Merge branch 'main' into issue-3127

Jtramey · Jul 8, 2024 · 072c2c5 · 072c2c5
2 parents a5bc693 + 53d5cad
commit 072c2c5
Show file tree

Hide file tree

Showing 19 changed files with 1,488 additions and 85 deletions.
diff --git a/.github/workflows/test_pr_and_main.yml b/.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
 
 

diff --git a/.github/workflows/typos.toml b/.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
diff --git a/.jenkins.sh b/.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

diff --git a/.codecov.yml → codecov.yml b/.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
diff --git a/pyomo/common/config.py b/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.
 

diff --git a/pyomo/common/dependencies.py b/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'):

diff --git a/pyomo/common/tests/test_dependencies.py b/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

diff --git a/pyomo/common/unittest.py b/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:

diff --git a/pyomo/core/base/set.py b/pyomo/core/base/set.py
@@ -1986,7 +1986,7 @@ class InsertionOrder(object):
     class SortedOrder(object):
         pass
 
-    _ValidOrderedAuguments = {True, False, InsertionOrder, SortedOrder}
+    _ValidOrderedArguments = {True, False, InsertionOrder, SortedOrder}
     _UnorderedInitializers = {set}
 
     @overload
@@ -2015,7 +2015,7 @@ def __new__(cls, *args, **kwds):
         ordered = kwds.get('ordered', Set.InsertionOrder)
         if ordered is True:
             ordered = Set.InsertionOrder
-        if ordered not in Set._ValidOrderedAuguments:
+        if ordered not in Set._ValidOrderedArguments:
             if inspect.isfunction(ordered):
                 ordered = Set.SortedOrder
             else:
@@ -2032,7 +2032,7 @@ def __new__(cls, *args, **kwds):
                             str(_)
                             for _ in sorted_robust(
                                 'Set.' + x.__name__ if isinstance(x, type) else x
-                                for x in Set._ValidOrderedAuguments.union(
+                                for x in Set._ValidOrderedArguments.union(
                                     {'<function>'}
                                 )
                             )

diff --git a/pyomo/core/kernel/register_numpy_types.py b/pyomo/core/kernel/register_numpy_types.py
@@ -45,10 +45,12 @@
     # Historically, the lists included several numpy aliases
     numpy_int_names.extend(('int_', 'intc', 'intp'))
     numpy_int.extend((numpy.int_, numpy.intc, numpy.intp))
-    numpy_float_names.append('float_')
-    numpy_float.append(numpy.float_)
-    numpy_complex_names.append('complex_')
-    numpy_complex.append(numpy.complex_)
+    if hasattr(numpy, 'float_'):
+        numpy_float_names.append('float_')
+        numpy_float.append(numpy.float_)
+    if hasattr(numpy, 'complex_'):
+        numpy_complex_names.append('complex_')
+        numpy_complex.append(numpy.complex_)
 
 # Re-build the old numpy_* lists
 for t in native_boolean_types:

diff --git a/pyomo/core/plugins/transform/radix_linearization.py b/pyomo/core/plugins/transform/radix_linearization.py
@@ -280,7 +280,7 @@ def _collect_bilinear(self, expr, bilin, quad):
         if type(expr) is PowExpression and value(expr._args[1]) == 2:
             # Note: directly testing the value of the exponent above is
             # safe: we have already verified that this expression is
-            # polynominal, so the exponent must be constant.
+            # polynomial, so the exponent must be constant.
             tmp = ProductExpression()
             tmp._numerator = [expr._args[0], expr._args[0]]
             tmp._denominator = []

diff --git a/pyomo/core/tests/unit/test_kernel_register_numpy_types.py b/pyomo/core/tests/unit/test_kernel_register_numpy_types.py
@@ -16,7 +16,10 @@
 # Boolean
 numpy_bool_names = []
 if numpy_available:
-    numpy_bool_names.append('bool_')
+    if numpy.__version__[0] == '2':
+        numpy_bool_names.append('bool')
+    else:
+        numpy_bool_names.append('bool_')
 # Integers
 numpy_int_names = []
 if numpy_available:
@@ -34,7 +37,8 @@
 # Reals
 numpy_float_names = []
 if numpy_available:
-    numpy_float_names.append('float_')
+    if hasattr(numpy, 'float_'):
+        numpy_float_names.append('float_')
     numpy_float_names.append('float16')
     numpy_float_names.append('float32')
     numpy_float_names.append('float64')
@@ -46,7 +50,8 @@
 # Complex
 numpy_complex_names = []
 if numpy_available:
-    numpy_complex_names.append('complex_')
+    if hasattr(numpy, 'complex_'):
+        numpy_complex_names.append('complex_')
     numpy_complex_names.append('complex64')
     numpy_complex_names.append('complex128')
     if hasattr(numpy, 'complex192'):

diff --git a/pyomo/core/tests/unit/test_numvalue.py b/pyomo/core/tests/unit/test_numvalue.py
@@ -552,10 +552,10 @@ def test_unknownNumericType(self):
 
