Merge remote-tracking branch 'refs/remotes/me/nlv2-presolve-defined-vars' into nlv2-presolve-defined-vars

jsiirola · jsiirola · commit 956c2014f6ef · 2024-05-29T11:30:09.000-06:00
diff --git a/.github/workflows/test_branches.yml b/.github/workflows/test_branches.yml
@@ -51,15 +51,16 @@ jobs:
       uses: urlstechie/urlchecker-action@0.0.34
       with:
         # A comma-separated list of file types to cover in the URL checks
-        file_types: .md,.rst
+        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
-        exclude_urls: https://pyomo-jenkins.sandia.gov/
+        # 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:
diff --git a/.github/workflows/test_pr_and_main.yml b/.github/workflows/test_pr_and_main.yml
@@ -61,15 +61,16 @@ jobs:
       uses: urlstechie/urlchecker-action@0.0.34
       with:
         # A comma-separated list of file types to cover in the URL checks
-        file_types: .md,.rst
+        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
-        exclude_urls: https://pyomo-jenkins.sandia.gov/
+        # 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:
@@ -85,6 +86,11 @@ jobs:
         other: [""]
         category: [""]
 
+        # win/3.8 conda builds no longer work due to environment not being able
+        # to resolve. We are skipping it now.
+        exclude:
+        - os: windows-latest
+          python: 3.8
         include:
         - os: ubuntu-latest
           TARGET: linux
diff --git a/examples/dae/ReactionKinetics.py b/examples/dae/ReactionKinetics.py
@@ -304,7 +304,10 @@ def regression_model():
 
     # Model & data from:
     #
-    # http://www.doiserbia.nb.rs/img/doi/0367-598X/2014/0367-598X1300037A.pdf
+    # https://doiserbia.nb.rs/img/doi/0367-598X/2014/0367-598X1300037A.pdf
+    # Almagrbi, A. M., Hatami, T., Glišić, S., & Orlović, A. (2014).
+    # Determination of kinetic parameters for complex transesterification
+    # reaction by standard optimisation methods.
     #
     model = ConcreteModel()
 
diff --git a/pyomo/common/gsl.py b/pyomo/common/gsl.py
@@ -23,8 +23,8 @@
 )
 def get_gsl(downloader):
     logger.info(
-        "As of February 9, 2023, AMPL GSL can no longer be downloaded\
-        through download-extensions. Visit https://portal.ampl.com/\
+        "As of February 9, 2023, AMPL GSL can no longer be downloaded \
+        through download-extensions. Visit https://portal.ampl.com/ \
         to download the AMPL GSL binaries."
     )
 
diff --git a/pyomo/core/plugins/transform/model.py b/pyomo/core/plugins/transform/model.py
@@ -16,10 +16,17 @@
 # because we may support an explicit matrix representation for models.
 #
 
+from pyomo.common.deprecation import deprecated
 from pyomo.core.base import Objective, Constraint
 import array
 
 
+@deprecated(
+    "to_standard_form() is deprecated.  "
+    "Please use WriterFactory('compile_standard_form')",
+    version='6.7.3.dev0',
+    remove_in='6.8.0',
+)
 def to_standard_form(self):
     """
     Produces a standard-form representation of the model. Returns
diff --git a/pyomo/dataportal/plugins/db_table.py b/pyomo/dataportal/plugins/db_table.py
@@ -385,8 +385,9 @@ def __init__(self, filename=None, data=None):
         will override that in the file.
         """
 
-        # ugh hardcoded strings. See following URL for info:
-        # http://publib.boulder.ibm.com/infocenter/idshelp/v10/index.jsp?topic=/com.ibm.odbc.doc/odbc58.htm
+        # Hardcoded string required here.
+        # See documentation:
+        # https://www.ibm.com/docs/en/informix-servers/12.10?topic=SSGU8G_12.1.0/com.ibm.odbc.doc/ids_odbc_062.html
         self.ODBC_DS_KEY = 'ODBC Data Sources'
         self.ODBC_INFO_KEY = 'ODBC'
 
diff --git a/pyomo/repn/tests/ampl/test_nlv2.py b/pyomo/repn/tests/ampl/test_nlv2.py
@@ -2657,11 +2657,15 @@ def test_presolve_defined_var_to_const(self):
         nl_writer.NLWriter().write(
             m, OUT, symbolic_solver_labels=True, linear_presolve=True
         )
+        # Note that the presolve will end up recognizing con3 as a
+        # linear constraint; however, it does not do so until processing
+        # the constraints after presolve (so the constraint is not
+        # actually removed and the eq variable still appears in the model)
         self.assertEqual(
             *nl_diff(
                 """g3 1 1 0	#problem unknown
  1 1 0 0 1	#vars, constraints, objectives, ranges, eqns
- 1 0 0 0 0 0	#nonlinear constrs, objs; ccons: lin, nonlin, nd, nzlb
+ 0 0 0 0 0 0	#nonlinear constrs, objs; ccons: lin, nonlin, nd, nzlb
  0 0	#network constraints: nonlinear, linear
  0 0 0	#nonlinear vars in constraints, objectives, both
  0 0 0 1	#linear network variables; functions; arith, flags
@@ -2670,13 +2674,11 @@ def test_presolve_defined_var_to_const(self):
  4 2	#max name lengths: constraints, variables
  0 0 0 0 0	#common exprs: b,c,o,c1,o1
 C0	#con3
-o3	#/
-n8
-n-4
+n0
 x1	#initial guess
 0 100	#eq
 r	#1 ranges (rhs's)
-4 0	#con3
+4 2.0	#con3
 b	#1 bounds (on variables)
 3	#eq
 k0	#intermediate Jacobian column lengths
diff --git a/pyomo/scripting/plugins/download.py b/pyomo/scripting/plugins/download.py
@@ -38,9 +38,9 @@ def _call_impl(self, args, unparsed, logger):
         self.downloader.cacert = args.cacert
         self.downloader.insecure = args.insecure
         logger.info(
-            "As of February 9, 2023, AMPL GSL can no longer be downloaded\
-                    through download-extensions. Visit https://portal.ampl.com/\
-                    to download the AMPL GSL binaries."
+            "As of February 9, 2023, AMPL GSL can no longer be downloaded \
+            through download-extensions. Visit https://portal.ampl.com/ \
+            to download the AMPL GSL binaries."
         )
         for target in DownloadFactory:
             try:
diff --git a/pyomo/solvers/plugins/solvers/CBCplugin.py b/pyomo/solvers/plugins/solvers/CBCplugin.py
@@ -455,7 +455,7 @@ def process_logfile(self):
             tokens = tuple(re.split('[ \t]+', line.strip()))
             n_tokens = len(tokens)
             if n_tokens > 1:
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L3769
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L3769
                 if n_tokens > 4 and tokens[:4] == (
                     'Continuous',
                     'objective',
@@ -539,7 +539,7 @@ def process_logfile(self):
                         results.problem.name = results.problem.name.split('/')[-1]
                     if '\\' in results.problem.name:
                         results.problem.name = results.problem.name.split('\\')[-1]
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L10840
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L10840
                 elif tokens[0] == 'Presolve':
                     if n_tokens > 9 and tokens[3] == 'rows,' and tokens[6] == 'columns':
                         results.problem.number_of_variables = int(tokens[4]) - int(
@@ -551,7 +551,7 @@ def process_logfile(self):
                         results.problem.number_of_objectives = 1
                     elif n_tokens > 6 and tokens[6] == 'infeasible':
                         soln.status = SolutionStatus.infeasible
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L11105
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L11105
                 elif (
                     n_tokens > 11
                     and tokens[:2] == ('Problem', 'has')
@@ -563,7 +563,7 @@ def process_logfile(self):
                     results.problem.number_of_constraints = int(tokens[2])
                     results.problem.number_of_nonzeros = int(tokens[6][1:])
                     results.problem.number_of_objectives = 1
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L10814
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L10814
                 elif (
                     n_tokens > 8
                     and tokens[:3] == ('Original', 'problem', 'has')
@@ -579,7 +579,7 @@ def process_logfile(self):
                     in ' '.join(tokens)
                 ):
                     results.problem.sense = maximize
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L3047
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L3047
                 elif n_tokens > 3 and tokens[:2] == ('Result', '-'):
                     if tokens[2:4] in [('Run', 'abandoned'), ('User', 'ctrl-c')]:
                         results.solver.termination_condition = (
@@ -609,15 +609,15 @@ def process_logfile(self):
                                 'solution': TerminationCondition.other,
                                 'iterations': TerminationCondition.maxIterations,
                             }.get(tokens[4], TerminationCondition.other)
-                    # perhaps from https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L12318
+                    # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L12318
                     elif n_tokens > 3 and tokens[2] == "Finished":
                         soln.status = SolutionStatus.optimal
                         optim_value = _float(tokens[4])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7904
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7904
                 elif n_tokens >= 3 and tokens[:2] == ('Objective', 'value:'):
                     # parser for log file generetated with discrete variable
                     optim_value = _float(tokens[2])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7904
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7904
                 elif n_tokens >= 4 and tokens[:4] == (
                     'No',
                     'feasible',
@@ -630,25 +630,25 @@ def process_logfile(self):
                         lower_bound is None
                     ):  # Only use if not already found since this is to less decimal places
                         results.problem.lower_bound = _float(tokens[2])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7918
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7918
                 elif tokens[0] == 'Gap:':
                     # This is relative and only to 2 decimal places - could calculate explicitly using lower bound
                     gap = _float(tokens[1])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7923
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7923
                 elif n_tokens > 2 and tokens[:2] == ('Enumerated', 'nodes:'):
                     nodes = int(tokens[2])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7926
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7926
                 elif n_tokens > 2 and tokens[:2] == ('Total', 'iterations:'):
                     results.solver.statistics.black_box.number_of_iterations = int(
                         tokens[2]
                     )
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7930
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7930
                 elif n_tokens > 3 and tokens[:3] == ('Time', '(CPU', 'seconds):'):
                     results.solver.system_time = _float(tokens[3])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L7933
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L7933
                 elif n_tokens > 3 and tokens[:3] == ('Time', '(Wallclock', 'Seconds):'):
                     results.solver.wallclock_time = _float(tokens[3])
-                # https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp?rev=2497#L10477
+                # https://github.com/coin-or/Cbc/blob/cb6bf98/Cbc/src/CbcSolver.cpp#L10477
                 elif n_tokens > 4 and tokens[:4] == (
                     'Total',
                     'time',
@@ -832,11 +832,15 @@ def process_soln_file(self, results):
             tokens = tuple(re.split('[ \t]+', line.strip()))
             n_tokens = len(tokens)
             #
-            # These are the only header entries CBC will generate (identified via browsing CbcSolver.cpp)
-            # See https://projects.coin-or.org/Cbc/browser/trunk/Cbc/src/CbcSolver.cpp
-            # Search for (no integer solution - continuous used)      Currently line 9912 as of rev2497
-            # Note that since this possibly also covers old CBC versions, we shall not be removing any functionality,
-            # even if it is not seen in the current revision
+            # These are the only header entries CBC will generate
+            # (identified via browsing CbcSolver.cpp).  See
+            #     https://github.com/coin-or/Cbc/tree/master/src/CbcSolver.cpp
+            # Search for "(no integer solution - continuous used)"
+            # (L10796 as of cb855c7)
+            #
+            # Note that since this possibly also supports old CBC
+            # versions, we shall not be removing any functionality, even
+            # if it is not seen in the current revision
             #
             if not header_processed:
                 if tokens[0] == 'Optimal':

