Merge pull request #509 from LCSB-BioCore/develop

Develop→master 20211108

.gitlab-ci.yml

@@ -38,6 +38,7 @@ variables:
 .global_trigger_compat_tests: &global_trigger_compat_tests
   rules:
     - if: $CI_COMMIT_BRANCH == "master"
+    - if: $CI_EXTERNAL_PULL_REQUEST_TARGET_BRANCH_NAME == "master"
 
 #
 # Test environment & platform settings
@@ -58,7 +59,7 @@ variables:
 .global_env_win: &global_env_win
   script:
     - $global:LASTEXITCODE = 0 # Note the global prefix.
-    - Invoke-Expression $Env:ARTENOLIS_SOFT_PATH"\julia\"$Env:JULIA_VER"\bin\julia" --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
+    - Invoke-Expression $Env:ARTENOLIS_SOFT_PATH"\julia\"$Env:JULIA_VER"\bin\julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'"
     - exit $LASTEXITCODE
 
 .global_env_win8: &global_env_win8

docs/src/notebooks/2_finding_balance.jl

@@ -155,6 +155,7 @@ dict_soln = parsimonious_flux_balance_analysis_dict(
     modifications = [
         silence, # silence the optimizer (OSQP is very verbose by default)
         change_constraint("R_EX_glc__D_e"; lb = -12, ub = -12),
+        change_optimizer_attribute("polish", true),
     ],
 )
 
@@ -248,6 +249,7 @@ moment_moma = minimize_metabolic_adjustment_analysis_dict(
     modifications = [
         silence,
         change_optimizer_attribute("polish", true),
+        change_optimizer_attribute("max-iter", 10_000),
         change_constraint("EX_glc__D_e", lb = -1000),
         change_constraint("CYTBD"; lb = 0, ub = 0),
         add_moment_constraints(ksas, protein_mass_fraction;),

test/analysis/minimize_metabolic_adjustment.jl

 @testset "MOMA" begin
-    model = load_model(StandardModel, model_paths["e_coli_core.json"])
+    model = test_toyModel()
 
-    sol = parsimonious_flux_balance_analysis_dict(
-        model,
-        OSQP.Optimizer;
-        modifications = [silence, change_optimizer_attribute("polish", true)],
-    )
+    sol = [looks_like_biomass_reaction(rid) ? 0.5 : 0.0 for rid in reactions(model)]
 
     moma = minimize_metabolic_adjustment_analysis_dict(
         model,
         sol,
         OSQP.Optimizer;
-        modifications = [
-            silence,
-            change_optimizer_attribute("polish", true),
-            change_constraint("CYTBD"; lb = 0.0, ub = 0.0),
-        ],
+        modifications = [silence, change_optimizer_attribute("polish", true)],
     )
 
-    @test isapprox(
-        moma["BIOMASS_Ecoli_core_w_GAM"],
-        0.06214149238730545,
-        atol = QP_TEST_TOLERANCE,
-    )
+    @test isapprox(moma["biomass1"], 0.07692307692307691, atol = QP_TEST_TOLERANCE)
 end

test/analysis/parsimonious_flux_balance_analysis.jl

 @testset "Parsimonious flux balance analysis with StandardModel" begin
-    model = load_model(StandardModel, model_paths["e_coli_core.json"])
+    model = test_toyModel()
+
     d = parsimonious_flux_balance_analysis_dict(
         model,
         Tulip.Optimizer;
         modifications = [
-            change_constraint("EX_glc__D_e"; lb = -12, ub = -12),
-            change_optimizer_attribute("IPM_IterationsLimit", 500),
-        ],
-        qp_modifications = [
-            change_optimizer(OSQP.Optimizer),
-            change_optimizer_attribute("polish", true),
-            silence,
-        ],
-    )
-    v = parsimonious_flux_balance_analysis_vec(
-        model,
-        Tulip.Optimizer;
-        modifications = [
-            change_constraint("EX_glc__D_e"; lb = -12, ub = -12),
+            change_constraint("EX_m1(e)", lb = -10.0),
             change_optimizer_attribute("IPM_IterationsLimit", 500),
         ],
         qp_modifications = [
@@ -29,6 +17,5 @@
 
     # The used optimizer doesn't really converge to the same answer everytime
     # here, we therefore tolerate a wide range of results.
-    @test isapprox(d["PGM"], -17.606459419216442, atol = QP_TEST_TOLERANCE)
-    @test isapprox(v[8], -17.606459419216442, atol = QP_TEST_TOLERANCE)
+    @test isapprox(d["biomass1"], 10.0, atol = QP_TEST_TOLERANCE)
 end