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
@@ -48,23 +50,69 @@ jobs:
         pip install -e . --no-build-isolation
 
     - 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: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies with optimization stack
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install pyomo idaes-pse
+        pip install -e . --no-build-isolation
+
+    - name: Install IPOPT solver via IDAES
+      run: |
+        echo "Installing IPOPT solver via IDAES extensions"
+        idaes get-extensions --extra petsc
+
+    - name: Run Pyomo tests
+      run: |
+        echo "Running Pyomo test suite (continue-on-error enabled)"
+        # Exit code 5 = no tests collected (pyomo tests added in later PRs)
+        pytest tests/ -n auto -v -m "pyomo" --cov=lyopronto --cov-report=term-missing || { rc=$?; [ $rc -eq 5 ] && echo "No pyomo-marked tests found yet (expected until PR #8)" && 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:
@@ -43,18 +51,39 @@ jobs:
         python -m pip install --upgrade pip setuptools wheel
         pip install .
         pip install .[dev]
+        if [ "${{ inputs.include_pyomo }}" == "true" ]; then
+          pip install pyomo idaes-pse
+        fi
         pip install -e . --no-build-isolation
 
+    - 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 +99,8 @@ 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:
@@ -33,23 +34,77 @@ jobs:
         pip install .[dev]
         pip install -e . --no-build-isolation
 
-    - 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: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies with optimization stack
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install pyomo idaes-pse
+        pip install -e . --no-build-isolation
+
+    - name: Install IPOPT solver via IDAES
+      run: |
+        echo "Installing IPOPT solver via IDAES extensions"
+        idaes get-extensions --extra petsc
+
+    - name: Run Pyomo tests
+      run: |
+        echo "Running Pyomo test suite"
+        echo "These tests require IPOPT solver and may be slower"
+        # Exit code 5 = no tests collected (pyomo tests added in later PRs)
+        pytest tests/ -n auto -v -m "pyomo" --cov=lyopronto --cov-report=xml --cov-report=term-missing || { rc=$?; [ $rc -eq 5 ] && echo "No pyomo-marked tests found yet (expected until PR #8)" && 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

@@ -63,7 +63,7 @@ def dry(vial,product,ht,Pchamber,Tshelf,dt):
     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) * 1000.0, 0.0, 0.0]])
 
     inputs = (vial, product, ht, Pch_t, Tsh_t, dt, Lpr0)
 

lyopronto/constant.py

@@ -25,15 +25,15 @@
 Torr_to_mTorr = 1000.0
 cal_To_J = 4.184
 
-rho_ice = 0.918 # g/mL
-rho_solute = 1.5 # g/mL
-rho_solution = 1.0  # g/mL
+rho_ice = 0.918 # [g/mL]
+rho_solute = 1.5 # [g/mL]
+rho_solution = 1.0  # [g/mL]
 
-dHs = 678.0 # Heat of sublimation in cal/g
-k_ice = 0.0059 # Thermal conductivity of ice in cal/cm/s/K
-dHf = 79.7 # Heat of fusion in cal/g
+dHs = 678.0 # Heat of sublimation [cal/g]
+k_ice = 0.0059 # Thermal conductivity of ice [cal/cm/s/K]
+dHf = 79.7 # Heat of fusion [cal/g]
 
-Cp_ice = 2030.0 # Constant pressure specific heat of ice in J/kg/K
-Cp_solution = 4000.0 # Constant pressure specific heat of water in J/kg/K
+Cp_ice = 2030.0 # Constant pressure specific heat of ice [J/kg/K]
+Cp_solution = 4000.0 # Constant pressure specific heat of water [J/kg/K]
 
 ##################################################

lyopronto/functions.py

@@ -287,14 +287,26 @@ def __init__(self, rampspec, count_ramp_against_dt=True):
             times = np.array([0.0, self.dt_setpt[0] / constant.hr_To_min])
         # Older logic: setpoint_dt includes the ramp time.
         # Kept for backward compatibility, but add a check if insufficient time allowed for ramp
-        if count_ramp_against_dt: 
+        if count_ramp_against_dt:
+            # In the no-init path, dt_setpt[0] is already consumed during
+            # initialization (times starts with [0, dt_setpt[0]]).  Start the
+            # loop index for dt_setpt at i (not i-1) so that dt_setpt[0] is
+            # not consumed a second time.  In the init path, times starts
+            # with just [0] and the loop correctly starts consuming at
+            # dt_setpt[0] via index i-1.
+            has_init = "init" in rampspec
             for i in range(1, len(self.setpt)):
-                # If less dt_setpt than setpt provided, repeat the last dt
-                totaltime = self.dt_setpt[min(len(self.dt_setpt)-1, i-1)] / constant.hr_To_min
+                # If fewer dt_setpt than setpt provided, repeat the last dt
+                dt_idx = i - 1 if has_init else i
+                totaltime = self.dt_setpt[min(len(self.dt_setpt) - 1, dt_idx)] / constant.hr_To_min
                 ramptime = abs((self.setpt[i] - self.setpt[i-1]) / self.ramp_rate) / constant.hr_To_min
                 holdtime = totaltime - ramptime
-                if ramptime > holdtime:
-                    warn(f"Ramp time from {self.setpt[i-1]:.2e} to {self.setpt[i]:.2e} exceeds total time for setpoint change, {totaltime}.")
+                if holdtime < 0:
+                    warn(f"Ramp time ({ramptime * constant.hr_To_min:.1f} min) from "
+                         f"{self.setpt[i-1]:.2e} to {self.setpt[i]:.2e} exceeds "
+                         f"total stage time ({totaltime * constant.hr_To_min:.1f} min). "
+                         f"Clamping hold time to 0.")
+                    holdtime = 0.0
                 times = np.append(times, [ramptime, holdtime])
         else:
         # Newer logic: setpoint_dt applies *after* the ramp is complete.
@@ -404,8 +416,9 @@ def fill_output(sol, inputs):
     interp_func = PchipInterpolator(sol.t, interp_points, axis=0)
     fullout = np.zeros((len(out_t), 7))
     for i, t in enumerate(out_t):
-        if np.any(sol.t == t):
-            fullout[i,:] = interp_points[sol.t == t, :]
+        mask = sol.t == t
+        if np.any(mask):
+            fullout[i,:] = interp_points[mask, :][0]
         else:
             fullout[i,:] = interp_func(t)
     return fullout