Original file line number	Diff line number	Diff line change
`@@ -304,7 +304,10 @@ def regression_model():`
`304`	`304`
`305`	`305`	`# Model & data from:`
`306`	`306`	`#`
`307`		`- # http://www.doiserbia.nb.rs/img/doi/0367-598X/2014/0367-598X1300037A.pdf`
	`307`	`+ # https://doiserbia.nb.rs/img/doi/0367-598X/2014/0367-598X1300037A.pdf`
	`308`	`+ # Almagrbi, A. M., Hatami, T., Glišić, S., & Orlović, A. (2014).`
	`309`	`+ # Determination of kinetic parameters for complex transesterification`
	`310`	`+ # reaction by standard optimisation methods.`
`308`	`311`	`#`
`309`	`312`	`model = ConcreteModel()`
`310`	`313`
Original file line number	Diff line number	Diff line change
`@@ -23,8 +23,8 @@`
`23`	`23`	`)`
`24`	`24`	`def get_gsl(downloader):`
`25`	`25`	`logger.info(`
`26`		`- "As of February 9, 2023, AMPL GSL can no longer be downloaded\`
`27`		`- through download-extensions. Visit https://portal.ampl.com/\`
	`26`	`+ "As of February 9, 2023, AMPL GSL can no longer be downloaded \`
	`27`	`+ through download-extensions. Visit https://portal.ampl.com/ \`
`28`	`28`	`to download the AMPL GSL binaries."`
`29`	`29`	`)`
`30`	`30`