Merge branch 'main' into solvers2

Author: michaelbynum

.codecov.yml

@@ -1,15 +1,18 @@
 codecov:
   notify:
     # GHA: 5, Jenkins: 11
-    # Accurate as of July 3, 2024
-    # Potential to change when Python versions change
-    after_n_builds: 16
-    wait_for_ci: true
+    # Accurate as of April 1, 2025
+    # Potential to change when Python versions change.  We will allow
+    # codecov to start reporting when 80% of the reports are in.  This
+    # will hopefully help avoid an issue where codecov is not tracking
+    # PR branches (see https://github.com/codecov/feedback/issues/692).
+    after_n_builds: 13
+    wait_for_ci: false
   require_ci_to_pass: false
+comment:
+  after_n_builds: 13
 coverage:
-  range:
-  - 50.0
-  - 100.0
+  range: 70..98
   status:
     patch:
       default:

.github/workflows/test_branches.yml

@@ -26,10 +26,14 @@ env:
   CACHE_VER: v221013.1
   NEOS_EMAIL: [email protected]
   SRC_REF: ${{ github.head_ref || github.ref }}
+  PYOMO_WORKFLOW: branch
 
 jobs:
   lint:
     name: lint/style-and-typos
+    if: |
+      ${{ ! ( contains(github.event.pull_request.title, '[WIP]') ||
+            github.event.pull_request.draft ) }}
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Pyomo source
@@ -48,6 +52,7 @@ jobs:
       with: 
         config: ./.github/workflows/typos.toml
     - name: URL Checker
+      if: env.PYOMO_WORKFLOW == 'branch'
       uses: urlstechie/[email protected]
       with:
         # A comma-separated list of file types to cover in the URL checks
@@ -805,7 +810,8 @@ jobs:
   cover:
     name: process-coverage-${{ matrix.TARGET }}
     needs: build
-    if: ${{ false }} # turn off for branches
+    # run even if a build job fails, but not if canceled (except for branches)
+    if: ${{ false }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
     strategy:
@@ -876,26 +882,6 @@ jobs:
         $PYTHON_EXE -c "from pyomo.dataportal.parse_datacmds import \
             parse_data_commands; parse_data_commands(data='')"
 
-    - name: Update codecov uploader
-      run: |
-        set +e
-        CODECOV="${GITHUB_WORKSPACE}/codecov.sh"
-        echo "CODECOV=$CODECOV" >> $GITHUB_ENV
-        for i in `seq 3`; do
-            echo "Downloading current codecov script (attempt ${i})"
-            curl -L https://codecov.io/bash -o $CODECOV
-            if test $? == 0; then
-                break
-            fi
-            DELAY=$(( RANDOM % 30 + 30))
-            echo "Pausing $DELAY seconds before re-attempting download"
-            sleep $DELAY
-        done
-        if test ! -e $CODECOV; then
-            echo "Failed to download codecov.sh"
-            exit 1
-        fi
-
     - name: Combine coverage reports
       if: github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main'
       run: |
@@ -934,7 +920,7 @@ jobs:
 
     - name: Upload codecov reports
       if: github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: coverage.xml
         token: ${{ secrets.PYOMO_CODECOV_TOKEN }}
@@ -946,7 +932,7 @@ jobs:
       if: |
         hashFiles('coverage-other.xml') != '' &&
         (github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main')
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: coverage-other.xml
         token: ${{ secrets.PYOMO_CODECOV_TOKEN }}

.github/workflows/test_pr_and_main.yml

@@ -34,13 +34,18 @@ env:
   CACHE_VER: v221013.1
   NEOS_EMAIL: [email protected]
   SRC_REF: ${{ github.head_ref || github.ref }}
+  PYOMO_WORKFLOW: |
+    ${{ ( contains(github.event.pull_request.title, '[WIP]') ||
+          github.event.pull_request.draft ) && 'draft_pr'
+        || github.event.pull_request.number && 'pr' || 'main' }}
 
 jobs:
   lint:
     name: lint/style-and-typos
-    runs-on: ubuntu-latest
     if: |
-      contains(github.event.pull_request.title, '[WIP]') != true && !github.event.pull_request.draft
+      ${{ ! ( contains(github.event.pull_request.title, '[WIP]') ||
+            github.event.pull_request.draft ) }}
+    runs-on: ubuntu-latest
     steps:
     - name: Checkout Pyomo source
       uses: actions/checkout@v4
@@ -57,6 +62,21 @@ jobs:
       uses: crate-ci/typos@master
       with: 
         config: ./.github/workflows/typos.toml
+    - name: URL Checker
+      if: env.PYOMO_WORKFLOW == 'branch'
+      uses: urlstechie/[email protected]
+      with:
+        # A comma-separated list of file types to cover in the URL checks
+        file_types: .md,.rst,.py
+        # Choose whether to include file with no URLs in the prints.
+        print_all: false
+        # More verbose summary at the end of a run
+        verbose: true
+        # How many times to retry a failed request (defaults to 1)
+        retry_count: 3
+        # Exclude Jenkins because it's behind a firewall; ignore RTD because
+        # a magically-generated string is triggering a failure
+        exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
 
 
   build:
@@ -843,7 +863,8 @@ jobs:
   cover:
     name: process-coverage-${{ matrix.TARGET }}
     needs: build
-    if: success() || failure() # run even if a build job fails, but not if cancelled
+    # run even if a build job fails, but not if canceled (except for branches)
+    if: success() || failure()
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
     strategy:
@@ -914,26 +935,6 @@ jobs:
         $PYTHON_EXE -c "from pyomo.dataportal.parse_datacmds import \
             parse_data_commands; parse_data_commands(data='')"
 
