Merge branch 'main' into sorted-robust-write

.codecov.yml

@@ -14,6 +14,6 @@ coverage:
 #    - !ci.appveyor.com
 codecov:
   notify:
-    # GHA: 5, Jenkins: 6
-    after_n_builds: 11  # all
+    # GHA: 4, Jenkins: 4
+    after_n_builds: 8  # all
     wait_for_ci: yes

.coin-or/projDesc.xml

@@ -107,7 +107,7 @@ Carl D. Laird, Chair, Pyomo Management Committee, cdlaird at sandia dot gov
                      license file directly.
                 -->
 		<projectLicenseURL>
-		  https://github.com/Pyomo/pyomo/blob/master/LICENSE.txt
+		  https://github.com/Pyomo/pyomo/blob/main/LICENSE.txt
 		</projectLicenseURL>
 
 		<!-- Below, you can list other COIN projects your project      -->

.coveragerc

@@ -7,6 +7,7 @@ omit =
 # The [run] section must be at the end, as the build harness will add a
 # "data_file" directive to the end of this file.
 [run]
+concurrency = multiprocessing,thread
 parallel = True
 source =
     pyomo

.github/workflows/pr_master_test.yml

@@ -3,10 +3,10 @@ name: GitHub CI
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
   workflow_dispatch:
     inputs:
       git-ref:
@@ -27,7 +27,7 @@ env:
       pint pyro4 pyyaml sphinx_rtd_theme sympy xlrd
       python-louvain
   PYTHON_NUMPY_PKGS: >
-      numpy scipy pyodbc pandas matplotlib seaborn numdifftools
+      numpy scipy pyodbc pandas matplotlib seaborn numdifftools casadi
   CACHE_VER: v3
   NEOS_EMAIL: tests@pyomo.org
 
@@ -62,7 +62,7 @@ jobs:
           PACKAGES: glpk
 
         - os: ubuntu-18.04
-          python: 3.7
+          python: 3.8
           other: /mpi
           mpi: 3
           skip_doctest: 1
@@ -88,11 +88,12 @@ jobs:
 
         - os: ubuntu-18.04
           python: 3.6
-          other: /parallel
-          category: parallel
+          other: /cython
+          setup_options: --with-cython
           skip_doctest: 1
           TARGET: linux
           PYENV: pip
+          PACKAGES: cython
 
         - os: ubuntu-18.04
           python: 3.7
@@ -102,15 +103,6 @@ jobs:
           TARGET: linux
           PYENV: pip
 
-        - os: ubuntu-18.04
-          python: 3.6
-          other: /cython
-          setup_options: --with-cython
-          skip_doctest: 1
-          TARGET: linux
-          PYENV: pip
-          PACKAGES: cython
-
         exclude:
         - {os: macos-latest, python: pypy3}
         - {os: windows-latest, python: pypy3}
@@ -203,7 +195,6 @@ jobs:
         for pkg in bash pkg-config unixodbc freetds glpk; do
             brew list $pkg || brew install $pkg
         done
-        #brew link --overwrite gcc
 
     - name: Update Linux
       if: matrix.TARGET == 'linux'
@@ -649,6 +640,11 @@ jobs:
     - name: Upload codecov reports
       run: |
         set +e
+        if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then
+            SHA=$(jq --raw-output .pull_request.head.sha "$GITHUB_EVENT_PATH")
+        else
+            SHA=$GITHUB_SHA
+        fi
         function upload {
             echo ""
             echo "Build group: $1"
@@ -667,17 +663,22 @@ jobs:
             i=0
             while : ; do
                 ((i+=1))
+                rm -f codecov.log
                 echo "Uploading coverage to codecov (attempt ${i})"
                 bash $CODECOV -Z -e TAG,GHA_OS_NAME -X gcov -X s3 \
-                    -f coverage.xml
+                    -f coverage.xml -C $SHA | tee codecov.log
                 if test $? == 0; then
                     echo "PASS $CODECOV_NAME" >> codecov.result
                     break
                 elif test $i -ge 2; then
-                    # Do not fail the build (yet) just because the codecov
-                    # upload fails
-                    echo "FAIL $CODECOV_NAME" >> codecov.result
-                    break
+                    if test `grep successfully codecov.log | wc -l` -gt 0; then
+                        echo "PASS $CODECOV_NAME (implied)" >> codecov.result
+                    else
+                        # Do not fail the build (yet) just because the
+                        # codecov upload fails
+                        echo "FAIL $CODECOV_NAME" >> codecov.result
+                        break
+                    fi
                 fi
                 DELAY=$(( RANDOM % 30 + 30))
                 echo "Pausing $DELAY seconds before re-attempting upload"

