Merge branch 'main' into doc-reorg

.github/workflows/test_branches.yml

@@ -519,7 +519,7 @@ jobs:
         $BARON_DIR = "${env:TPL_DIR}/baron"
         echo "$BARON_DIR" | `
             Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-        $URL = "https://www.minlp.com/downloads/xecs/baron/current/"
+        $URL = "https://minlp.com/downloads/xecs/baron/current/"
         if ( "${{matrix.TARGET}}" -eq "win" ) {
             $INSTALLER = "${env:DOWNLOAD_DIR}/baron_install.exe"
             $URL += "baron-win64.exe"

.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
 
 
@@ -561,7 +562,7 @@ jobs:
         $BARON_DIR = "${env:TPL_DIR}/baron"
         echo "$BARON_DIR" | `
             Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-        $URL = "https://www.minlp.com/downloads/xecs/baron/current/"
+        $URL = "https://minlp.com/downloads/xecs/baron/current/"
         if ( "${{matrix.TARGET}}" -eq "win" ) {
             $INSTALLER = "${env:DOWNLOAD_DIR}/baron_install.exe"
             $URL += "baron-win64.exe"

.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 +205,43 @@ 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
-            CODECOV_JOB_NAME=`echo ${JOB_NAME} | sed -r 's/^(.*autotest_)?Pyomo_([^\/]+).*/\2/'`.$BUILD_NUMBER.$python
+        if test -z "$PYOMO_SOURCE_SHA"; then
+            PYOMO_SOURCE_SHA=$GIT_COMMIT
+        fi
+        if test -n "$CODECOV_TOKEN" -a -n "$PYOMO_SOURCE_SHA"; then
+            CODECOV_JOB_NAME=$(echo ${JOB_NAME} \
+                | sed -r 's/^(.*autotest_)?Pyomo_([^\/]+).*/\2/').$BUILD_NUMBER.$python
+            if test -z "$CODECOV_REPO_OWNER"; then
+                if test -n "$PYOMO_SOURCE_REPO"; then
+                    CODECOV_REPO_OWNER=$(echo "$PYOMO_SOURCE_REPO" | cut -d '/' -f 4)
+                elif test -n "$GIT_URL"; then
+                    CODECOV_REPO_OWNER=$(echo "$GIT_URL" | cut -d '/' -f 4)
+                else
+                    CODECOV_REPO_OWNER=""
+                fi
+            fi
+            if test -z "$CODECOV_SOURCE_BRANCH"; then
+                CODECOV_SOURCE_BRANCH=$(git branch -av --contains "$PYOMO_SOURCE_SHA" \
+                    | grep "${PYOMO_SOURCE_SHA:0:7}" | grep "/origin/" \
+                    | cut -d '/' -f 3 | cut -d' ' -f 1)
+                if test -z "$CODECOV_SOURCE_BRANCH"; then
+                    CODECOV_SOURCE_BRANCH=main
+                fi
+            fi
             i=0
             while /bin/true; do
                 i=$[$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

.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

doc/Archive/contributed_packages/gdpopt.rst

@@ -93,10 +93,10 @@ An example that includes the modeling approach may be found below.
     Variables:
       x : Size=1, Index=None
           Key  : Lower : Value : Upper : Fixed : Stale : Domain
-          None :  -1.2 :   0.0 :     2 : False : False :  Reals
+          None :  -1.2 :     0 :     2 : False : False :  Reals
       y : Size=1, Index=None
           Key  : Lower : Value : Upper : Fixed : Stale : Domain
-          None :   -10 :   1.0 :    10 : False : False :  Reals
+          None :   -10 :     1 :    10 : False : False :  Reals
   <BLANKLINE>
     Objectives:
       objective : Size=1, Index=None, Active=True
@@ -106,7 +106,7 @@ An example that includes the modeling approach may be found below.
     Constraints:
       c : Size=1
           Key  : Lower : Body : Upper
-          None :   1.0 :  1.0 :   1.0
+          None :   1.0 :    1 :   1.0
 
 .. note:: 
 

examples/pyomo/tutorials/set.dat

@@ -16,3 +16,6 @@ set S[5] := 2 3;
 
 set T[2] := 1 3;
 set T[5] := 2 3;
+
+set X[2] := 1;
+set X[5] := 2 3;

examples/pyomo/tutorials/set.out

@@ -1,4 +1,4 @@
-23 Set Declarations
+24 Set Declarations
     A : Size=1, Index=None, Ordered=Insertion
         Key  : Dimen : Domain : Size : Members
         None :     1 :    Any :    3 : {1, 2, 3}
@@ -89,5 +89,9 @@
           2 :     1 :    Any :    5 : {1, 3, 5, 7, 9}
           3 :     1 :    Any :    5 : {1, 4, 7, 10, 13}
           4 :     1 :    Any :    5 : {1, 5, 9, 13, 17}
+    X : Size=2, Index=B, Ordered=Insertion
+        Key : Dimen : Domain : Size : Members
+          2 :     1 :   S[2] :    1 : {1,}
+          5 :     1 :   S[5] :    2 : {2, 3}
 
-23 Declarations: A B C D E F G H Hsub I J K K_2 L M N O P R S T U V
+24 Declarations: A B C D E F G H Hsub I J K K_2 L M N O P R S X T U V

examples/pyomo/tutorials/set.py

@@ -171,6 +171,13 @@ def P_init(model, i, j):
 #
 model.S = Set(model.B, within=model.A)
 
+#
+# Validation of a set array can also be linked to another set array. If so, the
+# elements under each index must also be found under the corresponding index in
+# the validation set array:
+#
+model.X = Set(model.B, within=model.S)
+
 
 #
 # Validation of set arrays can also be performed with the _validate_ option.

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:

pyomo/contrib/appsi/base.py

@@ -1007,7 +1007,7 @@ def add_constraints(self, cons: List[ConstraintData]):
                 raise ValueError(
                     'constraint {name} has already been added'.format(name=con.name)
                 )
-            self._active_constraints[con] = (con.lower, con.body, con.upper)
+            self._active_constraints[con] = con.expr
             if self.use_extensions and cmodel_available:
                 tmp = cmodel.prep_for_repn(con.body, self._expr_types)
             else:
@@ -1363,40 +1363,13 @@ def update(self, timer: HierarchicalTimer = None):
         cons_to_remove_and_add = dict()
         need_to_set_objective = False
         if config.update_constraints:
-            cons_to_update = list()
-            sos_to_update = list()
             for c in current_cons_dict.keys():
-                if c not in new_cons_set:
-                    cons_to_update.append(c)
+                if c not in new_cons_set and c.expr is not self._active_constraints[c]:
+                    cons_to_remove_and_add[c] = None
+            sos_to_update = []
             for c in current_sos_dict.keys():
                 if c not in new_sos_set:
                     sos_to_update.append(c)
-            for c in cons_to_update:
-                lower, body, upper = self._active_constraints[c]
-                new_lower, new_body, new_upper = c.lower, c.body, c.upper
-                if new_body is not body:
-                    cons_to_remove_and_add[c] = None
-                    continue
-                if new_lower is not lower:
-                    if (
-                        type(new_lower) is NumericConstant
-                        and type(lower) is NumericConstant
-                        and new_lower.value == lower.value
-                    ):
-                        pass
-                    else:
-                        cons_to_remove_and_add[c] = None
-                        continue
-                if new_upper is not upper:
-                    if (
-                        type(new_upper) is NumericConstant
-                        and type(upper) is NumericConstant
-                        and new_upper.value == upper.value
-                    ):
-                        pass
-                    else:
-                        cons_to_remove_and_add[c] = None
-                        continue
             self.remove_sos_constraints(sos_to_update)
             self.add_sos_constraints(sos_to_update)
         timer.stop('cons')

pyomo/contrib/appsi/cmodel/src/fbbt_model.cpp

@@ -205,7 +205,7 @@ void process_fbbt_constraints(FBBTModel *model, PyomoExprTypes &expr_types,
   py::handle con_body;
 
   for (py::handle c : cons) {
-    lower_body_upper = active_constraints[c];
+    lower_body_upper = c.attr("to_bounded_expression")();
     con_lb = lower_body_upper[0];
     con_body = lower_body_upper[1];
     con_ub = lower_body_upper[2];

pyomo/contrib/appsi/cmodel/src/lp_writer.cpp

@@ -289,7 +289,7 @@ void process_lp_constraints(py::list cons, py::object writer) {
   py::object nonlinear_expr;
   PyomoExprTypes expr_types = PyomoExprTypes();
   for (py::handle c : cons) {
-    lower_body_upper = active_constraints[c];
+    lower_body_upper = c.attr("to_bounded_expression")();
     cname = getSymbol(c, labeler);
     repn = generate_standard_repn(
         lower_body_upper[1], "compute_values"_a = false, "quadratic"_a = true);