CI/CD infrastructure and testing improvements

.github/workflows/pr-tests.yml

@@ -4,14 +4,16 @@ name: PR Tests
 # - Draft PRs: Fast tests only (no coverage) for rapid iteration
 # - Ready for Review: Full tests with coverage for quality assurance
 # - All subsequent commits: Continue with full coverage
+# - Pyomo tests run separately and don't block PRs
 
 on:
   pull_request:
     branches: [ main ]
     types: [ opened, synchronize, reopened, ready_for_review, converted_to_draft ]
 
 jobs:
-  test:
+  test-scipy:
+    name: SciPy Tests
     runs-on: ubuntu-latest
 
     steps:
@@ -26,7 +28,7 @@ jobs:
     - name: Determine test mode
       id: mode
       run: |
-        if [ "${{ github.event.pull_request.draft }}" ]; then
+        if [ "${{ github.event.pull_request.draft }}" = "true" ]; then
           echo "mode=fast" >> $GITHUB_OUTPUT
         else
           echo "mode=full" >> $GITHUB_OUTPUT
@@ -43,28 +45,70 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install .
-        pip install .[dev]
-        pip install -e . --no-build-isolation
-
+        pip install -e ".[dev]"
+
     - name: Run tests
-    # Currently this conditional branching doesn't actually do anything,
-    # since pyproject.toml adds these coverage arguments to the testing anyway
       run: |
         if [ "${{ steps.mode.outputs.mode }}" == "fast" ]; then
-          echo "⚡ Skipping notebook tests (marked with @pytest.mark.notebook) - these run separately"
-          pytest tests/ -n auto -v -m "not notebook" --cov=lyopronto --cov-report=term-missing
+          echo "Draft PR: Skipping notebook and pyomo tests for fast feedback"
+          pytest tests/ -n auto -v -m "not notebook and not pyomo"
         else
-          echo "⚡ Skipping notebook tests (marked with @pytest.mark.slow), not running coverage"
-          pytest tests/ -n auto -v -m "not notebook"
+          echo "Ready PR: Running full scipy test suite (excluding notebook and pyomo)"
+          pytest tests/ -n auto -v -m "not notebook and not pyomo" --cov=lyopronto --cov-report=xml:coverage.xml
         fi
 
-    - name: Upload coverage (if run)
-      if: steps.mode.outputs.coverage == 'true'
+    - name: Upload coverage
+      if: steps.mode.outputs.mode == 'full'
       uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: pr-tests
         name: pr-coverage
         fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
+
+  test-pyomo:
+    name: Pyomo Tests (Optional)
+    if: ${{ github.event.pull_request.draft == false }}
+    runs-on: ubuntu-latest
+    continue-on-error: true  # Pyomo tests are brittle, don't block PRs
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies with optimization stack
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -e ".[dev]"
+        pip install pyomo idaes-pse
+
+    - name: Install IPOPT solver via IDAES
+      run: |
+        echo "Installing IPOPT solver via IDAES extensions"
+        idaes get-extensions --extra petsc
+
+    - name: Run Pyomo tests
+      run: |
+        echo "Running Pyomo test suite (continue-on-error enabled)"
+        # Exit code 5 = no tests collected (pyomo tests added in later PRs)
+        pytest tests/ -n auto -v -m "pyomo" --cov=lyopronto --cov-report=term-missing || { rc=$?; [ $rc -eq 5 ] && echo "No pyomo-marked tests found yet" && exit 0; exit $rc; }
+
+    - name: Pyomo Test Summary
+      if: always()
+      run: |
+        echo "Pyomo tests completed"
+        echo "Failures here don't block PR merge"

.github/workflows/slow-tests.yml

@@ -17,6 +17,14 @@ on:
         options:
           - 'true'
           - 'false'
+      include_pyomo:
+        description: 'Include Pyomo tests (requires IPOPT)'
+        required: false
+        default: 'true'
+        type: choice
+        options:
+          - 'true'
+          - 'false'
 
 jobs:
   slow-tests:
@@ -41,20 +49,39 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install .
-        pip install .[dev]
-        pip install -e . --no-build-isolation
+        pip install -e ".[dev]"
+        if [ "${{ inputs.include_pyomo }}" == "true" ]; then
+          pip install pyomo idaes-pse
+        fi
+
+    - name: Install IPOPT solver via IDAES (if Pyomo enabled)
+      if: inputs.include_pyomo == 'true'
+      run: |
+        echo "Installing IPOPT solver via IDAES extensions"
+        idaes get-extensions --extra petsc
 
