Merge branch 'main' into scaling-uninitialized

.coin-or/projDesc.xml

@@ -227,8 +227,8 @@ Carl D. Laird, Chair, Pyomo Management Committee, claird at andrew dot cmu dot e
 			     Use explicit overrides to disable use of automated
 			     version reporting.
 			-->
-			<stableVersionNumber>6.7.2</stableVersionNumber>
-			<releaseNumber>6.7.2</releaseNumber>
+			<stableVersionNumber>6.7.3</stableVersionNumber>
+			<releaseNumber>6.7.3</releaseNumber>
 
 		</developmentStatus>
 

.github/workflows/test_pr_and_main.yml

@@ -68,8 +68,9 @@ jobs:
         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:
+        #  - Jenkins because it's behind a firewall
+        #  - RTD because a magically-generated string triggers failures
         exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
 
 

.github/workflows/typos.toml

@@ -38,6 +38,8 @@ caf = "caf"
 WRONLY = "WRONLY"
 # Ignore the name Hax
 Hax = "Hax"
+# Ignore dout (short for dual output in SAS solvers)
+dout = "dout"
 # Big Sur
 Sur = "Sur"
 # contrib package named mis and the acronym whence the name comes
@@ -67,4 +69,6 @@ RO = "RO"
 EOF = "EOF"
 # Ignore lst as shorthand for list
 lst = "lst"
+# Abbreviation of gamma (used in stochpdegas1_automatic.py)
+gam = "gam"
 # AS NEEDED: Add More Words Below

.jenkins.sh

@@ -20,8 +20,11 @@
 #
 # CODECOV_TOKEN: the token to use when uploading results to codecov.io
 #
-# CODECOV_ARGS: additional arguments to pass to the codecov uploader
-#     (e.g., to support SSL certificates)
+# CODECOV_SOURCE_BRANCH: passed to the 'codecov-cli' command; branch of Pyomo
+#     (e.g., to enable correct codecov uploads)
+#
+# CODECOV_REPO_OWNER: passed to the 'codecov-cli' command; owner of repo
+#     (e.g., to enable correct codecov uploads)
 #
 # DISABLE_COVERAGE: if nonempty, then coverage analysis is disabled
 #
@@ -202,22 +205,28 @@ if test -z "$MODE" -o "$MODE" == test; then
         # Note, that the PWD should still be $WORKSPACE/pyomo
         #
         coverage combine || exit 1
-        coverage report -i
+        coverage report -i || exit 1
+        coverage xml -i || exit 1
         export OS=`uname`
-        if test -z "$CODECOV_TOKEN"; then
-            coverage xml
-        else
+        if test -n "$CODECOV_TOKEN"; then
             CODECOV_JOB_NAME=`echo ${JOB_NAME} | sed -r 's/^(.*autotest_)?Pyomo_([^\/]+).*/\2/'`.$BUILD_NUMBER.$python
+            if test -z "$CODECOV_REPO_OWNER"; then
+                CODECOV_REPO_OWNER="pyomo"
+            fi
+            if test -z "CODECOV_SOURCE_BRANCH"; then
+                CODECOV_SOURCE_BRANCH="main"
+            fi
             i=0
             while /bin/true; do
                 i=$[$i+1]
                 echo "Uploading coverage to codecov (attempt $i)"
-                codecov -X gcovcodecov -X gcov -X s3 --no-color \
-                    -t $CODECOV_TOKEN --root `pwd` -e OS,python \
-                    --name $CODECOV_JOB_NAME $CODECOV_ARGS \
-                    | tee .cover.upload
-                if test $? == 0 -a `grep -i error .cover.upload \
-                        | grep -v branch= | wc -l` -eq 0; then
+                codecovcli -v upload-process --sha $PYOMO_SOURCE_SHA \
+                    --fail-on-error --git-service github --token $CODECOV_TOKEN \
+                    --slug pyomo/pyomo --file coverage.xml --disable-search \
+                    --name $CODECOV_JOB_NAME \
+                    --branch $CODECOV_REPO_OWNER:$CODECOV_SOURCE_BRANCH \
+                    --env OS,python --network-root-folder `pwd` --plugin noop
+                if test $? == 0; then
                     break
                 elif test $i -ge 4; then
                     exit 1

CHANGELOG.md

@@ -2,6 +2,22 @@ Pyomo CHANGELOG
 ===============
 
 
+-------------------------------------------------------------------------------
+Pyomo 6.7.3   (29 May 2024)
+-------------------------------------------------------------------------------
+
+- Core
+  - Deprecate `pyomo.core.plugins.transform.model.to_standard_form()` (#3265)
+  - Reorder definitions to avoid `NameError` in some situations (#3264)
+- Solver Interfaces
+  - NLv2: Fix linear presolver with constant defined vars/external fcns (#3276)
+- Testing
+  - Add URL checking to GHA linting job (#3259, #3261)
+  - Skip Windows Python 3.8 conda GHA job (#3269)
+- Contributed Packages
+  - DoE: Bug fixes for workshop (#3267)
+  - viewer: Update guard for pint import (#3277)
+
 -------------------------------------------------------------------------------
 Pyomo 6.7.2   (9 May 2024)
 -------------------------------------------------------------------------------
@@ -57,7 +73,7 @@ Pyomo 6.7.2   (9 May 2024)
   - CP: Add SequenceVar and other logical expressions for scheduling (#3227)
   - DoE: Bug fixes (#3245)
   - iis: Add minimal intractable system infeasibility diagnostics (#3172)
-  - incidence_analysis: Improve `solve_strongly_connected_components` 
+  - incidence_analysis: Improve `solve_strongly_connected_components`
     performance for models with named expressions (#3186)
   - incidence_analysis: Add function to plot incidence graph in
     Dulmage-Mendelsohn order (#3207)

