test_pr_and_main.yml

name: GitHub CI

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
    types:
      - opened
      - reopened
      - synchronize
      - ready_for_review
  workflow_dispatch:
    inputs:
      git-ref:
        description: Git Hash (Optional)
        required: false

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

defaults:
  run:
    shell: bash -l {0}

env:
  PYTHONWARNINGS: ignore::UserWarning
  PYTHON_CORE_PKGS: wheel
  PYPI_ONLY: z3-solver linear-tree
  PYPY_EXCLUDE: scipy numdifftools seaborn statsmodels linear-tree
  CACHE_VER: v221013.1
  NEOS_EMAIL: tests@pyomo.org
  SRC_REF: ${{ github.head_ref || github.ref }}

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
    steps:
    - name: Checkout Pyomo source
      uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: '3.10'
    - name: Black Formatting Check
      run: |
        # Note v24.4.1 fails due to a bug in the parser
        pip install 'black!=24.4.1'
        black . -S -C --check --diff --exclude examples/pyomobook/python-ch/BadIndent.py
    - name: Spell Check
      uses: crate-ci/typos@master
      with: 
        config: ./.github/workflows/typos.toml


  build:
    name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.other }}
    needs: lint  # the linter job is a prerequisite for PRs
    runs-on: ${{ matrix.os }}
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python: [ 3.9, '3.10', '3.11', '3.12', '3.13' ]
        other: [""]
        category: [""]

        include:
        - os: ubuntu-latest
          TARGET: linux
          PYENV: pip

        - os: macos-latest
          TARGET: osx
          PYENV: pip

        - os: windows-latest
          TARGET: win
          PYENV: conda
          PACKAGES: glpk pytest-qt filelock

        - os: ubuntu-latest
          python: '3.11'
          other: /conda
          skip_doctest: 1
          TARGET: linux
          PYENV: conda
          PACKAGES: pytest-qt

        - os: ubuntu-latest
          python: '3.10'
          other: /mpi
          mpi: 3
          skip_doctest: 1
          TARGET: linux
          PYENV: conda
          PACKAGES: openmpi mpi4py

        - os: ubuntu-latest
          python: '3.12'
          other: /cython
          setup_options: --with-cython
          skip_doctest: 1
          TARGET: linux
          PYENV: pip
          PACKAGES: cython

        - os: windows-latest
          python: 3.9
          other: /pip
          skip_doctest: 1
          TARGET: win
          PYENV: pip

        - os: ubuntu-latest
          python: '3.11'
          other: /singletest
          category: "-m 'neos or importtest'"
          skip_doctest: 1
          TARGET: linux
          PYENV: pip

        - os: ubuntu-latest
          python: 3.9
          other: /slim
          slim: 1
          skip_doctest: 1
          TARGET: linux
          PYENV: pip

        - os: ubuntu-latest
          python: 3.12
          other: /numpy2
          slim: 1
          skip_doctest: 1
          TARGET: linux
          PYENV: pip
          PACKAGES: "gurobipy dill numpy>2.0 scipy networkx"

        - os: ubuntu-latest
          python: '3.10'
          other: /pyutilib
          TARGET: linux
          PYENV: pip
          PACKAGES: pyutilib

        - os: ubuntu-latest
          python: pypy-3.9
          skip_doctest: 1
          TARGET: linux
          PYENV: pip

    steps:
    - name: Checkout Pyomo source
      uses: actions/checkout@v4

    - name: Configure job parameters
      run: |
        JOB="${{matrix.TARGET}}/${{matrix.python}}${{matrix.other}}"
        echo "GHA_JOBNAME=$JOB" | sed 's|/|_|g' >> $GITHUB_ENV
        if test -z "${{matrix.other}}"; then
            echo "GHA_JOBGROUP=${{matrix.TARGET}}" >> $GITHUB_ENV
        else
            echo "GHA_JOBGROUP=other" >> $GITHUB_ENV
        fi
        # Note: pandas 1.0.3 causes gams 29.1.0 import to fail in python 3.8
        EXTRAS=tests
        if test -z "${{matrix.slim}}"; then
            EXTRAS="$EXTRAS,docs,optional"
        fi
        echo "EXTRAS=$EXTRAS" >> $GITHUB_ENV
        PYTHON_PACKAGES="${{matrix.PACKAGES}}"
        echo "PYTHON_PACKAGES=$PYTHON_PACKAGES" \
            | tr '\n' ' ' | sed 's/ \+/ /g' >> $GITHUB_ENV

    #- name: Pip package cache
    #  uses: actions/cache@v4
    #  if: matrix.PYENV == 'pip'
    #  id: pip-cache
    #  with:
    #    path: cache/pip
    #    key: pip-${{env.CACHE_VER}}.0-${{runner.os}}-${{matrix.python}}

    #- name: OS package cache
    #  uses: actions/cache@v4
    #  if: matrix.TARGET != 'osx'
    #  id: os-cache
    #  with:
    #    path: cache/os
    #    key: pkg-${{env.CACHE_VER}}.0-${{runner.os}}

    - name: TPL package download cache
      uses: actions/cache@v4
      if: ${{ ! matrix.slim }}
      id: download-cache
      with:
        path: cache/download
        key: download-${{env.CACHE_VER}}.0-${{runner.os}}

    - name: Configure curl
      run: |
        CURLRC="$(cat <<EOF
           retry = 0
           max-time = 30
        EOF
        )"
        echo "$CURLRC" > ${GITHUB_WORKSPACE}/.curlrc
        echo "$CURLRC" > ${GITHUB_WORKSPACE}/_curlrc
        echo "CURL_HOME=$GITHUB_WORKSPACE" >> $GITHUB_ENV

    - name: Update OSX
      if: matrix.TARGET == 'osx'
      run: |
        mkdir -p ${GITHUB_WORKSPACE}/cache/os
        export HOMEBREW_CACHE=${GITHUB_WORKSPACE}/cache/os
        # Be cautious running brew update: it can break
        #    setup-python on OSX
        # brew update
        #
        # Notes:
        #  - install glpk
        #  - pyodbc needs: gcc pkg-config unixodbc freetds
        for pkg in bash pkg-config unixodbc freetds glpk ginac; do
            brew list $pkg || brew install $pkg
        done

    - name: Update Linux
      if: matrix.TARGET == 'linux'
      run: |
        mkdir -p ${GITHUB_WORKSPACE}/cache/os
        # Notes:
        #  - install glpk
        #  - ipopt needs: libopenblas-dev gfortran liblapack-dev
        sudo apt-get -o Dir::Cache=${GITHUB_WORKSPACE}/cache/os \
            install libopenblas-dev gfortran liblapack-dev glpk-utils \
            libginac-dev
        sudo chmod -R 777 ${GITHUB_WORKSPACE}/cache/os

    - name: Update Windows
      if: matrix.TARGET == 'win'
      run: |
        echo "SETUPTOOLS_USE_DISTUTILS=local" >> $GITHUB_ENV
        choco install pkgconfiglite

    - name: Set up Python ${{ matrix.python }}
      if: matrix.PYENV == 'pip'
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python }}

    - name: Set up Miniconda Python ${{ matrix.python }}
      if: matrix.PYENV == 'conda'
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: false
        python-version: ${{ matrix.python }}

    # This is necessary for qt (UI) tests; the package utilized here does not
    # have support for OSX.
    - name: Set up UI testing infrastructure
      if: ${{ matrix.TARGET != 'osx' }}
      uses: pyvista/setup-headless-display-action@v2
      with:
        qt: true
        pyvista: false

    # GitHub actions is very fragile when it comes to setting up various
    # Python interpreters, expecially the setup-miniconda interface.
    # Per the setup-miniconda documentation, it is important to always
    # invoke bash as a login shell ('shell: bash -l {0}') so that the
    # conda environment is properly activated.  However, running within
    # a login shell appears to foul up the link to python from
    # setup-python.  Further, we have anecdotal evidence that
    # subprocesses invoked through $(python -c ...) and `python -c ...`
    # will not pick up the python activated by setup-python on OSX.
    #
    # Our solution is to define a PYTHON_EXE environment variable that
    # can be explicitly called within subprocess calls to reach the
    # correct interpreter.  Note that we must explicitly run in a *non*
    # login shell to set up the environment variable for the
    # setup-python environments.

    - name: Install Python Packages (pip)
      if: matrix.PYENV == 'pip'
      shell: bash # DO NOT REMOVE: see note above
      run: |
        python -c 'import sys;print(sys.executable)'
        python -m pip install --cache-dir cache/pip --upgrade pip
        python -m pip install --cache-dir cache/pip setuptools
        PYOMO_DEPENDENCIES=`python setup.py dependencies \
            --extras "$EXTRAS" | tail -1`
        PACKAGES="${PYTHON_CORE_PKGS} ${PYTHON_PACKAGES} ${PYOMO_DEPENDENCIES} "
        if [[ ${{matrix.python}} == pypy* ]]; then
            EXCLUDE="$PYPY_EXCLUDE $EXCLUDE"
        fi
        EXCLUDE=`echo "$EXCLUDE" | xargs`
        if test -n "$EXCLUDE"; then
            for WORD in $EXCLUDE; do
                PACKAGES=${PACKAGES//$WORD / }
            done
        fi
        python -m pip install --cache-dir cache/pip ${PACKAGES}
        python -m pip install --cache-dir cache/pip pymysql || \
            python -m pip install --cache-dir cache/pip pymysql
        if test -z "${{matrix.slim}}"; then
            python -m pip install --cache-dir cache/pip cplex docplex \
                || echo "WARNING: CPLEX Community Edition is not available"
            python -m pip install --cache-dir cache/pip gurobipy \
                || echo "WARNING: Gurobi is not available"
            python -m pip install --cache-dir cache/pip xpress \
                || echo "WARNING: Xpress Community Edition is not available"
            python -m pip install --cache-dir cache/pip maingopy \
                || echo "WARNING: MAiNGO is not available"
            if [[ ${{matrix.python}} == pypy* ]]; then
                echo "skipping wntr for pypy"
            else
                python -m pip install wntr \
                    || echo "WARNING: WNTR is not available"
            fi
        fi
        python -c 'import sys; print("PYTHON_EXE=%s" \
            % (sys.executable,))' >> $GITHUB_ENV
        echo ""
        echo "Final pip environment:"
        python -m pip list | sed 's/^/    /'

    - name: Install Python packages (conda)
      if: matrix.PYENV == 'conda'
      run: |
        # Set up environment
        conda config --set always_yes yes
        conda config --set auto_update_conda false
        conda config --remove channels defaults
        conda config --append channels nodefaults
        conda config --append channels conda-forge
        # Try to install mamba
        conda install --update-deps -q -y -n base conda-libmamba-solver \
            || MAMBA_FAILED=1
        if test -z "$MAMBA_FAILED"; then
            echo "*** Activating the mamba environment solver ***"
            conda config --set solver libmamba
        fi
        # Add the rest of the channels
        conda config --append channels gurobi
        conda config --append channels ibmdecisionoptimization
        conda config --append channels fico-xpress
        # Print environment info
        echo "*** CONDA environment: ***"
        conda info
        conda config --show-sources
        conda config --show channels
        conda list --show-channel-urls
        which python
        python --version
        # Note: some pypi packages are not available through conda
        PYOMO_DEPENDENCIES=`python setup.py dependencies \
            --extras "$EXTRAS" | tail -1`
        PACKAGES="${PYTHON_CORE_PKGS} ${PYTHON_PACKAGES} ${PYOMO_DEPENDENCIES} "
        if [[ ${{matrix.python}} == pypy* ]]; then
            EXCLUDE="$PYPY_EXCLUDE $EXCLUDE"
        fi
        # HACK: Remove problem packages on conda+Linux
        if test "${{matrix.TARGET}}" == linux; then
            EXCLUDE="casadi numdifftools $EXCLUDE"
        fi
        if [[ "${{matrix.TARGET}}" == win && "${{matrix.python}}" == "3.13" ]]; then
            # As of Nov 7, 2024, qtconsole is not compatible with python 3.13 on win
            EXCLUDE="qtconsole $EXCLUDE"
        fi
        EXCLUDE=`echo "$EXCLUDE" | xargs`
        if test -n "$EXCLUDE"; then
            for WORD in $EXCLUDE; do
                PACKAGES=${PACKAGES//$WORD / }
            done
        fi
        for PKG in $PACKAGES; do
            if [[ " $PYPI_ONLY " == *" $PKG "* ]]; then
                PYPI_DEPENDENCIES="$PYPI_DEPENDENCIES $PKG"
            else
                CONDA_DEPENDENCIES="$CONDA_DEPENDENCIES $PKG"
            fi
        done
        echo ""
        echo "*** Install Pyomo dependencies ***"
        # For windows, cannot use newer setuptools because of APPSI compilation issues
        if test "${{matrix.TARGET}}" == 'win'; then
            CONDA_DEPENDENCIES="$CONDA_DEPENDENCIES setuptools<74.0.0"
        fi
        # Note: this will fail the build if any installation fails (or
        # possibly if it outputs messages to stderr)
        conda install --update-deps -q -y $CONDA_DEPENDENCIES
        if test -z "${{matrix.slim}}"; then
            PYVER=$(echo "py${{matrix.python}}" | sed 's/\.//g')
            echo "Installing for $PYVER"
            for PKG in 'cplex>=12.10' docplex gurobi xpress cyipopt pymumps scip; do
                echo ""
                echo "*** Install $PKG ***"
                # conda can literally take an hour to determine that a
                # package is not available.  Perform a quick search to see
                # if the package is available for this interpreter before
                # attempting an install.
                # NOTE: conda search will attempt approximate matches.
                _PKGLIST=$(conda search -f "$PKG") || echo "Package $PKG not found"
                echo "$_PKGLIST"
                _BASE=$(echo "$PKG" | sed 's/[=<>].*//')
                _BUILDS=$(echo "$_PKGLIST" | grep "^$_BASE " \
                    | sed -r 's/\s+/ /g' | cut -d\  -f3) || echo ""
                if test -n "$_BUILDS"; then
                    _ISPY=$(echo "$_BUILDS" | grep "^py") \
                        || echo "INFO: No python build detected."
                    _PYOK=$(echo "$_BUILDS" | grep -E "^($PYVER|pyh)") \
                        || echo "INFO: No python build matching $PYVER detected."
                    if test -z "$_ISPY" -o -n "$_PYOK"; then
                        echo ""
                        echo "... INSTALLING $PKG"
                        conda install -y "$PKG" || _BUILDS=""
                    fi
                fi
                if test -z "$_BUILDS"; then
                    echo "WARNING: $PKG is not available"
                fi
            done
        fi
        # Re-try Pyomo (optional) dependencies with pip
        if test -n "$PYPI_DEPENDENCIES"; then
            python -m pip install --cache-dir cache/pip $PYPI_DEPENDENCIES
        fi
        # remember this python interpreter
        python -c 'import sys; print("PYTHON_EXE=%s" \
            % (sys.executable,))' >> $GITHUB_ENV
        #
        # conda activate puts itself first in the PATH, which overrides
        # any paths we add through GITHUB_PATH.  We will update .profile
        # to move the local runner paths back to the front (before conda).
        for profile in $HOME/.profile $HOME/.bash_profile; do
            if test ! -e $profile; then
                continue
            fi
            echo '' >> $profile
            echo 'export PATH=`echo "$PATH" \
                | tr ":" "\\n" | grep runner | tr "\n" ":"`:`echo "$PATH" \
                | tr ":" "\\n" | grep -v runner | tr "\n" ":"`' >> $profile
        done
        echo ""
        echo "Final conda environment:"
        conda list | sed 's/^/    /'

    - name: Setup TPL package directories
      run: |
        TPL_DIR="${GITHUB_WORKSPACE}/cache/tpl"
        mkdir -p "$TPL_DIR"
        DOWNLOAD_DIR="${GITHUB_WORKSPACE}/cache/download"
        mkdir -p "$DOWNLOAD_DIR"
        echo "TPL_DIR=$TPL_DIR" >> $GITHUB_ENV
        echo "DOWNLOAD_DIR=$DOWNLOAD_DIR" >> $GITHUB_ENV

    - name: Install Ipopt
      if: ${{ ! matrix.slim }}
      run: |
        IPOPT_DIR=$TPL_DIR/ipopt
        echo "$IPOPT_DIR" >> $GITHUB_PATH
        echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$IPOPT_DIR" >> $GITHUB_ENV
        mkdir -p $IPOPT_DIR
        IPOPT_TAR=${DOWNLOAD_DIR}/ipopt.tar.gz
        if test ! -e $IPOPT_TAR; then
            echo "...downloading Ipopt"
            if test "${{matrix.TARGET}}" == osx; then
                echo "IDAES Ipopt not available on OSX"
                exit 0
            fi
            URL=https://github.com/IDAES/idaes-ext
            RELEASE=$(curl --max-time 150 --retry 8 \
                -L -s -H 'Accept: application/json' ${URL}/releases/latest)
            VER=$(echo $RELEASE | sed -e 's/.*"tag_name":"\([^"]*\)".*/\1/')
            URL=${URL}/releases/download/$VER
            if test "${{matrix.TARGET}}" == linux; then
                curl --max-time 150 --retry 8 \
                    -L $URL/idaes-solvers-ubuntu2004-x86_64.tar.gz \
                    > $IPOPT_TAR
            else
                curl --max-time 150 --retry 8 \
                    -L $URL/idaes-solvers-windows-x86_64.tar.gz \
                    $URL/idaes-lib-windows-x86_64.tar.gz > $IPOPT_TAR
            fi
        fi
        cd $IPOPT_DIR
        tar -xzi < $IPOPT_TAR
        echo ""
        echo "$IPOPT_DIR"
        ls -l $IPOPT_DIR

    - name: Install GAMS
      if: ${{ ! matrix.slim }}
      # We install using Powershell because the GAMS installer hangs
      # when launched from bash on Windows
      shell: pwsh
      run: |
        $GAMS_DIR = "${env:TPL_DIR}/gams"
        echo "$GAMS_DIR" | `
            Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
        echo "LD_LIBRARY_PATH=${env:LD_LIBRARY_PATH}:$GAMS_DIR" `
            Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
        echo "DYLD_LIBRARY_PATH=${env:DYLD_LIBRARY_PATH}:$GAMS_DIR" `
            Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
        $INSTALLER = "${env:DOWNLOAD_DIR}/gams_install.exe"
        # We are pinning to 29.1.0 because a license is required for
        # versions after this in order to run in demo mode.
        $URL = "https://d37drm4t2jghv5.cloudfront.net/distributions/29.1.0"
        if ( "${{matrix.TARGET}}" -eq "win" ) {
            $URL = "$URL/windows/windows_x64_64.exe"
        } elseif ( "${{matrix.TARGET}}" -eq "osx" ) {
            $URL = "$URL/macosx/osx_x64_64_sfx.exe"
        } else {
            $URL = "$URL/linux/linux_x64_64_sfx.exe"
        }
        if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
            echo "...downloading GAMS"
            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
        }
        echo "...installing GAMS"
        if ( "${{matrix.TARGET}}" -eq "win" ) {
            Start-Process -FilePath "$INSTALLER" -ArgumentList `
                "/SP- /NORESTART /VERYSILENT /DIR=$GAMS_DIR /NOICONS" `
                -Wait
        } else {
            chmod 777 $INSTALLER
            Start-Process -FilePath "$INSTALLER" -ArgumentList `
                "-q -d $GAMS_DIR" -Wait
            mv $GAMS_DIR/*/* $GAMS_DIR/.
        }
        echo ""
        echo "$GAMS_DIR"
        ls -l $GAMS_DIR

    - name: Install GAMS Python bindings
      if: ${{ ! matrix.slim }}
      run: |
        GAMS_DIR="${env:TPL_DIR}/gams"
        py_ver=$($PYTHON_EXE -c 'import sys;v="_%s%s" % sys.version_info[:2] \
            ;print(v if v != "_27" else "")')
        if test -e $GAMS_DIR/apifiles/Python/api$py_ver; then
            echo "Installing GAMS Python bindings"
            pushd $GAMS_DIR/apifiles/Python/api$py_ver
            $PYTHON_EXE setup.py install
            popd
        fi

    - name: Install BARON
      if: ${{ ! matrix.slim }}
      shell: pwsh
      run: |
        $BARON_DIR = "${env:TPL_DIR}/baron"
        echo "$BARON_DIR" | `
            Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
        $URL = "https://minlp-downloads.nyc3.cdn.digitaloceanspaces.com/xecs/baron/current/"
        if ( "${{matrix.TARGET}}" -eq "win" ) {
            $INSTALLER = "${env:DOWNLOAD_DIR}/baron_install.exe"
            $URL += "baron-win64.exe"
        } elseif ( "${{matrix.TARGET}}" -eq "osx" ) {
            $INSTALLER = "${env:DOWNLOAD_DIR}/baron_install.zip"
            $URL += "baron-osx64.zip"
        } else {
            $INSTALLER = "${env:DOWNLOAD_DIR}/baron_install.zip"
            $URL += "baron-lin64.zip"
        }
        if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
            echo "...downloading BARON ($URL)"
            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
        }
        echo "...installing BARON"
        if ( "${{matrix.TARGET}}" -eq "win" ) {
            Start-Process -FilePath "$INSTALLER" -ArgumentList `
                "/SP- /NORESTART /VERYSILENT /DIR=$BARON_DIR /NOICONS" `
                -Wait
        } else {
            unzip -q $INSTALLER
            mv baron-* $BARON_DIR
        }
        echo ""
        echo "$BARON_DIR"
        ls -l $BARON_DIR

    - name: Install GJH_ASL_JSON
      if: ${{ ! matrix.slim && matrix.TARGET != 'win' }}
      run: |
        GJH_DIR="$TPL_DIR/gjh"
        echo "${GJH_DIR}" >> $GITHUB_PATH
        INSTALL_DIR="${DOWNLOAD_DIR}/gjh"
        if test ! -e "$INSTALL_DIR/bin"; then
            mkdir -p "$INSTALL_DIR"
            INSTALLER="$INSTALL_DIR/gjh_asl_json.zip"
            URL="https://codeload.github.com/ghackebeil/gjh_asl_json/zip/master"
            curl --max-time 150 --retry 8 -L $URL > $INSTALLER
            cd $INSTALL_DIR
            unzip -q $INSTALLER
            cd gjh_asl_json-master/Thirdparty
            ./get.ASL
            cd ..
            make
            mv bin "$INSTALL_DIR/bin"
        fi
        cp -rp "$INSTALL_DIR/bin" "$GJH_DIR"
        echo ""
        echo "$GJH_DIR"
        ls -l $GJH_DIR

    - name: Install Pyomo
      run: |
        echo ""
        echo "Clone Pyomo-model-libraries..."
        URL=https://github.com/Pyomo/pyomo-model-libraries.git
        git clone -b ${SRC_REF##*/} $URL || git clone -b main $URL
        echo ""
        echo "Install Pyomo..."
        echo ""
        $PYTHON_EXE setup.py develop ${{matrix.setup_options}}
        echo ""
        echo "Set custom PYOMO_CONFIG_DIR"
        echo ""
        echo "PYOMO_CONFIG_DIR=${GITHUB_WORKSPACE}/config" >> $GITHUB_ENV

    # this has to be done after Pyomo is installed because highspy 
    # depends on pyomo's find_library function
    - name: Install HiGHS
      if: ${{ ! matrix.slim }}
      shell: bash
      run: |
        echo "NOTE: temporarily pinning to highspy pre-release for testing"
        $PYTHON_EXE -m pip install --cache-dir cache/pip "highspy>=1.7.1.dev1" \
            || echo "WARNING: highspy is not available"

    - name: Set up coverage tracking
      run: |
        if test "${{matrix.TARGET}}" == win; then
            COVERAGE_BASE=${GITHUB_WORKSPACE}\\.cover
        else
            COVERAGE_BASE=${GITHUB_WORKSPACE}/.cover
        fi
        COVERAGE_RC=${COVERAGE_BASE}_rc
        echo "COVERAGE_RCFILE=$COVERAGE_RC" >> $GITHUB_ENV
        echo "COVERAGE_PROCESS_START=$COVERAGE_RC" >> $GITHUB_ENV
        cp ${GITHUB_WORKSPACE}/.coveragerc ${COVERAGE_RC}
        echo "data_file=${COVERAGE_BASE}age" >> ${COVERAGE_RC}
        SITE_PACKAGES=$($PYTHON_EXE -c \
            "import sysconfig; print(sysconfig.get_path('purelib'))")
        echo "Python site-packages: $SITE_PACKAGES"
        echo 'import coverage; coverage.process_startup()' \
            > ${SITE_PACKAGES}/run_coverage_at_startup.pth

    - name: Download and install extensions
      if: ${{ ! matrix.slim }}
      run: |
        echo ""
        echo "Pyomo download-extensions"
        echo ""
        pyomo download-extensions || exit 1
        echo ""
        echo "Pyomo build-extensions"
        echo ""
        pyomo build-extensions --parallel 2

    - name: Report pyomo plugin information
      run: |
        echo "$PATH"
        pyomo help --solvers || exit 1
        pyomo help --transformations || exit 1
        pyomo help --writers || exit 1

    - name: Run Pyomo tests
      if: matrix.mpi == 0
      run: |
        $PYTHON_EXE -m pytest -v \
            -W ignore::Warning ${{matrix.category}} \
            pyomo `pwd`/pyomo-model-libraries \
            `pwd`/examples `pwd`/doc --junitxml="TEST-pyomo.xml"

    - name: Run Pyomo MPI tests
      if: matrix.mpi != 0
      run: |
        # Manually invoke the DAT parser so that parse_table_datacmds.py
        # is fully generated by a single process before invoking MPI
        $PYTHON_EXE -c "from pyomo.dataportal.parse_datacmds import \
            parse_data_commands; parse_data_commands(data='')"
        # Note: if we are testing with openmpi, add '--oversubscribe'
        mpirun -np ${{matrix.mpi}} -oversubscribe pytest -v \
            --junit-xml=TEST-pyomo-mpi.xml \
            -m "mpi" -W ignore::Warning \
            pyomo `pwd`/pyomo-model-libraries

    - name: Run documentation tests
      if: matrix.skip_doctest == 0
      run: |
        make -C doc/OnlineDocs doctest -d

    - name: Process code coverage report
      run: |
        coverage combine
        coverage report -i
        coverage xml -i

    - name: Record build artifacts
      uses: actions/upload-artifact@v4
      with:
        name: ${{github.job}}_${{env.GHA_JOBGROUP}}-${{env.GHA_JOBNAME}}
        include-hidden-files: true
        path: |
          .coverage
          coverage.xml
          # In general, do not record test results as artifacts to
          #   manage total artifact storage
          # TEST-*.xml


  bare-python-env:
    name: linux/3.9/bare-env
    needs: lint  # the linter job is a prerequisite for PRs
    runs-on: ubuntu-latest
    timeout-minutes: 10
    steps:
    - name: Checkout Pyomo source
      uses: actions/checkout@v4

    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: 3.9

    - name: Install Pyomo
      run: |
        echo ""
        echo "Install Pyomo..."
        echo ""
        python setup.py develop
        echo ""
        echo "Set custom PYOMO_CONFIG_DIR"
        echo ""
        echo "PYOMO_CONFIG_DIR=${GITHUB_WORKSPACE}/config" >> $GITHUB_ENV

    - name: Report pyomo plugin information
      run: |
        echo "$PATH"
        pyomo help --solvers || exit 1
        pyomo help --transformations || exit 1
        pyomo help --writers || exit 1

    - name: Run Pyomo standalone test
      run: |
        echo ""
        echo "Running standalone Pyomo test"
        echo ""
        python `pwd`/pyomo/environ/tests/standalone_minimal_pyomo_driver.py \
            || exit 1


  cover:
    name: process-coverage-${{ matrix.TARGET }}
    needs: build
    if: success() || failure() # run even if a build job fails, but not if cancelled
    runs-on: ${{ matrix.os }}
    timeout-minutes: 10
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-13, windows-latest]

        include:
        - os: ubuntu-latest
          TARGET: linux
        - os: macos-13
          TARGET: osx
        - os: windows-latest
          TARGET: win

    steps:
    - name: Checkout Pyomo source
      uses: actions/checkout@v4
      # We need the source for .codecov.yml and running "coverage xml"

    #- name: Pip package cache
    #  uses: actions/cache@v4
    #  id: pip-cache
    #  with:
    #    path: cache/pip
    #    key: pip-${{env.CACHE_VER}}.0-${{runner.os}}-3.9

    - name: Download build artifacts
      uses: actions/download-artifact@v4
      with:
        path: artifacts

    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: 3.9

    - name: Install Python Packages (pip)
      shell: bash # DO NOT REMOVE: see note above
      run: |
        python -c 'import sys;print(sys.executable)'
        python -m pip install --cache-dir cache/pip --upgrade pip
        PYOMO_DEPENDENCIES=`python setup.py dependencies \
            --extras "tests" | tail -1`
        python -m pip install --cache-dir cache/pip \
            ${PYTHON_CORE_PKGS} ${PYOMO_DEPENDENCIES}
        python -c 'import sys; print("PYTHON_EXE=%s" \
            % (sys.executable,))' >> $GITHUB_ENV

    - name: Install Pyomo
      run: |
        echo ""
        echo "Clone Pyomo-model-libraries..."
        git clone https://github.com/Pyomo/pyomo-model-libraries.git
        echo ""
        echo "Install Pyomo..."
        echo ""
        $PYTHON_EXE setup.py develop ${{matrix.setup_options}}
        echo ""
        echo "Set custom PYOMO_CONFIG_DIR"
        echo ""
        echo "PYOMO_CONFIG_DIR=${GITHUB_WORKSPACE}/config" >> $GITHUB_ENV

    - name: Generate parse_table_datacmds
      run: |
        # Manually invoke the DAT parser so that parse_table_datacmds.py
        # is generated before running "coverage xml"
        $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: |
        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
        for ARTIFACT in artifacts/*_*${{matrix.TARGET}}_*; do
            NAME=`echo $ARTIFACT | cut -d/ -f2`
            cp -v $ARTIFACT/.coverage .coverage-$NAME
        done
        rm -vf .coverage coverage.xml
        echo "Build: ${{ matrix.TARGET }}/other"
        echo ""
        FILES=.coverage-*_other-*
        coverage combine --debug=dataio $FILES
        if test ! -e .coverage; then
            echo "No coverage to upload."
        else
            coverage xml || coverage xml -i
            mv -v coverage.xml coverage-other.xml
        fi
        echo ""
        echo "Build: ${{ matrix.TARGET }}"
        echo ""
        FILES=.coverage-*_${{matrix.TARGET}}-*
        coverage combine --debug=dataio $FILES
        rm -vf artifacts/*/*.xml
        if test ! -e .coverage; then
            echo "No coverage to upload."
        else
            coverage xml || coverage xml -i
        fi

    - name: Upload codecov reports
      if: github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main'
      uses: codecov/codecov-action@v4
      with:
        files: coverage.xml
        token: ${{ secrets.PYOMO_CODECOV_TOKEN }}
        name: ${{ matrix.TARGET }}
        flags: ${{ matrix.TARGET }}
        fail_ci_if_error: true

    - name: Upload other coverage reports
      if: |
        hashFiles('coverage-other.xml') != '' &&
        (github.repository_owner == 'Pyomo' || github.ref != 'refs/heads/main')
      uses: codecov/codecov-action@v4
      with:
        files: coverage-other.xml
        token: ${{ secrets.PYOMO_CODECOV_TOKEN }}
        name: ${{ matrix.TARGET }}/other
        flags: ${{ matrix.TARGET }},other
        fail_ci_if_error: true