.github/workflows/push_branch_test.yml

@@ -3,7 +3,7 @@ name: GitHub Branch CI
 on:
   push:
     branches-ignore:
-      - master
+      - main
   workflow_dispatch:
     inputs:
       git-ref:
@@ -24,7 +24,7 @@ env:
       pint pyro4 pyyaml sphinx_rtd_theme sympy xlrd
       python-louvain
   PYTHON_NUMPY_PKGS: >
-      numpy scipy pyodbc pandas matplotlib seaborn numdifftools
+      numpy scipy pyodbc pandas matplotlib seaborn numdifftools casadi
   CACHE_VER: v3
   NEOS_EMAIL: tests@pyomo.org
 
@@ -87,14 +87,6 @@ jobs:
 
         - os: ubuntu-18.04
           python: 3.6
-          other: /parallel
-          category: parallel
-          skip_doctest: 1
-          TARGET: linux
-          PYENV: pip
-
-        - os: ubuntu-18.04
-          python: 3.7
           other: /cython
           setup_options: --with-cython
           skip_doctest: 1
@@ -190,7 +182,6 @@ jobs:
         for pkg in bash pkg-config unixodbc freetds glpk; do
             brew list $pkg || brew install $pkg
         done
-        #brew link --overwrite gcc
 
     - name: Update Linux
       if: matrix.TARGET == 'linux'
@@ -636,6 +627,11 @@ jobs:
     - name: Upload codecov reports
       run: |
         set +e
+        if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then
+            SHA=$(jq --raw-output .pull_request.head.sha "$GITHUB_EVENT_PATH")
+        else
+            SHA=$GITHUB_SHA
+        fi
         function upload {
             echo ""
             echo "Build group: $1"
@@ -654,17 +650,22 @@ jobs:
             i=0
             while : ; do
                 ((i+=1))
+                rm -f codecov.log
                 echo "Uploading coverage to codecov (attempt ${i})"
                 bash $CODECOV -Z -e TAG,GHA_OS_NAME -X gcov -X s3 \
-                    -f coverage.xml
+                    -f coverage.xml -C $SHA | tee codecov.log
                 if test $? == 0; then
                     echo "PASS $CODECOV_NAME" >> codecov.result
                     break
                 elif test $i -ge 2; then
-                    # Do not fail the build (yet) just because the codecov
-                    # upload fails
-                    echo "FAIL $CODECOV_NAME" >> codecov.result
-                    break
+                    if test `grep successfully codecov.log | wc -l` -gt 0; then
+                        echo "PASS $CODECOV_NAME (implied)" >> codecov.result
+                    else
+                        # Do not fail the build (yet) just because the
+                        # codecov upload fails
+                        echo "FAIL $CODECOV_NAME" >> codecov.result
+                        break
+                    fi
                 fi
                 DELAY=$(( RANDOM % 30 + 30))
                 echo "Pausing $DELAY seconds before re-attempting upload"

README.md

@@ -1,8 +1,7 @@
 [![Github Actions Status](https://github.com/Pyomo/pyomo/workflows/GitHub%20CI/badge.svg?event=push)](https://github.com/Pyomo/pyomo/actions?query=event%3Apush+workflow%3A%22GitHub+CI%22)
 [![Jenkins Status](https://img.shields.io/jenkins/s/https/software.sandia.gov/downloads/pub/pyomo/jenkins/Pyomo_trunk.svg?logo=jenkins&logoColor=white)](https://jenkins-srn.sandia.gov/job/Pyomo_trunk)
-[![codecov](https://codecov.io/gh/Pyomo/pyomo/branch/master/graph/badge.svg)](https://codecov.io/gh/Pyomo/pyomo)
+[![codecov](https://codecov.io/gh/Pyomo/pyomo/branch/main/graph/badge.svg)](https://codecov.io/gh/Pyomo/pyomo)
 [![Documentation Status](https://readthedocs.org/projects/pyomo/badge/?version=latest)](http://pyomo.readthedocs.org/en/latest/)
-
 [![GitHub contributors](https://img.shields.io/github/contributors/pyomo/pyomo.svg)](https://github.com/pyomo/pyomo/graphs/contributors)
 [![Merged PRs](https://img.shields.io/github/issues-pr-closed-raw/pyomo/pyomo.svg?label=merged+PRs)](https://github.com/pyomo/pyomo/pulls?q=is:pr+is:merged)
 [![Issue stats](http://isitmaintained.com/badge/resolution/pyomo/pyomo.svg)](http://isitmaintained.com/project/pyomo/pyomo)
@@ -11,7 +10,13 @@
 [![a COIN-OR project](https://www.coin-or.org/GitHub/coin-or-badge.png)](https://www.coin-or.org)
 
 ## Pyomo Overview
-Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. Pyomo can be used to define symbolic problems, create concrete problem instances, and solve these instances with standard solvers. Pyomo supports a wide range of problem types, including:
+
+Pyomo is a Python-based open-source software package that supports a
+diverse set of optimization capabilities for formulating and analyzing
+optimization models. Pyomo can be used to define symbolic problems,
+create concrete problem instances, and solve these instances with
+standard solvers. Pyomo supports a wide range of problem types,
+including:
 
  -  Linear programming
  -  Quadratic programming
@@ -24,7 +29,14 @@ Pyomo is a Python-based open-source software package that supports a diverse set
  -  Differential algebraic equations
  -  Mathematical programming with equilibrium constraints
 
-Pyomo supports analysis and scripting within a full-featured programming language. Further, Pyomo has also proven an effective framework for developing high-level optimization and analysis tools.  For example, the PySP package provides generic solvers for stochastic programming. PySP leverages the fact that Pyomo's modeling objects are embedded within a full-featured high-level programming language, which allows for transparent parallelization of subproblems using Python parallel communication libraries.
+Pyomo supports analysis and scripting within a full-featured programming
+language. Further, Pyomo has also proven an effective framework for
+developing high-level optimization and analysis tools.  For example, the
+[`mpi-sppy`](https://github.com/Pyomo/mpi-sppy) package provides generic
+solvers for stochastic programming. `mpi-sppy` leverages the fact that
+Pyomo's modeling objects are embedded within a full-featured high-level
+programming language, which allows for transparent parallelization of
+subproblems using Python parallel communication libraries.
 
 * [Pyomo Home](http://www.pyomo.org)
 * [About Pyomo](http://www.pyomo.org/about)
@@ -68,9 +80,15 @@ Pyomo is currently tested with the following Python implementations:
 ### Developers
 
 Pyomo development moved to this repository in June, 2016 from
-Sandia National Laboratories. Developer discussions are hosted by [google groups](https://groups.google.com/forum/#!forum/pyomo-developers).
+Sandia National Laboratories. Developer discussions are hosted by
+[google groups](https://groups.google.com/forum/#!forum/pyomo-developers).
 
-By contributing to this software project, you are agreeing to the following terms and conditions for your contributions:
+By contributing to this software project, you are agreeing to the
+following terms and conditions for your contributions:
 
 1. You agree your contributions are submitted under the BSD license. 
-2. You represent you are authorized to make the contributions and grant the license. If your employer has rights to intellectual property that includes your contributions, you represent that you have received permission to make contributions and grant the required license on behalf of that employer. 
+2. You represent you are authorized to make the contributions and grant
+   the license. If your employer has rights to intellectual property that
+   includes your contributions, you represent that you have received
+   permission to make contributions and grant the required license on
+   behalf of that employer.

doc/OnlineDocs/advanced_topics/index.rst

@@ -5,6 +5,5 @@ Advanced Topics
    :maxdepth: 1
 
    persistent_solvers.rst
-   pysp_rapper/index.rst
    units_container.rst
    linearexpression.rst