     - name: Run slow tests
+      env:
+        RUN_SLOW_TESTS: "1"
       run: |
+        # Helper: allow exit code 5 (no tests collected) to pass gracefully
+        run_pytest() { "$@" || { rc=$?; [ $rc -eq 5 ] && echo "No matching tests found (exit 5 is OK)" && return 0; return $rc; }; }
         if [ "${{ inputs.run_all }}" == "true" ]; then
-          echo "🔍 Running ALL tests (including slow optimization tests)"
-          echo "⏱️ This may take 30-40 minutes on CI"
-          pytest tests/ -n auto -v --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          echo "Running ALL tests (including slow optimization tests)"
+          echo "This may take 30-40 minutes on CI"
+          if [ "${{ inputs.include_pyomo }}" == "true" ]; then
+            run_pytest pytest tests/ -n auto -v --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          else
+            run_pytest pytest tests/ -n auto -v -m "not pyomo" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          fi
         else
-          echo "🐌 Running ONLY slow tests (marked with @pytest.mark.slow)"
-          echo "⏱️ This focuses on optimization tests that take minutes"
-          pytest tests/ -n auto -v -m "slow" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          echo "Running ONLY slow tests (marked with @pytest.mark.slow)"
+          echo "This focuses on optimization tests that take minutes"
+          if [ "${{ inputs.include_pyomo }}" == "true" ]; then
+            run_pytest pytest tests/ -n auto -v -m "slow" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          else
+            run_pytest pytest tests/ -n auto -v -m "slow and not pyomo" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+          fi
         fi
 
     - name: Upload coverage
@@ -70,8 +97,8 @@ jobs:
       if: always()
       run: |
         if [ "${{ inputs.run_all }}" == "true" ]; then
-          echo "✅ Complete test suite finished"
+          echo "Complete test suite finished"
         else
-          echo "🐌 Slow tests completed"
+          echo "Slow tests completed"
         fi
-        echo "📊 Coverage uploaded to Codecov"
+        echo "Coverage uploaded to Codecov"

.github/workflows/tests.yml

@@ -1,14 +1,15 @@
 name: Main Branch Tests
 
 # Full tests with coverage for main branch
-# (PRs are handled by pr-tests.yml)
+# Runs both scipy tests and Pyomo tests in separate jobs
 
 on:
   push:
-    branches: [ main, dev-pyomo ]
+    branches: [ main ]
 
 jobs:
-  test:
+  test-scipy:
+    name: SciPy Tests
     runs-on: ubuntu-latest
 
     steps:
@@ -29,27 +30,77 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        pip install .
-        pip install .[dev]
-        pip install -e . --no-build-isolation
+        pip install -e ".[dev]"
 
-    - name: Run ALL tests with pytest and coverage (including slow tests)
+    - name: Run SciPy tests (excluding Pyomo tests)
       run: |
-        echo "🔍 Running complete test suite including slow tests"
-        echo "⏱️ This may take 30-40 minutes on CI (includes optimization tests)"
-        pytest tests/ -n auto -v --cov=lyopronto --cov-report=xml --cov-report=term-missing
+        echo "Running SciPy test suite (excluding Pyomo tests)"
+        pytest tests/ -n auto -v -m "not pyomo" --cov=lyopronto --cov-report=xml --cov-report=term-missing
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
+        flags: scipy-tests
+        name: scipy-coverage
         fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Coverage Summary
       if: always()
       run: |
-        echo "✅ Full coverage tests completed for main branch"
-        echo "📊 Coverage metrics updated in Codecov"
+        echo "SciPy tests completed for main branch"
+        echo "Coverage metrics updated in Codecov"
+
+  test-pyomo:
+    name: Pyomo Tests
+    runs-on: ubuntu-latest
+    continue-on-error: true  # Pyomo tests are brittle, don't block merges
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies with optimization stack
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -e ".[dev]"
+        pip install pyomo idaes-pse
+
+    - name: Install IPOPT solver via IDAES
+      run: |
+        echo "Installing IPOPT solver via IDAES extensions"
+        idaes get-extensions --extra petsc
+
+    - name: Run Pyomo tests
+      run: |
+        echo "Running Pyomo test suite"
+        echo "These tests require IPOPT solver and may be slower"
+        # Exit code 5 = no tests collected (pyomo tests added in later PRs)
+        pytest tests/ -n auto -v -m "pyomo" --cov=lyopronto --cov-report=xml --cov-report=term-missing || { rc=$?; [ $rc -eq 5 ] && echo "No pyomo-marked tests found yet" && exit 0; exit $rc; }
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: pyomo-tests
+        name: pyomo-coverage
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Pyomo Test Summary
+      if: always()
+      run: |
+        echo "Pyomo tests completed (continue-on-error enabled)"
+        echo "Coverage metrics updated in Codecov"

.gitignore

@@ -2,6 +2,29 @@
 #
 # Python precompiled files
 *.pyc
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
 # Data files
 *.csv
 

lyopronto/calc_knownRp.py

@@ -49,7 +49,7 @@ def dry(vial,product,ht,Pchamber,Tshelf,dt):
     ##################  Initialization ################
 
     # Initial fill height
-    Lpr0 = functions.Lpr0_FUN(vial['Vfill'],vial['Ap'],product['cSolid'])   # cm
+    Lpr0 = functions.Lpr0_FUN(vial['Vfill'],vial['Ap'],product['cSolid'])   # [cm]
 
     # Time-dependent functions for Pchamber and Tshelf, take time in hours
     Pch_t = functions.RampInterpolator(Pchamber)
@@ -58,12 +58,12 @@ def dry(vial,product,ht,Pchamber,Tshelf,dt):
     # Get maximum simulation time based on shelf and chamber setpoints
     # This may not really be necessary, but is part of legacy behavior
     # Could remove in a future release
-    max_t = max(Pch_t.max_time(), Tsh_t.max_time())   # hr, add buffer
+    max_t = max(Pch_t.max_time(), Tsh_t.max_time())   # [hr], add buffer
 
     if Pch_t.max_setpt() > functions.Vapor_pressure(Tsh_t.max_setpt()):
         warn("Chamber pressure setpoint exceeds vapor pressure at shelf temperature " +\
         "setpoint(s). Drying cannot proceed.")
-        return np.array([[0.0, Tsh_t(0), Tsh_t(0), Tsh_t(0), Pch_t(0), 0.0, 0.0]])
+        return np.array([[0.0, Tsh_t(0), Tsh_t(0), Tsh_t(0), Pch_t(0) * constant.Torr_to_mTorr, 0.0, 0.0]])
 
     inputs = (vial, product, ht, Pch_t, Tsh_t, dt, Lpr0)
 
@@ -75,21 +75,21 @@ def dry(vial,product,ht,Pchamber,Tshelf,dt):
     # taking them as arguments.
     def calc_dLdt(t, u):
         # Time in hours
-        Lck = u[0] # cm
+        Lck = u[0] # [cm]
         Tsh = Tsh_t(t)
         Pch = Pch_t(t)
-        Kv = functions.Kv_FUN(ht['KC'],ht['KP'],ht['KD'],Pch)  # Vial heat transfer coefficient in cal/s/K/cm^2
-        Rp = functions.Rp_FUN(Lck,product['R0'],product['A1'],product['A2'])  # Product resistance in cm^2-hr-Torr/g
-        Tsub = fsolve(functions.T_sub_solver_FUN, T0, args = (Pch,vial['Av'],vial['Ap'],Kv,Lpr0,Lck,Rp,Tsh))[0] # Sublimation front temperature array in degC
-        dmdt = functions.sub_rate(vial['Ap'],Rp,Tsub,Pch)   # Total sublimation rate array in kg/hr
+        Kv = functions.Kv_FUN(ht['KC'],ht['KP'],ht['KD'],Pch)  # Vial heat transfer coefficient [cal/s/K/cm^2]
+        Rp = functions.Rp_FUN(Lck,product['R0'],product['A1'],product['A2'])  # Product resistance [cm^2-hr-Torr/g]
+        Tsub = fsolve(functions.T_sub_solver_FUN, T0, args = (Pch,vial['Av'],vial['Ap'],Kv,Lpr0,Lck,Rp,Tsh))[0] # Sublimation front temperature [degC]
+        dmdt = functions.sub_rate(vial['Ap'],Rp,Tsub,Pch)   # Total sublimation rate [kg/hr]
         if dmdt<0:
             # print("Shelf temperature is too low for sublimation.")
             dmdt = 0.0
             dLdt = 0
             return [dLdt]
         # Tbot = functions.T_bot_FUN(Tsub,Lpr0,Lck,Pch,Rp)    # Vial bottom temperature array in degC
 
-        dLdt = (dmdt*constant.kg_To_g)/(1-product['cSolid']*constant.rho_solution/constant.rho_solute)/(vial['Ap']*constant.rho_ice)*(1-product['cSolid']*(constant.rho_solution-constant.rho_ice)/constant.rho_solute) # cm/hr
+        dLdt = (dmdt*constant.kg_To_g)/(1-product['cSolid']*constant.rho_solution/constant.rho_solute)/(vial['Ap']*constant.rho_ice)*(1-product['cSolid']*(constant.rho_solution-constant.rho_ice)/constant.rho_solute) # [cm/hr]
         return [dLdt]
 
     ### ------ Condition for ending simulation: completed drying