Merge branch 'main' into ldsda_documentation

Author: blnicho

.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 }}

pyomo/common/tests/test_tee.py

@@ -578,7 +578,18 @@ def test_exit_on_del(self):
         stack = T.context_stack
         self.assertGreater(len(stack), 0)
         del T
-        gc.collect()
+        # This is a bit tricky: for cpython, T should be immediately
+        # deallocated (including calling __del__) through reference
+        # counting.  pypy is trickier: because it lacks
+        # reference-counting, it must rely on the GC.  We have seen
+        # cases on GHA where a single call to gc.collect() was sometimes
+        # insufficient to ensure that T was collected (but unable to
+        # reproduce it locally).  We will try up to 4 times (1 more than
+        # the number of generations in the GC)
+        remaining_attempts = 4
+        while len(stack) and remaining_attempts:
+            gc.collect()
+            remaining_attempts -= 1
         self.assertEqual(len(stack), 0)
 
     def test_deadlock(self):