work-around equalities in coupling bounds in MAT

.github/workflows/ci.yml

@@ -1,9 +1,10 @@
 name: CI
+
 on:
   push:
     branches:
       - master
-      - develop
+  pull_request:
 
 jobs:
   test:
@@ -13,8 +14,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6' # Oldest supported version for COBREXA.jl
           - '1' # This is always the latest stable release in the 1.X series
+          - '1.6' # LTS
           #- 'nightly'
         os:
           - ubuntu-latest
@@ -23,28 +24,20 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@latest
       - run: |
           git config --global user.name Tester
           git config --global user.email [email protected]
       - uses: julia-actions/julia-runtest@latest
         continue-on-error: ${{ matrix.version == 'nightly' }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

src/base/solver.jl

@@ -24,8 +24,16 @@ function make_optimization_model(model::MetabolicModel, optimizer; sense = MAX_S
     C = coupling(model) # empty if no coupling
     isempty(C) || begin
         cl, cu = coupling_bounds(model)
-        @constraint(optimization_model, c_lbs, cl .<= C * x) # coupling lower bounds
-        @constraint(optimization_model, c_ubs, C * x .<= cu) # coupling upper bounds
+        @constraint(
+            optimization_model,
+            c_lbs,
+            cl[isfinite.(cl)] .<= C[isfinite.(cl), :] * x
+        ) # coupling lower bounds
+        @constraint(
+            optimization_model,
+            c_ubs,
+            C[isfinite.(cu), :] * x .<= cu[isfinite.(cu)]
+        ) # coupling upper bounds
     end
 
     return optimization_model