-    - name: Update codecov uploader
-      run: |
-        set +e
-        CODECOV="${GITHUB_WORKSPACE}/codecov.sh"
-        echo "CODECOV=$CODECOV" >> $GITHUB_ENV
-        for i in `seq 3`; do
-            echo "Downloading current codecov script (attempt ${i})"
-            curl -L https://codecov.io/bash -o $CODECOV
-            if test $? == 0; then
-                break
-            fi
-            DELAY=$(( RANDOM % 30 + 30))
-            echo "Pausing $DELAY seconds before re-attempting download"
-            sleep $DELAY
-        done
-        if test ! -e $CODECOV; then
-            echo "Failed to download codecov.sh"
-            exit 1
-        fi
-
     - name: Combine coverage reports
       if: github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main'
       run: |
@@ -972,7 +973,7 @@ jobs:
 
     - name: Upload codecov reports
       if: github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: coverage.xml
         token: ${{ secrets.PYOMO_CODECOV_TOKEN }}
@@ -984,7 +985,7 @@ jobs:
       if: |
         hashFiles('coverage-other.xml') != '' &&
         (github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main')
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: coverage-other.xml
         token: ${{ secrets.PYOMO_CODECOV_TOKEN }}

doc/OnlineDocs/contribution_guide.rst

@@ -413,7 +413,7 @@ provides an example of how this can be done, including a directory
 for plugins and package tests.  For example, this package can be
 imported as a subpackage of ``pyomo.contrib``::
 
-    from pyomo.environ import *
+    import pyomo.environ as pyo
     from pyomo.contrib.example import a
 
     # Print the value of 'a' defined by this package

doc/OnlineDocs/explanation/analysis/sensitivity_toolbox.rst

@@ -31,25 +31,25 @@ Here :math:`x_1`, :math:`x_2`, and :math:`x_3` are the decision variables while
 .. doctest:: python
 
     # Import Pyomo and the sensitivity toolbox
-    >>> from pyomo.environ import *
+    >>> import pyomo.environ as pyo
     >>> from pyomo.contrib.sensitivity_toolbox.sens import sensitivity_calculation
 
     # Create a concrete model
-    >>> m = ConcreteModel()
+    >>> m = pyo.ConcreteModel()
 
     # Define the variables with bounds and initial values
-    >>> m.x1 = Var(initialize = 0.15, within=NonNegativeReals)
-    >>> m.x2 = Var(initialize = 0.15, within=NonNegativeReals)
-    >>> m.x3 = Var(initialize = 0.0, within=NonNegativeReals)
+    >>> m.x1 = pyo.Var(initialize = 0.15, within=pyo.NonNegativeReals)
+    >>> m.x2 = pyo.Var(initialize = 0.15, within=pyo.NonNegativeReals)
+    >>> m.x3 = pyo.Var(initialize = 0.0, within=pyo.NonNegativeReals)
 
     # Define the parameters
-    >>> m.eta1 = Param(initialize=4.5,mutable=True)
-    >>> m.eta2 = Param(initialize=1.0,mutable=True)
+    >>> m.eta1 = pyo.Param(initialize=4.5,mutable=True)
+    >>> m.eta2 = pyo.Param(initialize=1.0,mutable=True)
 
     # Define the constraints and objective
-    >>> m.const1 = Constraint(expr=6*m.x1+3*m.x2+2*m.x3-m.eta1 ==0)
-    >>> m.const2 = Constraint(expr=m.eta2*m.x1+m.x2-m.x3-1 ==0)
-    >>> m.cost = Objective(expr=m.x1**2+m.x2**2+m.x3**2)
+    >>> m.const1 = pyo.Constraint(expr=6*m.x1+3*m.x2+2*m.x3-m.eta1 ==0)
+    >>> m.const2 = pyo.Constraint(expr=m.eta2*m.x1+m.x2-m.x3-1 ==0)
+    >>> m.cost = pyo.Objective(expr=m.x1**2+m.x2**2+m.x3**2)
 
 
 The solution of this optimization problem is :math:`x_1^* = 0.5`, :math:`x_2^* = 0.5`, and :math:`x_3^* = 0.0`. But what if we change the parameter values to :math:`\hat{p}_1 = 4.0` and :math:`\hat{p}_2 = 1.0`? Is there a quick way to approximate the new solution :math:`\hat{x}_1^*`, :math:`\hat{x}_2^*`, and :math:`\hat{x}_3^*`? Yes! This is the main functionality of sIPOPT and k_aug.
@@ -58,8 +58,8 @@ Next we define the perturbed parameter values :math:`\hat{p}_1` and :math:`\hat{
 
 .. doctest:: python
 
-    >>> m.perturbed_eta1 = Param(initialize = 4.0)
-    >>> m.perturbed_eta2 = Param(initialize = 1.0)
+    >>> m.perturbed_eta1 = pyo.Param(initialize = 4.0)
+    >>> m.perturbed_eta2 = pyo.Param(initialize = 1.0)
 
 And finally we call sIPOPT or k_aug: