Merge branch 'Pyomo:main' into parmest_obj_regularization

Author: sscini

.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 }}

doc/OnlineDocs/explanation/solvers/gdpopt.rst

@@ -20,7 +20,7 @@ Three algorithms are available in GDPopt:
 
 Usage and implementation details for GDPopt can be found in the PSE 2018 paper
 (`Chen et al., 2018`_), or via its
-`preprint <http://egon.cheme.cmu.edu/Papers/Chen_Pyomo_GDP_PSE2018.pdf>`_.
+`preprint <https://egon.cheme.cmu.edu/Papers/Chen_Pyomo_GDP_PSE2018.pdf>`_.
 
 Credit for prototyping and development can be found in the ``GDPopt`` class documentation, below.
 

doc/OnlineDocs/explanation/solvers/mindtpy.rst

@@ -17,10 +17,10 @@ The following algorithms are currently available in MindtPy:
 
 Usage and early implementation details for MindtPy can be found in the PSE 2018 paper Bernal et al.,
 (`ref <https://doi.org/10.1016/B978-0-444-64241-7.50144-0>`_,
-`preprint <http://egon.cheme.cmu.edu/Papers/Bernal_Chen_MindtPy_PSE2018Paper.pdf>`_).
+`preprint <https://egon.cheme.cmu.edu/Papers/Bernal_Chen_MindtPy_PSE2018Paper.pdf>`_).
 This solver implementation has been developed by `David Bernal <https://github.com/bernalde>`_
 and `Zedong Peng <https://github.com/ZedongPeng>`_ as part of research efforts at the `Bernal Research Group 
-<https://bernalde.github.io/>`_ and the `Grossmann Research Group <http://egon.cheme.cmu.edu/>`_
+<https://bernalde.github.io/>`_ and the `Grossmann Research Group <https://egon.cheme.cmu.edu/>`_
 at Purdue University and Carnegie Mellon University.
 
 .. _Duran & Grossmann, 1986: https://dx.doi.org/10.1007/BF02592064

doc/OnlineDocs/explanation/solvers/persistent.rst

@@ -24,16 +24,16 @@ Using Persistent Solvers
 The first step in using a persistent solver is to create a Pyomo model
 as usual.
 
->>> import pyomo.environ as pe
->>> m = pe.ConcreteModel()
->>> m.x = pe.Var()
->>> m.y = pe.Var()
->>> m.obj = pe.Objective(expr=m.x**2 + m.y**2)
->>> m.c = pe.Constraint(expr=m.y >= -2*m.x + 5)
+>>> import pyomo.environ as pyo
+>>> m = pyo.ConcreteModel()
+>>> m.x = pyo.Var()
+>>> m.y = pyo.Var()
+>>> m.obj = pyo.Objective(expr=m.x**2 + m.y**2)
+>>> m.c = pyo.Constraint(expr=m.y >= -2*m.x + 5)
 
 You can create an instance of a persistent solver through the SolverFactory.
 
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 
 This returns an instance of :py:class:`GurobiPersistent`. Now we need
 to tell the solver about our model.
@@ -48,7 +48,7 @@ variables and constraints. We can now solve the model.
 We can also add or remove variables, constraints, blocks, and
 objectives. For example,
 
->>> m.c2 = pe.Constraint(expr=m.y >= m.x)  # doctest: +SKIP
+>>> m.c2 = pyo.Constraint(expr=m.y >= m.x)  # doctest: +SKIP
 >>> opt.add_constraint(m.c2)  # doctest: +SKIP
 
 This tells the solver to add one new constraint but otherwise leave
@@ -69,29 +69,29 @@ code will run without error, but the solver will have an extra
 constraint. The solver will have both y >= -2*x + 5 and y <= x, which
 is not what was intended!
 
->>> m = pe.ConcreteModel()  # doctest: +SKIP
->>> m.x = pe.Var()  # doctest: +SKIP
->>> m.y = pe.Var()  # doctest: +SKIP
->>> m.c = pe.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> m = pyo.ConcreteModel()  # doctest: +SKIP
+>>> m.x = pyo.Var()  # doctest: +SKIP
+>>> m.y = pyo.Var()  # doctest: +SKIP
+>>> m.c = pyo.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 >>> opt.set_instance(m)  # doctest: +SKIP
 >>> # WRONG:
 >>> del m.c  # doctest: +SKIP
->>> m.c = pe.Constraint(expr=m.y <= m.x)  # doctest: +SKIP
+>>> m.c = pyo.Constraint(expr=m.y <= m.x)  # doctest: +SKIP
 >>> opt.add_constraint(m.c)  # doctest: +SKIP
 
 The correct way to do this is:
 
->>> m = pe.ConcreteModel()  # doctest: +SKIP
->>> m.x = pe.Var()  # doctest: +SKIP
->>> m.y = pe.Var()  # doctest: +SKIP
->>> m.c = pe.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> m = pyo.ConcreteModel()  # doctest: +SKIP
+>>> m.x = pyo.Var()  # doctest: +SKIP
+>>> m.y = pyo.Var()  # doctest: +SKIP
+>>> m.c = pyo.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 >>> opt.set_instance(m)  # doctest: +SKIP
 >>> # Correct:
 >>> opt.remove_constraint(m.c)  # doctest: +SKIP
 >>> del m.c  # doctest: +SKIP
->>> m.c = pe.Constraint(expr=m.y <= m.x)  # doctest: +SKIP
+>>> m.c = pyo.Constraint(expr=m.y <= m.x)  # doctest: +SKIP
 >>> opt.add_constraint(m.c)  # doctest: +SKIP
 
 .. warning:: Components removed from a pyomo model must be removed
@@ -100,14 +100,14 @@ The correct way to do this is:
 Additionally, unexpected behavior may result if a component is
 modified before being removed.
 
->>> m = pe.ConcreteModel()  # doctest: +SKIP
->>> m.b = pe.Block()  # doctest: +SKIP
->>> m.b.x = pe.Var()  # doctest: +SKIP
->>> m.b.y = pe.Var()  # doctest: +SKIP
->>> m.b.c = pe.Constraint(expr=m.b.y >= -2*m.b.x + 5)  # doctest: +SKIP
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> m = pyo.ConcreteModel()  # doctest: +SKIP
+>>> m.b = pyo.Block()  # doctest: +SKIP
+>>> m.b.x = pyo.Var()  # doctest: +SKIP
+>>> m.b.y = pyo.Var()  # doctest: +SKIP
+>>> m.b.c = pyo.Constraint(expr=m.b.y >= -2*m.b.x + 5)  # doctest: +SKIP
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 >>> opt.set_instance(m)  # doctest: +SKIP
->>> m.b.c2 = pe.Constraint(expr=m.b.y <= m.b.x)  # doctest: +SKIP
+>>> m.b.c2 = pyo.Constraint(expr=m.b.y <= m.b.x)  # doctest: +SKIP
 >>> # ERROR: The constraint referenced by m.b.c2 does not
 >>> # exist in the solver model.
 >>> opt.remove_block(m.b)  # doctest: +SKIP 
@@ -117,12 +117,12 @@ the solver instance, modify it with Pyomo, and then add it back to the
 solver instance. The only exception is with variables. Variables may
 be modified and then updated with with solver:
 
->>> m = pe.ConcreteModel()  # doctest: +SKIP
->>> m.x = pe.Var()  # doctest: +SKIP
->>> m.y = pe.Var()  # doctest: +SKIP
->>> m.obj = pe.Objective(expr=m.x**2 + m.y**2)  # doctest: +SKIP
->>> m.c = pe.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> m = pyo.ConcreteModel()  # doctest: +SKIP
+>>> m.x = pyo.Var()  # doctest: +SKIP
+>>> m.y = pyo.Var()  # doctest: +SKIP
+>>> m.obj = pyo.Objective(expr=m.x**2 + m.y**2)  # doctest: +SKIP
+>>> m.c = pyo.Constraint(expr=m.y >= -2*m.x + 5)  # doctest: +SKIP
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 >>> opt.set_instance(m)  # doctest: +SKIP
 >>> m.x.setlb(1.0)  # doctest: +SKIP
 >>> opt.update_var(m.x)  # doctest: +SKIP
@@ -160,13 +160,13 @@ Persistent Solver Performance
 In order to get the best performance out of the persistent solvers, use the
 "save_results" flag:
 
->>> import pyomo.environ as pe
->>> m = pe.ConcreteModel()
->>> m.x = pe.Var()
->>> m.y = pe.Var()
->>> m.obj = pe.Objective(expr=m.x**2 + m.y**2)
->>> m.c = pe.Constraint(expr=m.y >= -2*m.x + 5)
->>> opt = pe.SolverFactory('gurobi_persistent')  # doctest: +SKIP
+>>> import pyomo.environ as pyo
+>>> m = pyo.ConcreteModel()
+>>> m.x = pyo.Var()
+>>> m.y = pyo.Var()
+>>> m.obj = pyo.Objective(expr=m.x**2 + m.y**2)
+>>> m.c = pyo.Constraint(expr=m.y >= -2*m.x + 5)
+>>> opt = pyo.SolverFactory('gurobi_persistent')  # doctest: +SKIP
 >>> opt.set_instance(m)  # doctest: +SKIP
 >>> results = opt.solve(save_results=False)  # doctest: +SKIP
 

doc/OnlineDocs/explanation/solvers/pynumero/tutorial.nlp_interfaces.rst

@@ -10,7 +10,7 @@ Relevant imports
 .. doctest::
    :skipif: not numpy_available or not scipy_available or not asl_available
 
-   >>> import pyomo.environ as pe
+   >>> import pyomo.environ as pyo
    >>> from pyomo.contrib.pynumero.interfaces.pyomo_nlp import PyomoNLP
    >>> import numpy as np
 
@@ -19,12 +19,12 @@ Create a Pyomo model
 .. doctest::
    :skipif: not numpy_available or not scipy_available or not asl_available
 
-   >>> m = pe.ConcreteModel()
-   >>> m.x = pe.Var(bounds=(-5, None))
-   >>> m.y = pe.Var(initialize=2.5)
-   >>> m.obj = pe.Objective(expr=m.x**2 + m.y**2)
-   >>> m.c1 = pe.Constraint(expr=m.y == (m.x - 1)**2)
-   >>> m.c2 = pe.Constraint(expr=m.y >= pe.exp(m.x))
+   >>> m = pyo.ConcreteModel()
+   >>> m.x = pyo.Var(bounds=(-5, None))
+   >>> m.y = pyo.Var(initialize=2.5)
+   >>> m.obj = pyo.Objective(expr=m.x**2 + m.y**2)
+   >>> m.c1 = pyo.Constraint(expr=m.y == (m.x - 1)**2)
+   >>> m.c2 = pyo.Constraint(expr=m.y >= pyo.exp(m.x))
 
 Create a :py:class:`pyomo.contrib.pynumero.interfaces.pyomo_nlp.PyomoNLP` instance
 

examples/gdp/small_lit/ex1_Lee.py

@@ -13,7 +13,7 @@
 Taken from Example 1 of the paper "New Algorithms for Nonlinear Generalized Disjunctive Programming" by Lee and Grossmann
 
 This GDP problem has one disjunction containing three terms, and exactly one of them must be true. The literature can be found here:
-http://egon.cheme.cmu.edu/Papers/LeeNewAlgo.pdf
+https://egon.cheme.cmu.edu/Papers/LeeNewAlgo.pdf
 
 """