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/test/analysis/fba.jl b/test/analysis/fba.jl
index 4e92b0c53..3aecc1f11 100644
--- a/test/analysis/fba.jl
+++ b/test/analysis/fba.jl
@@ -2,19 +2,19 @@
     cp = test_simpleLP()
     (lp, x) = flux_balance_analysis(cp, GLPK.Optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test sol ≈ [1.0, 2.0]
 
     (lp, x) = flux_balance_analysis(cp, Clp.Optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test sol ≈ [1.0, 2.0]
 
     # test the maximization of the objective
     cp = test_simpleLP2()
     (lp, x) = flux_balance_analysis(cp, GLPK.Optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test sol ≈ [-1.0, 2.0]
 
     # test with a more biologically meaningfull model
@@ -29,7 +29,7 @@
 
     (lp, x) = flux_balance_analysis(cp, GLPK.Optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test objective_value(lp) ≈ expected_optimum
     @test cp.c' * sol ≈ expected_optimum
 
@@ -54,7 +54,7 @@ end
     # FBA
     biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
     cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
-    optimizer = Tulip.Optimizer # quiet by default
+    optimizer = COBREXA.Tulip.Optimizer # quiet by default
     sol = fba(model, optimizer; objective_func = biomass, constraints = cons)
     pfl = findfirst(model.reactions, "PFL")
     solmulti = fba(model, optimizer; objective_func = [biomass, pfl], weights = [0.8, 0.2]) # classic flux balance analysis
diff --git a/test/analysis/fva.jl b/test/analysis/fva.jl
index 671e66da3..8c555dc8c 100644
--- a/test/analysis/fva.jl
+++ b/test/analysis/fva.jl
@@ -74,7 +74,7 @@ end
     pfl = findfirst(model.reactions, "PFL")
 
     # FVA
-    optimizer = Tulip.Optimizer
+    optimizer = COBREXA.Tulip.Optimizer
     atts = Dict("IPM_IterationsLimit" => 500)
     cons = Dict("EX_glc__D_e" => (-10.0, -10.0))
     fva_max, fva_min =
diff --git a/test/analysis/pfba.jl b/test/analysis/pfba.jl
index 4d9987a52..fffd674fe 100644
--- a/test/analysis/pfba.jl
+++ b/test/analysis/pfba.jl
@@ -27,7 +27,7 @@
     ) # just see if it works - OSQP is a terrible LP solver
     sol = pfba(
         model,
-        [Tulip.Optimizer, OSQP.Optimizer];
+        [COBREXA.Tulip.Optimizer, COBREXA.OSQP.Optimizer];
         objective_func = biomass,
         solver_attributes = Dict("opt1" => Dict{Any,Any}(), "opt2" => atts),
     ) # try two optimizers
diff --git a/test/base/solver.jl b/test/base/solver.jl
index 3208c7e9f..bcfce612d 100644
--- a/test/base/solver.jl
+++ b/test/base/solver.jl
@@ -4,12 +4,12 @@
     optimizer = GLPK.Optimizer
     (lp, x) = optimize_model(cp, optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test sol ≈ [1.0, 2.0]
 
     optimizer = Clp.Optimizer
     (lp, x) = optimize_model(cp, optimizer)
     @test termination_status(lp) === MOI.OPTIMAL
-    sol = JuMP.value.(x)
+    sol = COBREXA.JuMP.value.(x)
     @test sol ≈ [1.0, 2.0]
 end
diff --git a/test/runtests.jl b/test/runtests.jl
index 5baeae3e3..e3811f527 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -14,7 +14,6 @@ using OSQP
 using Statistics
 using JSON
 using Measurements
-using Downloads
 
 function run_test_file(path...)
     fn = joinpath(path...)
@@ -42,7 +41,7 @@ function download_data_file(url, path, hash)
         return path
     end
 
-    Downloads.download(url, path)
+    COBREXA.Downloads.download(url, path)
     check_data_file_hash(path, hash)
     return path
 end
diff --git a/test/sampling/sampling_tools_test.jl b/test/sampling/sampling_tools_test.jl
index 0886946fa..92611296b 100644
--- a/test/sampling/sampling_tools_test.jl
+++ b/test/sampling/sampling_tools_test.jl
@@ -8,7 +8,7 @@
         ),
     )
 
-    optimizer = Tulip.Optimizer
+    optimizer = COBREXA.Tulip.Optimizer
     biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
     cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
     atts = Dict("IPM_IterationsLimit" => 110)
-- 
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