RELEASE.md

@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.7.2.
+We are pleased to announce the release of Pyomo 6.7.3.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing

.codecov.yml → codecov.yml

@@ -1,19 +1,21 @@
+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
 coverage:
-  range: "50...100"
+  range:
+  - 50.0
+  - 100.0
   status:
+    patch:
+      default:
+        # Force patches to be covered at the level of the codebase
+        threshold: 0.0
     project:
       default:
         # Allow overall coverage to drop to avoid failures due to code
         # cleanup or CI unavailability/lag
-        threshold: 5%
-    patch:
-      default:
-        # Force patches to be covered at the level of the codebase
-        threshold: 0%
-#  ci:
-#    - !ci.appveyor.com
-codecov:
-  notify:
-    # GHA: 4, Jenkins: 8
-    after_n_builds: 12  # all
-    wait_for_ci: yes
+        threshold: 5.0

pyomo/common/config.py

@@ -996,7 +996,7 @@ class will still create ``c`` instances that only have the single
 :py:meth:`generate_documentation()`.  The simplest is
 :py:meth:`display()`, which prints out the current values of the
 configuration object (and if it is a container type, all of it's
-children).  :py:meth:`generate_yaml_template` is simular to
+children).  :py:meth:`generate_yaml_template` is similar to
 :py:meth:`display`, but also includes the description fields as
 formatted comments.
 

pyomo/common/dependencies.py

@@ -999,10 +999,13 @@ def _finalize_numpy(np, available):
         # registration here (to bypass the deprecation warning) until we
         # finally remove all support for it
         numeric_types._native_boolean_types.add(t)
-    _floats = [np.float_, np.float16, np.float32, np.float64]
+    _floats = [np.float16, np.float32, np.float64]
     # float96 and float128 may or may not be defined in this particular
     # numpy build (it depends on platform and version).
     # Register them only if they are present
+    if hasattr(np, 'float_'):
+        # Prepend to preserve previous functionality
+        _floats.insert(0, np.float_)
     if hasattr(np, 'float96'):
         _floats.append(np.float96)
     if hasattr(np, 'float128'):
@@ -1013,10 +1016,13 @@ def _finalize_numpy(np, available):
         # registration here (to bypass the deprecation warning) until we
         # finally remove all support for it
         numeric_types._native_boolean_types.add(t)
-    _complex = [np.complex_, np.complex64, np.complex128]
+    _complex = [np.complex64, np.complex128]
     # complex192 and complex256 may or may not be defined in this
     # particular numpy build (it depends on platform and version).
     # Register them only if they are present
+    if hasattr(np, 'np.complex_'):
+        # Prepend to preserve functionality
+        _complex.insert(0, np.complex_)
     if hasattr(np, 'complex192'):
         _complex.append(np.complex192)
     if hasattr(np, 'complex256'):

pyomo/common/tests/test_dependencies.py

@@ -209,7 +209,7 @@ def test_and_or(self):
         _and_or = avail0 & avail1 | avail2
         self.assertTrue(_and_or)
 
-        # Verify operator prescedence
+        # Verify operator precedence
         _or_and = avail0 | avail2 & avail2
         self.assertTrue(_or_and)
         _or_and = (avail0 | avail2) & avail2

pyomo/common/unittest.py

@@ -783,6 +783,7 @@ def filter_fcn(self, line):
         return False
 
     def filter_file_contents(self, lines, abstol=None):
+        _numpy_scalar_re = re.compile(r'np.(int|float)\d+\(([^\)]+)\)')
         filtered = []
         deprecated = None
         for line in lines:
@@ -807,29 +808,49 @@ def filter_file_contents(self, lines, abstol=None):
             item_list = []
             items = line.strip().split()
             for i in items:
+                # Split up lists, dicts, and sets
+                while i and i[0] in '[{':
+                    item_list.append(i[0])
+                    i = i[1:]
+                tail = []
+                while i and i[-1] in ',:]}':
+                    tail.append(i[-1])
+                    i = i[:-1]
+
                 # A few substitutions to get tests passing on pypy3
                 if ".inf" in i:
                     i = i.replace(".inf", "inf")
                 if "null" in i:
                     i = i.replace("null", "None")
 
                 try:
-                    item_list.append(float(i))
+                    # Numpy 2.x changed the repr for scalars.  Convert
+                    # the new scalar reprs back to the original (which
+                    # were indistinguishable from python floats/ints)
+                    np_match = _numpy_scalar_re.match(i)
+                    if np_match:
+                        item_list.append(float(np_match.group(2)))
+                    else:
+                        item_list.append(float(i))
                 except:
                     item_list.append(i)
+                if tail:
+                    tail.reverse()
+                    item_list.extend(tail)
 
             # We can get printed results objects where the baseline is
             # exactly 0 (and omitted) and the test is slightly non-zero.
             # We will look for the pattern of values printed from
             # results objects and remote them if they are within
             # tolerance of 0
             if (
-                len(item_list) == 2
-                and item_list[0] == 'Value:'
-                and type(item_list[1]) is float
-                and abs(item_list[1]) < (abstol or 0)
-                and len(filtered[-1]) == 1
-                and filtered[-1][0][-1] == ':'
+                len(item_list) == 3
+                and item_list[0] == 'Value'
+                and item_list[1] == ':'
+                and type(item_list[2]) is float
+                and abs(item_list[2]) < (abstol or 0)
+                and len(filtered[-1]) == 2
+                and filtered[-1][1] == ':'
             ):
                 filtered.pop()
             else: