From f63820d4c5357a1ff398a4b872afd2e15de0182e Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 25 Jun 2020 11:32:00 -0600
Subject: [PATCH 01/46] Adding Pyutilib testing

---
 .github/workflows/pr_master_test.yml | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .github/workflows/pr_master_test.yml

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
new file mode 100644
index 00000000..2fd09eff
--- /dev/null
+++ b/.github/workflows/pr_master_test.yml
@@ -0,0 +1 @@
+name: GitHub CI

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

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

env:
  PYTHONWARNINGS: ignore::UserWarning
  PYTHON_BASE_PKGS: >
      coverage xlrd codecov

jobs:
  pyomo-tests:
    name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.NAME }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python: [2.7, 3.5, 3.6, 3.7, 3.8, pypy2, pypy3]
        include:
        - os: ubuntu-latest
          TARGET: linux
          PYENV: pip

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

        - os: windows-latest
          TARGET: win
          PYENV: conda
          PACKAGES: setuptools, coverage, nose, xlrd

        exclude:
        - {os: macos-latest, python: pypy2}
        - {os: macos-latest, python: pypy3}
        - {os: windows-latest, python: pypy2}
        - {os: windows-latest, python: pypy3}

    steps:
    - uses: actions/checkout@v2

    # Ideally we would cache the conda downloads; however, each cache is
    # over 850MB, and with 5 python versions, that would consume 4.2 of
    # the 5 GB GitHub allows.
    #
    #- name: Conda package cache
    #  uses: actions/cache@v1
    #  if: matrix.PYENV == 'conda'
    #  id: conda-cache
    #  with:
    #    path: cache/conda
    #    key: conda-v2-${{runner.os}}-${{matrix.python}}

    - name: Pip package cache
      uses: actions/cache@v1
      if: matrix.PYENV == 'pip'
      id: pip-cache
      with:
        path: cache/pip
        key: pip-v2-${{runner.os}}-${{matrix.python}}

    - name: OS package cache
      uses: actions/cache@v1
      id: os-cache
      with:
        path: cache/os
        key: pkg-v2-${{runner.os}}

    - name: TPL package download cache
      uses: actions/cache@v1
      id: download-cache
      with:
        path: cache/download
        key: download-v3-${{runner.os}}

    - name: Set up Python ${{ matrix.python }}
      if: matrix.PYENV == 'pip'
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python }}

    - name: Set up Miniconda Python ${{ matrix.python }}
      if: matrix.PYENV == 'conda'
      uses: goanpeca/setup-miniconda@v1
      with:
        auto-update-conda: true
        python-version: ${{ matrix.python }}

    # 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
      run: |
        python -m pip install --cache-dir cache/pip --upgrade pip
        pip install --cache-dir cache/pip ${PYTHON_BASE_PKGS} 
        if [[ ${{matrix.python}} == pypy  ]] || [[ ${{matrix.python}} == 2.7 ]]; then
            pip install --cache-dir cache/pip pyro
        else
            pip install --cache-dir cache/pip pyro4
        fi
        if [[ ${{matrix.python}} == 3.4 ]]; then
            pip install --cache-dir cache/pip pyyaml<=5.2
        elif [[ ${{matrix.python}} != 3.6 ]]; then
            pip install --cache-dir cache/pip pyyaml
        fi
        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
            % (sys.executable,))'

    - name: Install Python packages (conda)
      if: matrix.PYENV == 'conda'
      run: |
        mkdir -p $GITHUB_WORKSPACE/cache/conda
        conda config --set always_yes yes
        conda config --set auto_update_conda false
        conda config --prepend pkgs_dirs $GITHUB_WORKSPACE/cache/conda
        conda info
        conda config --show-sources
        conda list --show-channel-urls
        conda install -q -y -c conda-forge ${{matrix.PACKAGES}}
        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
            % (sys.executable,))'

    - name: Run Pyutilib tests
      run: |
        test.pyutilib --cat=all --cov

    - name: Process code coverage report
      env:
        CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
      run: |
        while : ; do
            curl --retry 8 -L https://codecov.io/bash -o codecov.sh
            bash codecov.sh -Z -X gcov -f coverage.xml
            if test $? == 0; then
                break
            elif test $i -ge 4; then
                exit 1
            fi
            DELAY=$(( RANDOM % 30 + 30))
            echo "Pausing $DELAY seconds before re-attempting upload"
            sleep $DELAY
        done
\ No newline at end of file

From 575fa0e6151b05d60d07c14188733547a997f930 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <55767766+mrmundt@users.noreply.github.com>
Date: Thu, 25 Jun 2020 11:35:18 -0600
Subject: [PATCH 02/46] Removing unnecessary caches

---
 .github/workflows/pr_master_test.yml | 154 ++++++++++++++++++++++++++-
 1 file changed, 153 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 2fd09eff..26565106 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -1 +1,153 @@
-name: GitHub CI

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

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

env:
  PYTHONWARNINGS: ignore::UserWarning
  PYTHON_BASE_PKGS: >
      coverage xlrd codecov

jobs:
  pyomo-tests:
    name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.NAME }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python: [2.7, 3.5, 3.6, 3.7, 3.8, pypy2, pypy3]
        include:
        - os: ubuntu-latest
          TARGET: linux
          PYENV: pip

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

        - os: windows-latest
          TARGET: win
          PYENV: conda
          PACKAGES: setuptools, coverage, nose, xlrd

        exclude:
        - {os: macos-latest, python: pypy2}
        - {os: macos-latest, python: pypy3}
        - {os: windows-latest, python: pypy2}
        - {os: windows-latest, python: pypy3}

    steps:
    - uses: actions/checkout@v2

    # Ideally we would cache the conda downloads; however, each cache is
    # over 850MB, and with 5 python versions, that would consume 4.2 of
    # the 5 GB GitHub allows.
    #
    #- name: Conda package cache
    #  uses: actions/cache@v1
    #  if: matrix.PYENV == 'conda'
    #  id: conda-cache
    #  with:
    #    path: cache/conda
    #    key: conda-v2-${{runner.os}}-${{matrix.python}}

    - name: Pip package cache
      uses: actions/cache@v1
      if: matrix.PYENV == 'pip'
      id: pip-cache
      with:
        path: cache/pip
        key: pip-v2-${{runner.os}}-${{matrix.python}}

    - name: OS package cache
      uses: actions/cache@v1
      id: os-cache
      with:
        path: cache/os
        key: pkg-v2-${{runner.os}}

    - name: TPL package download cache
      uses: actions/cache@v1
      id: download-cache
      with:
        path: cache/download
        key: download-v3-${{runner.os}}

    - name: Set up Python ${{ matrix.python }}
      if: matrix.PYENV == 'pip'
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python }}

    - name: Set up Miniconda Python ${{ matrix.python }}
      if: matrix.PYENV == 'conda'
      uses: goanpeca/setup-miniconda@v1
      with:
        auto-update-conda: true
        python-version: ${{ matrix.python }}

    # 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
      run: |
        python -m pip install --cache-dir cache/pip --upgrade pip
        pip install --cache-dir cache/pip ${PYTHON_BASE_PKGS} 
        if [[ ${{matrix.python}} == pypy  ]] || [[ ${{matrix.python}} == 2.7 ]]; then
            pip install --cache-dir cache/pip pyro
        else
            pip install --cache-dir cache/pip pyro4
        fi
        if [[ ${{matrix.python}} == 3.4 ]]; then
            pip install --cache-dir cache/pip pyyaml<=5.2
        elif [[ ${{matrix.python}} != 3.6 ]]; then
            pip install --cache-dir cache/pip pyyaml
        fi
        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
            % (sys.executable,))'

    - name: Install Python packages (conda)
      if: matrix.PYENV == 'conda'
      run: |
        mkdir -p $GITHUB_WORKSPACE/cache/conda
        conda config --set always_yes yes
        conda config --set auto_update_conda false
        conda config --prepend pkgs_dirs $GITHUB_WORKSPACE/cache/conda
        conda info
        conda config --show-sources
        conda list --show-channel-urls
        conda install -q -y -c conda-forge ${{matrix.PACKAGES}}
        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
            % (sys.executable,))'

    - name: Run Pyutilib tests
      run: |
        test.pyutilib --cat=all --cov

    - name: Process code coverage report
      env:
        CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
      run: |
        while : ; do
            curl --retry 8 -L https://codecov.io/bash -o codecov.sh
            bash codecov.sh -Z -X gcov -f coverage.xml
            if test $? == 0; then
                break
            elif test $i -ge 4; then
                exit 1
            fi
            DELAY=$(( RANDOM % 30 + 30))
            echo "Pausing $DELAY seconds before re-attempting upload"
            sleep $DELAY
        done
\ No newline at end of file
+name: GitHub CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+env:
+  PYTHONWARNINGS: ignore::UserWarning
+  PYTHON_BASE_PKGS: >
+      coverage xlrd codecov
+
+jobs:
+  pyomo-tests:
+    name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.NAME }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: [2.7, 3.5, 3.6, 3.7, 3.8, pypy2, pypy3]
+        include:
+        - os: ubuntu-latest
+          TARGET: linux
+          PYENV: pip
+
+        - os: macos-latest
+          TARGET: osx
+          PYENV: pip
+
+        - os: windows-latest
+          TARGET: win
+          PYENV: conda
+          PACKAGES: setuptools, coverage, nose, xlrd
+
+        exclude:
+        - {os: macos-latest, python: pypy2}
+        - {os: macos-latest, python: pypy3}
+        - {os: windows-latest, python: pypy2}
+        - {os: windows-latest, python: pypy3}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    # Ideally we would cache the conda downloads; however, each cache is
+    # over 850MB, and with 5 python versions, that would consume 4.2 of
+    # the 5 GB GitHub allows.
+    #
+    #- name: Conda package cache
+    #  uses: actions/cache@v1
+    #  if: matrix.PYENV == 'conda'
+    #  id: conda-cache
+    #  with:
+    #    path: cache/conda
+    #    key: conda-v2-${{runner.os}}-${{matrix.python}}
+
+    - name: Pip package cache
+      uses: actions/cache@v1
+      if: matrix.PYENV == 'pip'
+      id: pip-cache
+      with:
+        path: cache/pip
+        key: pip-v2-${{runner.os}}-${{matrix.python}}
+
+    - name: Set up Python ${{ matrix.python }}
+      if: matrix.PYENV == 'pip'
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Set up Miniconda Python ${{ matrix.python }}
+      if: matrix.PYENV == 'conda'
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python }}
+
+    # 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
+      run: |
+        python -m pip install --cache-dir cache/pip --upgrade pip
+        pip install --cache-dir cache/pip ${PYTHON_BASE_PKGS} 
+        if [[ ${{matrix.python}} == pypy  ]] || [[ ${{matrix.python}} == 2.7 ]]; then
+            pip install --cache-dir cache/pip pyro
+        else
+            pip install --cache-dir cache/pip pyro4
+        fi
+        if [[ ${{matrix.python}} == 3.4 ]]; then
+            pip install --cache-dir cache/pip pyyaml<=5.2
+        elif [[ ${{matrix.python}} != 3.6 ]]; then
+            pip install --cache-dir cache/pip pyyaml
+        fi
+        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
+            % (sys.executable,))'
+
+    - name: Install Python packages (conda)
+      if: matrix.PYENV == 'conda'
+      run: |
+        mkdir -p $GITHUB_WORKSPACE/cache/conda
+        conda config --set always_yes yes
+        conda config --set auto_update_conda false
+        conda config --prepend pkgs_dirs $GITHUB_WORKSPACE/cache/conda
+        conda info
+        conda config --show-sources
+        conda list --show-channel-urls
+        conda install -q -y -c conda-forge ${{matrix.PACKAGES}}
+        python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
+            % (sys.executable,))'
+
+    - name: Run Pyutilib tests
+      run: |
+        test.pyutilib --cat=all --cov
+
+    - name: Process code coverage report
+      env:
+        CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
+      run: |
+        while : ; do
+            curl --retry 8 -L https://codecov.io/bash -o codecov.sh
+            bash codecov.sh -Z -X gcov -f coverage.xml
+            if test $? == 0; then
+                break
+            elif test $i -ge 4; then
+                exit 1
+            fi
+            DELAY=$(( RANDOM % 30 + 30))
+            echo "Pausing $DELAY seconds before re-attempting upload"
+            sleep $DELAY
+        done

From 7b618f0fe2c2ab5f92245f68a0e08e2949bfc1ce Mon Sep 17 00:00:00 2001
From: Miranda Mundt <55767766+mrmundt@users.noreply.github.com>
Date: Thu, 25 Jun 2020 11:39:43 -0600
Subject: [PATCH 03/46] Pyutilib was not actually installed

---
 .github/workflows/pr_master_test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 26565106..7f435627 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -131,6 +131,10 @@ jobs:
         python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
             % (sys.executable,))'
 
+    - name: Install Pyutilib
+      run: |
+        python setup.py develop
+
     - name: Run Pyutilib tests
       run: |
         test.pyutilib --cat=all --cov

From 3dae484887ed52fffc48f8302660c60dc5d04216 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 25 Jun 2020 11:46:00 -0600
Subject: [PATCH 04/46] Attempting to get coverage working

---
 .github/workflows/pr_master_test.yml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 7f435627..cb39b670 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -135,6 +135,24 @@ jobs:
       run: |
         python setup.py develop
 
+    - 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 "::set-env name=COVERAGE_RCFILE::$COVERAGE_RC"
+        echo "::set-env name=COVERAGE_PROCESS_START::$COVERAGE_RC"
+        cp ${GITHUB_WORKSPACE}/.coveragerc ${COVERAGE_RC}
+        echo "data_file=${COVERAGE_BASE}age" >> ${COVERAGE_RC}
+        SITE_PACKAGES=$($PYTHON_EXE -c "from distutils.sysconfig import \
+            get_python_lib; print(get_python_lib())")
+        echo "Python site-packages: $SITE_PACKAGES"
+        echo 'import coverage; coverage.process_startup()' \
+            > ${SITE_PACKAGES}/run_coverage_at_startup.pth
+
     - name: Run Pyutilib tests
       run: |
         test.pyutilib --cat=all --cov
@@ -143,6 +161,10 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
+        coverage combine
+        coverage report -i
+        coverage xml -i
+        i=0
         while : ; do
             curl --retry 8 -L https://codecov.io/bash -o codecov.sh
             bash codecov.sh -Z -X gcov -f coverage.xml

From 7a84afce066867fa734a5eb402f98b5351cdaf21 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 25 Jun 2020 11:51:19 -0600
Subject: [PATCH 05/46] Coverage is causing issues

---
 .github/workflows/pr_master_test.yml | 35 +---------------------------
 1 file changed, 1 insertion(+), 34 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index cb39b670..294463a8 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -135,24 +135,6 @@ jobs:
       run: |
         python setup.py develop
 
-    - 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 "::set-env name=COVERAGE_RCFILE::$COVERAGE_RC"
-        echo "::set-env name=COVERAGE_PROCESS_START::$COVERAGE_RC"
-        cp ${GITHUB_WORKSPACE}/.coveragerc ${COVERAGE_RC}
-        echo "data_file=${COVERAGE_BASE}age" >> ${COVERAGE_RC}
-        SITE_PACKAGES=$($PYTHON_EXE -c "from distutils.sysconfig import \
-            get_python_lib; print(get_python_lib())")
-        echo "Python site-packages: $SITE_PACKAGES"
-        echo 'import coverage; coverage.process_startup()' \
-            > ${SITE_PACKAGES}/run_coverage_at_startup.pth
-
     - name: Run Pyutilib tests
       run: |
         test.pyutilib --cat=all --cov
@@ -161,19 +143,4 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
-        coverage combine
-        coverage report -i
-        coverage xml -i
-        i=0
-        while : ; do
-            curl --retry 8 -L https://codecov.io/bash -o codecov.sh
-            bash codecov.sh -Z -X gcov -f coverage.xml
-            if test $? == 0; then
-                break
-            elif test $i -ge 4; then
-                exit 1
-            fi
-            DELAY=$(( RANDOM % 30 + 30))
-            echo "Pausing $DELAY seconds before re-attempting upload"
-            sleep $DELAY
-        done
+        codecov

From dea076a629085cd752c24c231afcecb20e303f2d Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 25 Jun 2020 12:02:16 -0600
Subject: [PATCH 06/46] Trying upload again

---
 .github/workflows/pr_master_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 294463a8..ff653b01 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -137,10 +137,10 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
-        test.pyutilib --cat=all --cov
+        test.pyutilib --cat=all --cov -v
 
     - name: Process code coverage report
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
-        codecov
+        bash codecov.sh -Z -X gcov -f TEST-pyutilib.xml

From b19117b7382bfc2f44ff557ceb6db34184868804 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 25 Jun 2020 12:06:00 -0600
Subject: [PATCH 07/46] Was missing one step

---
 .github/workflows/pr_master_test.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index ff653b01..41460ec3 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -38,7 +38,7 @@ jobs:
         - os: windows-latest
           TARGET: win
           PYENV: conda
-          PACKAGES: setuptools, coverage, nose, xlrd
+          PACKAGES: setuptools coverage nose xlrd
 
         exclude:
         - {os: macos-latest, python: pypy2}
@@ -127,7 +127,7 @@ jobs:
         conda info
         conda config --show-sources
         conda list --show-channel-urls
-        conda install -q -y -c conda-forge ${{matrix.PACKAGES}}
+        conda install -q -y -c conda-forge -c anaconda ${{matrix.PACKAGES}}
         python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
             % (sys.executable,))'
 
@@ -143,4 +143,5 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
+        curl --retry 8 -L https://codecov.io/bash -o codecov.sh
         bash codecov.sh -Z -X gcov -f TEST-pyutilib.xml

From 05a6076e0c700bfd6f9287441e01971005b1c057 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Tue, 30 Jun 2020 11:13:57 -0600
Subject: [PATCH 08/46] Updating with better codecov retry

---
 .github/workflows/pr_master_test.yml | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 41460ec3..36d50fbf 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -143,5 +143,15 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
-        curl --retry 8 -L https://codecov.io/bash -o codecov.sh
-        bash codecov.sh -Z -X gcov -f TEST-pyutilib.xml
+        while : ; do
+            curl --retry 8 -L https://codecov.io/bash -o codecov.sh \
+                && bash codecov.sh -Z -X gcov -f coverage.xml
+            if test $? == 0; then
+                break
+            elif test $i -ge 4; then
+                exit 1
+            fi
+            DELAY=$(( RANDOM % 30 + 30))
+            echo "Pausing $DELAY seconds before re-attempting upload"
+            sleep $DELAY
+        done

From da5a7998f3d71743f7620fe2e6f97fc175ec2d97 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Tue, 30 Jun 2020 11:18:18 -0600
Subject: [PATCH 09/46] Accident - wrong XML file name

---
 .github/workflows/pr_master_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 36d50fbf..4917ccfb 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -145,7 +145,7 @@ jobs:
       run: |
         while : ; do
             curl --retry 8 -L https://codecov.io/bash -o codecov.sh \
-                && bash codecov.sh -Z -X gcov -f coverage.xml
+                && bash codecov.sh -Z -X gcov -f TEST-pyutilib.xml
             if test $? == 0; then
                 break
             elif test $i -ge 4; then

From 981cf9523dc085b6528fe6f7708538be88866e14 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Tue, 30 Jun 2020 11:40:55 -0600
Subject: [PATCH 10/46] Incorporating suggested changes

---
 .github/workflows/pr_master_test.yml | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 4917ccfb..66dec12e 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -135,17 +135,40 @@ jobs:
       run: |
         python setup.py develop
 
+    - 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 "::set-env name=COVERAGE_RCFILE::$COVERAGE_RC"
+        echo "::set-env name=COVERAGE_PROCESS_START::$COVERAGE_RC"
+        cp ${GITHUB_WORKSPACE}/.coveragerc ${COVERAGE_RC}
+        echo "data_file=${COVERAGE_BASE}age" >> ${COVERAGE_RC}
+        SITE_PACKAGES=$($PYTHON_EXE -c "from distutils.sysconfig import \
+            get_python_lib; print(get_python_lib())")
+        echo "Python site-packages: $SITE_PACKAGES"
+        echo 'import coverage; coverage.process_startup()' \
+            > ${SITE_PACKAGES}/run_coverage_at_startup.pth
+
     - name: Run Pyutilib tests
       run: |
-        test.pyutilib --cat=all --cov -v
+        test.pyutilib --cat=all -v
 
     - name: Process code coverage report
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
+        coverage combine
+        coverage report -i
+        coverage xml -i
+        i=0
+        set +e
         while : ; do
             curl --retry 8 -L https://codecov.io/bash -o codecov.sh \
-                && bash codecov.sh -Z -X gcov -f TEST-pyutilib.xml
+                && bash codecov.sh -Z -X gcov -f coverage.xml
             if test $? == 0; then
                 break
             elif test $i -ge 4; then

From 44c2b97eafa9002083d15310ee3e915fc9a391b8 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Tue, 30 Jun 2020 12:26:20 -0600
Subject: [PATCH 11/46] Changing Python call for install

---
 .github/workflows/pr_master_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 66dec12e..06c1fa75 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -133,7 +133,7 @@ jobs:
 
     - name: Install Pyutilib
       run: |
-        python setup.py develop
+        $PYTHON_EXE setup.py develop
 
     - name: Set up coverage tracking
       run: |

From 53282d9f591ad0281c338dc90904332918832dce Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Tue, 30 Jun 2020 13:21:32 -0600
Subject: [PATCH 12/46] Removing codecov

---
 .github/workflows/pr_master_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 06c1fa75..4dc8e5d3 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -15,7 +15,7 @@ defaults:
 env:
   PYTHONWARNINGS: ignore::UserWarning
   PYTHON_BASE_PKGS: >
-      coverage xlrd codecov
+      coverage xlrd
 
 jobs:
   pyomo-tests:

From bffaf979e16aec019629b8784c5a7191fc558475 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 08:47:44 -0600
Subject: [PATCH 13/46] Adding Pyomo master script changes

---
 .github/workflows/pr_master_test.yml | 41 ++++++++++++++++++++++------
 1 file changed, 33 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 4dc8e5d3..0a7339e5 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -3,10 +3,10 @@ name: GitHub CI
 on:
   push:
     branches:
-      - master
-  pull_request:
-    branches:
-      - master
+      - github_actions
+  # pull_request:
+  #   branches:
+  #     - master
 
 defaults:
   run:
@@ -69,6 +69,17 @@ jobs:
         path: cache/pip
         key: pip-v2-${{runner.os}}-${{matrix.python}}
 
+    - name: Configure curl
+      run: |
+        CURLRC="$(cat <<EOF
+           retry = 0
+           max-time = 30
+        EOF
+        )"
+        echo "$CURLRC" > ${GITHUB_WORKSPACE}/.curlrc
+        echo "$CURLRC" > ${GITHUB_WORKSPACE}/_curlrc
+        echo "::set-env name=CURL_HOME::$GITHUB_WORKSPACE"
+
     - name: Set up Python ${{ matrix.python }}
       if: matrix.PYENV == 'pip'
       uses: actions/setup-python@v1
@@ -164,14 +175,28 @@ jobs:
         coverage combine
         coverage report -i
         coverage xml -i
-        i=0
         set +e
+        # Always attempt to update the codecov script, but fall back on
+        # the previously cached script if it fails
+        CODECOV="${GITHUB_WORKSPACE}/cache/download/codecov.sh"
+        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
+        i=0
         while : ; do
-            curl --retry 8 -L https://codecov.io/bash -o codecov.sh \
-                && bash codecov.sh -Z -X gcov -f coverage.xml
+            ((i+=1))
+            echo "Uploading coverage to codecov (attempt ${i})"
+            bash $CODECOV -Z -X gcov -X s3 -f coverage.xml
             if test $? == 0; then
                 break
-            elif test $i -ge 4; then
+            elif test $i -ge 5; then
                 exit 1
             fi
             DELAY=$(( RANDOM % 30 + 30))

From 9a7b45e0943638a00875e34d9febf51feaccaaf7 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 09:15:22 -0600
Subject: [PATCH 14/46] What is in the coverage file

---
 .github/workflows/pr_master_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 0a7339e5..41c401a8 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -163,6 +163,7 @@ jobs:
         echo "Python site-packages: $SITE_PACKAGES"
         echo 'import coverage; coverage.process_startup()' \
             > ${SITE_PACKAGES}/run_coverage_at_startup.pth
+        cat ${COVERAGE_RC}
 
     - name: Run Pyutilib tests
       run: |

From a6e875c7039bc5b58e0b92e929199e916a3bfff1 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 09:17:02 -0600
Subject: [PATCH 15/46] Adding one more line

---
 .github/workflows/pr_master_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 41c401a8..8c36bbab 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -157,6 +157,7 @@ jobs:
         echo "::set-env name=COVERAGE_RCFILE::$COVERAGE_RC"
         echo "::set-env name=COVERAGE_PROCESS_START::$COVERAGE_RC"
         cp ${GITHUB_WORKSPACE}/.coveragerc ${COVERAGE_RC}
+        echo "[run]" >> ${COVERAGE_RC}
         echo "data_file=${COVERAGE_BASE}age" >> ${COVERAGE_RC}
         SITE_PACKAGES=$($PYTHON_EXE -c "from distutils.sysconfig import \
             get_python_lib; print(get_python_lib())")

From e2995eac3da48d2a95c257bca858611acaf5df6f Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 09:23:16 -0600
Subject: [PATCH 16/46] What's going on with the coverage

---
 .github/workflows/pr_master_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 8c36bbab..e01982b7 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -174,6 +174,7 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
+        ls
         coverage combine
         coverage report -i
         coverage xml -i

From a17c65a8aad1cd167468995b6bdfcfc5d7d93345 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 09:40:57 -0600
Subject: [PATCH 17/46] Adding cache

---
 .github/workflows/pr_master_test.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index e01982b7..0042be80 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -69,6 +69,13 @@ jobs:
         path: cache/pip
         key: pip-v2-${{runner.os}}-${{matrix.python}}
 
+    - name: TPL package download cache
+      uses: actions/cache@v1
+      id: download-cache
+      with:
+        path: cache/download
+        key: download-v4-${{runner.os}}
+
     - name: Configure curl
       run: |
         CURLRC="$(cat <<EOF
@@ -174,7 +181,7 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
-        ls
+        ls -la
         coverage combine
         coverage report -i
         coverage xml -i

From 603b75cc0b7c960fc8e47d5f9d5860b94fd6dc5c Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 09:58:57 -0600
Subject: [PATCH 18/46] Trying again:

---
 .github/workflows/pr_master_test.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 0042be80..3ceef288 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -69,7 +69,7 @@ jobs:
         path: cache/pip
         key: pip-v2-${{runner.os}}-${{matrix.python}}
 
-    - name: TPL package download cache
+    - name: Download cache
       uses: actions/cache@v1
       id: download-cache
       with:
@@ -182,16 +182,17 @@ jobs:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
         ls -la
-        coverage combine
+        ls -la ${GITHUB_WORKSPACE}/cache
         coverage report -i
         coverage xml -i
+        ls -la
         set +e
         # Always attempt to update the codecov script, but fall back on
         # the previously cached script if it fails
         CODECOV="${GITHUB_WORKSPACE}/cache/download/codecov.sh"
         for i in `seq 3`; do
             echo "Downloading current codecov script (attempt ${i})"
-            curl -L https://codecov.io/bash -o $CODECOV
+            curl -L https://codecov.io/bash -O $CODECOV
             if test $? == 0; then
                 break
             fi

From 53c5544dc44da1e19232f016ba4a0fb334b56cd0 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 10:56:05 -0600
Subject: [PATCH 19/46] Trying again:

With changes
---
 .github/workflows/pr_master_test.yml | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 3ceef288..7b3373ce 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -49,20 +49,8 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    # Ideally we would cache the conda downloads; however, each cache is
-    # over 850MB, and with 5 python versions, that would consume 4.2 of
-    # the 5 GB GitHub allows.
-    #
-    #- name: Conda package cache
-    #  uses: actions/cache@v1
-    #  if: matrix.PYENV == 'conda'
-    #  id: conda-cache
-    #  with:
-    #    path: cache/conda
-    #    key: conda-v2-${{runner.os}}-${{matrix.python}}
-
     - name: Pip package cache
-      uses: actions/cache@v1
+      uses: actions/cache@v2
       if: matrix.PYENV == 'pip'
       id: pip-cache
       with:
@@ -70,7 +58,7 @@ jobs:
         key: pip-v2-${{runner.os}}-${{matrix.python}}
 
     - name: Download cache
-      uses: actions/cache@v1
+      uses: actions/cache@v2
       id: download-cache
       with:
         path: cache/download
@@ -181,8 +169,6 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
-        ls -la
-        ls -la ${GITHUB_WORKSPACE}/cache
         coverage report -i
         coverage xml -i
         ls -la
@@ -192,7 +178,7 @@ jobs:
         CODECOV="${GITHUB_WORKSPACE}/cache/download/codecov.sh"
         for i in `seq 3`; do
             echo "Downloading current codecov script (attempt ${i})"
-            curl -L https://codecov.io/bash -O $CODECOV
+            curl -L https://codecov.io/bash -o $CODECOV
             if test $? == 0; then
                 break
             fi
@@ -200,6 +186,7 @@ jobs:
             echo "Pausing $DELAY seconds before re-attempting download"
             sleep $DELAY
         done
+        ls -la ${GITHUB_WORKSPACE}/cache/
         i=0
         while : ; do
             ((i+=1))

From 89700454876083915679478668b735fa1a80ccd0 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 11:07:59 -0600
Subject: [PATCH 20/46] Make directory if it doesn't exist

---
 .github/workflows/pr_master_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 7b3373ce..1657f8d6 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -169,6 +169,7 @@ jobs:
       env:
         CODECOV_NAME: ${{matrix.TARGET}}/${{matrix.python}}${{matrix.NAME}}
       run: |
+        [ ! -d ${GITHUB_WORKSPACE}/cache/download ] && mkdir -pv ${GITHUB_WORKSPACE}/cache/download
         coverage report -i
         coverage xml -i
         ls -la

From 8748956f67fe770ffba565d7463004efed4281f0 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:16:39 -0600
Subject: [PATCH 21/46] Getting CWD for failing tests

---
 doc/workflow/examples/driver1.py | 3 +++
 doc/workflow/examples/driver2.py | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index 8651b07d..d1dfa8f1 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,3 +1,6 @@
+import os
+print(os.getcwd())
+
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index ee9fd62f..f46d3faf 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,3 +1,6 @@
+import os
+print(os.getcwd())
+
 import pyutilib.workflow
 import tasks_yz
 

From 205db586cd546639f707df06a26102a08e2018f5 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:21:46 -0600
Subject: [PATCH 22/46] Show me the PYTHONPATH

---
 .github/workflows/pr_master_test.yml | 2 +-
 doc/workflow/examples/driver1.py     | 1 +
 doc/workflow/examples/driver2.py     | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 1657f8d6..2d5dba11 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -163,7 +163,7 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
-        test.pyutilib --cat=all -v
+        test.pyutilib --cat=all -v -s
 
     - name: Process code coverage report
       env:
diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index d1dfa8f1..3f8d9902 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,5 +1,6 @@
 import os
 print(os.getcwd())
+print(os.environ['PYTHONPATH'].split(os.pathsep))
 
 import pyutilib.workflow
 import tasks_yz
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index f46d3faf..53237154 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,5 +1,6 @@
 import os
 print(os.getcwd())
+print(os.environ['PYTHONPATH'].split(os.pathsep))
 
 import pyutilib.workflow
 import tasks_yz

From 18c368a4fd5823b32d8122b1a77b7d460a5c842f Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:30:34 -0600
Subject: [PATCH 23/46] -s doesn't exist

---
 .github/workflows/pr_master_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 2d5dba11..1657f8d6 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -163,7 +163,7 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
-        test.pyutilib --cat=all -v -s
+        test.pyutilib --cat=all -v
 
     - name: Process code coverage report
       env:

From 698b0d3b09445f007654b2df31250190dc23f198 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:35:18 -0600
Subject: [PATCH 24/46] PYTHONPATH is not defined

---
 doc/workflow/examples/driver1.py | 4 +++-
 doc/workflow/examples/driver2.py | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index 3f8d9902..e31ff24d 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,6 +1,8 @@
 import os
 print(os.getcwd())
-print(os.environ['PYTHONPATH'].split(os.pathsep))
+import sys
+for p in sys.path:
+    print(p)
 
 import pyutilib.workflow
 import tasks_yz
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 53237154..2775ae12 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,6 +1,8 @@
 import os
 print(os.getcwd())
-print(os.environ['PYTHONPATH'].split(os.pathsep))
+import sys
+for p in sys.path:
+    print(p)
 
 import pyutilib.workflow
 import tasks_yz

From d2943978ae0b4ba7158dc367000f868fe561a4a3 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:40:27 -0600
Subject: [PATCH 25/46] Different

---
 doc/workflow/examples/driver1.py | 3 +--
 doc/workflow/examples/driver2.py | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index e31ff24d..d90c7330 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,5 +1,4 @@
-import os
-print(os.getcwd())
+
 import sys
 for p in sys.path:
     print(p)
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 2775ae12..a1f834ae 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,5 +1,4 @@
-import os
-print(os.getcwd())
+
 import sys
 for p in sys.path:
     print(p)

From 9ddc2a2390ae941316978b334aee48cdaef63309 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:48:31 -0600
Subject: [PATCH 26/46] Reverting changes

---
 doc/workflow/examples/driver1.py | 4 ----
 doc/workflow/examples/driver2.py | 4 ----
 2 files changed, 8 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index d90c7330..da817911 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,8 +1,4 @@
 
-import sys
-for p in sys.path:
-    print(p)
-
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index a1f834ae..87662ab7 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,8 +1,4 @@
 
-import sys
-for p in sys.path:
-    print(p)
-
 import pyutilib.workflow
 import tasks_yz
 

From 3a2fdb2f6f5c6f3e66a277b9091d30e0d7b7d1a1 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 13:59:46 -0600
Subject: [PATCH 27/46] Finding PATH

---
 doc/workflow/examples/driver1.py | 3 ++-
 doc/workflow/examples/driver2.py | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index da817911..5b6a0163 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,4 +1,5 @@
-
+import os
+print(os.environ(['PATH']))
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 87662ab7..13c8ecbe 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,4 +1,5 @@
-
+import os
+print(os.environ(['PATH']))
 import pyutilib.workflow
 import tasks_yz
 

From eced783c60e7d363ef425575e317e8533d46f399 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 14:01:23 -0600
Subject: [PATCH 28/46] Syntax:

---
 doc/workflow/examples/driver1.py | 2 +-
 doc/workflow/examples/driver2.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index 5b6a0163..066e5dd1 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,5 +1,5 @@
 import os
-print(os.environ(['PATH']))
+print(os.environ['PATH'])
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 13c8ecbe..1f095d5b 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,5 +1,5 @@
 import os
-print(os.environ(['PATH']))
+print(os.environ['PATH'])
 import pyutilib.workflow
 import tasks_yz
 

From 5c043d9530130be3cc5f6a6d2a7ddb4178b49961 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 14:05:53 -0600
Subject: [PATCH 29/46] Python versions

---
 .github/workflows/pr_master_test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 1657f8d6..b240ac57 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -163,6 +163,10 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
+        which python
+        which $PYTHON_EXE
+        echo ""
+        echo "###########################################"
         test.pyutilib --cat=all -v
 
     - name: Process code coverage report

From 4c56c9ff6c8769d48fba231921213537ab13ded0 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 14:21:19 -0600
Subject: [PATCH 30/46] Rewriting the driver scripts

---
 doc/workflow/examples/driver1.py    | 3 +--
 doc/workflow/examples/driver2.py    | 3 +--
 doc/workflow/examples/driver_1.sh   | 2 +-
 doc/workflow/examples/driver_2.sh   | 2 +-
 doc/workflow/examples/driver_3.sh   | 2 +-
 pyutilib/workflow/tests/test_doc.py | 2 +-
 6 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index 066e5dd1..da817911 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,5 +1,4 @@
-import os
-print(os.environ['PATH'])
+
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 1f095d5b..87662ab7 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,5 +1,4 @@
-import os
-print(os.environ['PATH'])
+
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver_1.sh b/doc/workflow/examples/driver_1.sh
index a18d26a5..6af2f102 100755
--- a/doc/workflow/examples/driver_1.sh
+++ b/doc/workflow/examples/driver_1.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-python driver1.py TaskZ --x=3 --y=4
+$PYTHON_EXE driver1.py TaskZ --x=3 --y=4
 # @:code
diff --git a/doc/workflow/examples/driver_2.sh b/doc/workflow/examples/driver_2.sh
index 84b1d83b..a2a7d517 100755
--- a/doc/workflow/examples/driver_2.sh
+++ b/doc/workflow/examples/driver_2.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-python driver2.py TaskZ --help
+$PYTHON_EXE driver2.py TaskZ --help
 # @:code
diff --git a/doc/workflow/examples/driver_3.sh b/doc/workflow/examples/driver_3.sh
index 67d72079..1b0ed0a4 100755
--- a/doc/workflow/examples/driver_3.sh
+++ b/doc/workflow/examples/driver_3.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-python driver2.py --help
+$PYTHON_EXE driver2.py --help
 # @:code
diff --git a/pyutilib/workflow/tests/test_doc.py b/pyutilib/workflow/tests/test_doc.py
index 8767e4e8..3e58267e 100644
--- a/pyutilib/workflow/tests/test_doc.py
+++ b/pyutilib/workflow/tests/test_doc.py
@@ -1,7 +1,7 @@
 # Imports
 import sys
 import os
-from os.path import dirname, abspath, abspath
+from os.path import dirname, abspath
 
 import pyutilib.th as unittest
 

From 8b4be2e9bcac75328a71281047fdb0d1b9bd0a41 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 14:24:36 -0600
Subject: [PATCH 31/46] Now Win is broken

---
 .github/workflows/pr_master_test.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index b240ac57..1657f8d6 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -163,10 +163,6 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
-        which python
-        which $PYTHON_EXE
-        echo ""
-        echo "###########################################"
         test.pyutilib --cat=all -v
 
     - name: Process code coverage report

From 5fc6d305a92f94f7854910b8a5b24fa21848fa34 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 14:42:31 -0600
Subject: [PATCH 32/46] Finalizing

---
 .github/workflows/pr_master_test.yml | 8 ++++----
 doc/workflow/examples/driver1.py     | 1 -
 doc/workflow/examples/driver2.py     | 1 -
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 1657f8d6..9262533f 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -3,10 +3,10 @@ name: GitHub CI
 on:
   push:
     branches:
-      - github_actions
-  # pull_request:
-  #   branches:
-  #     - master
+      - master
+  pull_request:
+    branches:
+      - master
 
 defaults:
   run:
diff --git a/doc/workflow/examples/driver1.py b/doc/workflow/examples/driver1.py
index da817911..8651b07d 100644
--- a/doc/workflow/examples/driver1.py
+++ b/doc/workflow/examples/driver1.py
@@ -1,4 +1,3 @@
-
 import pyutilib.workflow
 import tasks_yz
 
diff --git a/doc/workflow/examples/driver2.py b/doc/workflow/examples/driver2.py
index 87662ab7..ee9fd62f 100644
--- a/doc/workflow/examples/driver2.py
+++ b/doc/workflow/examples/driver2.py
@@ -1,4 +1,3 @@
-
 import pyutilib.workflow
 import tasks_yz
 

From 70cd2bfe95fedf1217775a9a863db1266e71efe0 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 15:00:10 -0600
Subject: [PATCH 33/46] Fix the path before the test runs

---
 doc/workflow/examples/driver_1.sh     |  2 +-
 doc/workflow/examples/driver_2.sh     |  2 +-
 doc/workflow/examples/driver_3.sh     |  2 +-
 doc/workflow/examples/test_example.py | 12 ++++++++++--
 4 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/doc/workflow/examples/driver_1.sh b/doc/workflow/examples/driver_1.sh
index 6af2f102..91777a08 100755
--- a/doc/workflow/examples/driver_1.sh
+++ b/doc/workflow/examples/driver_1.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-$PYTHON_EXE driver1.py TaskZ --x=3 --y=4
+python  driver1.py TaskZ --x=3 --y=4
 # @:code
diff --git a/doc/workflow/examples/driver_2.sh b/doc/workflow/examples/driver_2.sh
index a2a7d517..84b1d83b 100755
--- a/doc/workflow/examples/driver_2.sh
+++ b/doc/workflow/examples/driver_2.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-$PYTHON_EXE driver2.py TaskZ --help
+python driver2.py TaskZ --help
 # @:code
diff --git a/doc/workflow/examples/driver_3.sh b/doc/workflow/examples/driver_3.sh
index 1b0ed0a4..67d72079 100755
--- a/doc/workflow/examples/driver_3.sh
+++ b/doc/workflow/examples/driver_3.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-$PYTHON_EXE driver2.py --help
+python driver2.py --help
 # @:code
diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index 18b7ee16..356beb6f 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -11,8 +11,16 @@
 def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
-# Declare an empty TestCase class
-class Test(unittest.TestCase): pass
+class Test(unittest.TestCase):
+
+    def setUp(self):
+        self._path = os.environ['PATH']
+        os.environ['PATH'] = os.pathsep.join(
+            os.path.dirname(sys.executable), os.environ['PATH']
+        )
+
+    def tearDown(self):
+        os.environ['PATH'] = self._path
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):

From 35b248171c06d427c7c0ae0e2ade3d789b79cba5 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 15:04:23 -0600
Subject: [PATCH 34/46] Changing to join

---
 doc/workflow/examples/test_example.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index 356beb6f..e2a450a8 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -15,7 +15,7 @@ class Test(unittest.TestCase):
 
     def setUp(self):
         self._path = os.environ['PATH']
-        os.environ['PATH'] = os.pathsep.join(
+        os.environ['PATH'] = os.path.join(
             os.path.dirname(sys.executable), os.environ['PATH']
         )
 

From 4ef842fbf9d242ad539fdfe5f54dfb1529e69aff Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 15:09:04 -0600
Subject: [PATCH 35/46] Trying to prepend path with sys executable

---
 doc/workflow/examples/test_example.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index e2a450a8..6a0e009a 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -5,6 +5,8 @@
 from os.path import dirname, abspath, abspath, basename
 import sys
 
+sys.path.insert(0, sys.executable)
+
 currdir = dirname(abspath(__file__))+os.sep
 datadir = currdir
 
@@ -12,15 +14,7 @@ def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
 class Test(unittest.TestCase):
-
-    def setUp(self):
-        self._path = os.environ['PATH']
-        os.environ['PATH'] = os.path.join(
-            os.path.dirname(sys.executable), os.environ['PATH']
-        )
-
-    def tearDown(self):
-        os.environ['PATH'] = self._path
+    pass
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):

From c90741fcce0d6c8df2a064f7e9c9061134b7a1a1 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Wed, 1 Jul 2020 15:14:11 -0600
Subject: [PATCH 36/46] Trying a different way of inserting to sys.path

---
 doc/workflow/examples/test_example.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index 6a0e009a..7cbe76e0 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -5,8 +5,6 @@
 from os.path import dirname, abspath, abspath, basename
 import sys
 
-sys.path.insert(0, sys.executable)
-
 currdir = dirname(abspath(__file__))+os.sep
 datadir = currdir
 
@@ -14,7 +12,13 @@ def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
 class Test(unittest.TestCase):
-    pass
+
+    def setUp(self):
+        self._path = os.environ['PATH']
+        sys.path.insert(0, sys.executable)
+
+    def tearDown(self):
+        os.environ['PATH'] = self._path
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):

From 5d16f87a839b68ceb7ec837e80e42d8b615c2ef4 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 07:59:39 -0600
Subject: [PATCH 37/46] Trying a different way to invoke sys.path changes

---
 doc/workflow/examples/test_example.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index 7cbe76e0..eb70b453 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -12,13 +12,7 @@ def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
 class Test(unittest.TestCase):
-
-    def setUp(self):
-        self._path = os.environ['PATH']
-        sys.path.insert(0, sys.executable)
-
-    def tearDown(self):
-        os.environ['PATH'] = self._path
+    pass
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):
@@ -42,4 +36,9 @@ def tearDown(self):
 
 # Execute the tests
 if __name__ == '__main__':
+    _path = os.environ['PATH']
+    sys.path.insert(0, sys.executable)
+
     unittest.main()
+
+    os.environ['PATH'] = _path

From c48ef0d8864ba5d6847e5541af0ca3fa5f6d226d Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 08:28:54 -0600
Subject: [PATCH 38/46] Correcting the pathsep

---
 doc/workflow/examples/test_example.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index eb70b453..8997d244 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -12,7 +12,15 @@ def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
 class Test(unittest.TestCase):
-    pass
+
+    def setUp(self):
+        self._path = os.environ['PATH']
+        os.environ['PATH'] = os.pathsep.join([
+            os.path.dirname(sys.executable), os.environ['PATH']
+        ])
+
+    def tearDown(self):
+        os.environ['PATH'] = self._path
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):
@@ -36,9 +44,5 @@ class Test(unittest.TestCase):
 
 # Execute the tests
 if __name__ == '__main__':
-    _path = os.environ['PATH']
-    sys.path.insert(0, sys.executable)
 
     unittest.main()
-
-    os.environ['PATH'] = _path

From 8e61b3b00052d239f32b2a5fa1e795c4fa256d4c Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 08:52:59 -0600
Subject: [PATCH 39/46] Changing path in GA workflow JUST for Mac

---
 .github/workflows/pr_master_test.yml  |  6 ++++++
 doc/workflow/examples/test_example.py | 10 +---------
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 9262533f..2a347737 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -137,6 +137,12 @@ jobs:
         python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
             % (sys.executable,))'
 
+    - name: Correct MacOS path
+      if: matrix.TARGET == 'osx'
+      run: |
+        PYTHON_DIR=`dirname $PYTHON_EXE`
+        echo "::set-env PATH::$PYTHON_DIR:$PATH"
+
     - name: Install Pyutilib
       run: |
         $PYTHON_EXE setup.py develop
diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index 8997d244..c3281a68 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -12,15 +12,7 @@ def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
 class Test(unittest.TestCase):
-
-    def setUp(self):
-        self._path = os.environ['PATH']
-        os.environ['PATH'] = os.pathsep.join([
-            os.path.dirname(sys.executable), os.environ['PATH']
-        ])
-
-    def tearDown(self):
-        os.environ['PATH'] = self._path
+    pass
 
 # Find all example*.py files, and use them to define baseline tests
 for file in glob.glob(datadir+'example*.py'):

From ddf00fdd545072eb5b03ba991b01009f6daeff9e Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 08:54:40 -0600
Subject: [PATCH 40/46] name = PATH

---
 .github/workflows/pr_master_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 2a347737..dab02032 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -141,7 +141,7 @@ jobs:
       if: matrix.TARGET == 'osx'
       run: |
         PYTHON_DIR=`dirname $PYTHON_EXE`
-        echo "::set-env PATH::$PYTHON_DIR:$PATH"
+        echo "::set-env name=PATH::$PYTHON_DIR:$PATH"
 
     - name: Install Pyutilib
       run: |

From 000f9266df855faff47fd599fba81cbc3e16492a Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 08:56:52 -0600
Subject: [PATCH 41/46] What is going on with the PATH

---
 .github/workflows/pr_master_test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index dab02032..2123d2dc 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -141,7 +141,9 @@ jobs:
       if: matrix.TARGET == 'osx'
       run: |
         PYTHON_DIR=`dirname $PYTHON_EXE`
+        echo $PYTHON_DIR
         echo "::set-env name=PATH::$PYTHON_DIR:$PATH"
+        which python
 
     - name: Install Pyutilib
       run: |

From 638abdbb0f8c768bdf7206762e77916aa3a7446d Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 08:59:12 -0600
Subject: [PATCH 42/46] Let's try again

---
 .github/workflows/pr_master_test.yml  | 4 ++--
 doc/workflow/examples/test_example.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 2123d2dc..10e27cae 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -141,12 +141,12 @@ jobs:
       if: matrix.TARGET == 'osx'
       run: |
         PYTHON_DIR=`dirname $PYTHON_EXE`
-        echo $PYTHON_DIR
         echo "::set-env name=PATH::$PYTHON_DIR:$PATH"
-        which python
 
     - name: Install Pyutilib
       run: |
+        echo $PATH
+        which python
         $PYTHON_EXE setup.py develop
 
     - name: Set up coverage tracking
diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index c3281a68..e03a2186 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -32,7 +32,7 @@ class Test(unittest.TestCase):
     for file in glob.glob(datadir+'*.sh'):
         bname = basename(file)
         name=bname.split('.')[0]
-        Test.add_baseline_test(cmd='cd %s; /usr/bin/env sh %s' % (datadir, file),  baseline=datadir+name+'.txt', name=name, filter=filter)
+        Test.add_baseline_test(cmd='cd %s; /usr/bin/env bash %s' % (datadir, file),  baseline=datadir+name+'.txt', name=name, filter=filter)
 
 # Execute the tests
 if __name__ == '__main__':

From c9edff0c9a786ebff8829446fe536165754aebb4 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 09:06:40 -0600
Subject: [PATCH 43/46] What python is being accessed at the beginning of tests

---
 .github/workflows/pr_master_test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 10e27cae..e7267daa 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -145,8 +145,6 @@ jobs:
 
     - name: Install Pyutilib
       run: |
-        echo $PATH
-        which python
         $PYTHON_EXE setup.py develop
 
     - name: Set up coverage tracking
@@ -171,6 +169,7 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
+        which python
         test.pyutilib --cat=all -v
 
     - name: Process code coverage report

From 89050ce1f73438fcc8b903201233cf088ebf3c8d Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 09:13:51 -0600
Subject: [PATCH 44/46] Moving the prepending

---
 .github/workflows/pr_master_test.yml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index e7267daa..53666c40 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -137,12 +137,6 @@ jobs:
         python -c 'import sys; print("::set-env name=PYTHON_EXE::%s" \
             % (sys.executable,))'
 
-    - name: Correct MacOS path
-      if: matrix.TARGET == 'osx'
-      run: |
-        PYTHON_DIR=`dirname $PYTHON_EXE`
-        echo "::set-env name=PATH::$PYTHON_DIR:$PATH"
-
     - name: Install Pyutilib
       run: |
         $PYTHON_EXE setup.py develop
@@ -169,7 +163,12 @@ jobs:
 
     - name: Run Pyutilib tests
       run: |
-        which python
+        if [ ${{matrix.TARGET}} == 'osx' ]; then
+          which python
+          PYTHON_DIR=`dirname $PYTHON_EXE`
+          export PATH=$PYTHON_DIR:$PATH
+          which python
+        fi
         test.pyutilib --cat=all -v
 
     - name: Process code coverage report

From 3bcdf8c02d7b6f35d72874ab3c94d804164dcfc8 Mon Sep 17 00:00:00 2001
From: Miranda Mundt <mmundt@sandia.gov>
Date: Thu, 2 Jul 2020 09:16:33 -0600
Subject: [PATCH 45/46] Finalizing for real

---
 .github/workflows/pr_master_test.yml  | 2 --
 doc/workflow/examples/test_example.py | 1 +
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pr_master_test.yml b/.github/workflows/pr_master_test.yml
index 53666c40..d6211b09 100644
--- a/.github/workflows/pr_master_test.yml
+++ b/.github/workflows/pr_master_test.yml
@@ -164,10 +164,8 @@ jobs:
     - name: Run Pyutilib tests
       run: |
         if [ ${{matrix.TARGET}} == 'osx' ]; then
-          which python
           PYTHON_DIR=`dirname $PYTHON_EXE`
           export PATH=$PYTHON_DIR:$PATH
-          which python
         fi
         test.pyutilib --cat=all -v
 
diff --git a/doc/workflow/examples/test_example.py b/doc/workflow/examples/test_example.py
index e03a2186..a6834ff7 100644
--- a/doc/workflow/examples/test_example.py
+++ b/doc/workflow/examples/test_example.py
@@ -11,6 +11,7 @@
 def filter(line):
     return 'Running' in line or "IGNORE" in line or line.startswith('usage:') or 'Sub-commands' in line
 
+# Declare an empty TestCase class
 class Test(unittest.TestCase):
     pass
 

From 3e0139c012028eb5611a70156105073f99622a2e Mon Sep 17 00:00:00 2001
From: John Siirola <jsiirola@users.noreply.github.com>
Date: Thu, 2 Jul 2020 09:22:03 -0600
Subject: [PATCH 46/46] Removing whitespace added during development

---
 doc/workflow/examples/driver_1.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/workflow/examples/driver_1.sh b/doc/workflow/examples/driver_1.sh
index 91777a08..a18d26a5 100755
--- a/doc/workflow/examples/driver_1.sh
+++ b/doc/workflow/examples/driver_1.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
 # @code:
-python  driver1.py TaskZ --x=3 --y=4
+python driver1.py TaskZ --x=3 --y=4
 # @:code