     @unittest.skipUnless(numpy_available, "This test requires NumPy")
     def test_numpy_basic_float_registration(self):
-        self.assertIn(numpy.float_, native_numeric_types)
-        self.assertNotIn(numpy.float_, native_integer_types)
-        self.assertIn(numpy.float_, _native_boolean_types)
-        self.assertIn(numpy.float_, native_types)
+        self.assertIn(numpy.float64, native_numeric_types)
+        self.assertNotIn(numpy.float64, native_integer_types)
+        self.assertIn(numpy.float64, _native_boolean_types)
+        self.assertIn(numpy.float64, native_types)
 
     @unittest.skipUnless(numpy_available, "This test requires NumPy")
     def test_numpy_basic_int_registration(self):

diff --git a/pyomo/core/tests/unit/test_sets.py b/pyomo/core/tests/unit/test_sets.py
@@ -1051,7 +1051,7 @@ def setUp(self):
         self.instance = self.model.create_instance(currdir + "setA.dat")
         self.e1 = numpy.bool_(1)
         self.e2 = numpy.int_(2)
-        self.e3 = numpy.float_(3.0)
+        self.e3 = numpy.float64(3.0)
         self.e4 = numpy.int_(4)
         self.e5 = numpy.int_(5)
         self.e6 = numpy.int_(6)
@@ -1068,7 +1068,7 @@ def test_numpy_int(self):
 
     def test_numpy_float(self):
         model = ConcreteModel()
-        model.A = Set(initialize=[numpy.float_(1.0), numpy.float_(0.0)])
+        model.A = Set(initialize=[numpy.float64(1.0), numpy.float64(0.0)])
         self.assertEqual(model.A.bounds(), (0, 1))
 
 
@@ -3213,7 +3213,7 @@ def test_numpy_membership(self):
         self.assertEqual(numpy.int_(1) in Boolean, True)
         self.assertEqual(numpy.bool_(True) in Boolean, True)
         self.assertEqual(numpy.bool_(False) in Boolean, True)
-        self.assertEqual(numpy.float_(1.1) in Boolean, False)
+        self.assertEqual(numpy.float64(1.1) in Boolean, False)
         self.assertEqual(numpy.int_(2) in Boolean, False)
 
         self.assertEqual(numpy.int_(0) in Integers, True)
@@ -3222,7 +3222,7 @@ def test_numpy_membership(self):
         # identically to 1
         self.assertEqual(numpy.bool_(True) in Integers, True)
         self.assertEqual(numpy.bool_(False) in Integers, True)
-        self.assertEqual(numpy.float_(1.1) in Integers, False)
+        self.assertEqual(numpy.float64(1.1) in Integers, False)
         self.assertEqual(numpy.int_(2) in Integers, True)
 
         self.assertEqual(numpy.int_(0) in Reals, True)
@@ -3231,14 +3231,14 @@ def test_numpy_membership(self):
         # identically to 1
         self.assertEqual(numpy.bool_(True) in Reals, True)
         self.assertEqual(numpy.bool_(False) in Reals, True)
-        self.assertEqual(numpy.float_(1.1) in Reals, True)
+        self.assertEqual(numpy.float64(1.1) in Reals, True)
         self.assertEqual(numpy.int_(2) in Reals, True)
 
         self.assertEqual(numpy.int_(0) in Any, True)
         self.assertEqual(numpy.int_(1) in Any, True)
         self.assertEqual(numpy.bool_(True) in Any, True)
         self.assertEqual(numpy.bool_(False) in Any, True)
-        self.assertEqual(numpy.float_(1.1) in Any, True)
+        self.assertEqual(numpy.float64(1.1) in Any, True)
         self.assertEqual(numpy.int_(2) in Any, True)
 
     def test_setargs1(self):