From bf347986f8faa1529ee123beda70ae39fa04a9a2 Mon Sep 17 00:00:00 2001
From: "Stefan K. Seritan" <sserita@sandia.gov>
Date: Thu, 11 Jan 2024 13:41:38 -0800
Subject: [PATCH 1/4] Adjust main unit tests runners.

Only run MacOS tests on beta/master,
and only run lowest/highest Python versions on bugfix/feature branches.
Should address #387.
---
 .github/workflows/main-mac.yml     |  77 ++++++++++++++++++++++
 .github/workflows/main-minimal.yml | 101 +++++++++++++++++++++++++++++
 .github/workflows/main.yml         |   8 +--
 3 files changed, 181 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/main-mac.yml
 create mode 100644 .github/workflows/main-minimal.yml

diff --git a/.github/workflows/main-mac.yml b/.github/workflows/main-mac.yml
new file mode 100644
index 000000000..44a2a4dca
--- /dev/null
+++ b/.github/workflows/main-mac.yml
@@ -0,0 +1,77 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build and run tests (MacOS only, all Python versions)
+
+on:
+  push:
+    # Mac runners are expensive and oversubscribed. Only run on beta and master
+    branches: [ "beta", "master" ]
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+env:
+  SKIP_DEAP: 1
+
+jobs:
+  build: # Main build + unit test check
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-11]
+        python-version: [3.8, 3.9, '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up installation environment (Ubuntu or Windows)
+      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      run: |
+        ./.github/ci-scripts/before_install.sh
+    - name: Set up installation environment (MacOS)
+      if: ${{matrix.os == 'macos-11'}}
+      run: |
+        ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip packages
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install flake8
+        python -m pip install -e .[testing]
+        python setup.py build_ext --inplace
+        # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
+    - name: Lint with flake8
+      if: ${{matrix.os != 'windows-2019'}}
+      run: |
+        # Critical errors, exit on failure
+        flake8 . --count --show-source --statistics --config=.flake8-critical
+        # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
+        flake8 . --exit-zero --statistics
+    - name: Run unit tests ubuntu
+      if: ${{matrix.os == 'ubuntu-20.04'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    - name: Run unit tests windows  
+      if: ${{matrix.os == 'windows-2019'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    - name: Run unit tests MacOS  
+      if: ${{matrix.os == 'macos-11'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+
+
+
+
diff --git a/.github/workflows/main-minimal.yml b/.github/workflows/main-minimal.yml
new file mode 100644
index 000000000..752d41982
--- /dev/null
+++ b/.github/workflows/main-minimal.yml
@@ -0,0 +1,101 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build and run tests (no MacOS, low/high Python versions only)
+
+on:
+  push:
+    # Intended to be fast checks on non-main branches
+    branches-ignore: [ "beta", "develop", "master" ]
+  # Hacky way to only run pull requests from forked repositories (assumes : is not used in branch names unless forked)
+  # https://github.community/t/how-to-trigger-an-action-on-push-or-pull-request-but-not-both/16662/10
+  pull_request:
+    branches: [ "**:**" ]
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+env:
+  SKIP_DEAP: 1
+
+jobs:
+  build: # Main build + unit test check
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019]
+        python-version: [3.8,'3.11']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up installation environment (Ubuntu or Windows)
+      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      run: |
+        ./.github/ci-scripts/before_install.sh
+    - name: Set up installation environment (MacOS)
+      if: ${{matrix.os == 'macos-11'}}
+      run: |
+        ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip packages
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install flake8
+        python -m pip install -e .[testing]
+        python setup.py build_ext --inplace
+        # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
+    - name: Lint with flake8
+      if: ${{matrix.os != 'windows-2019'}}
+      run: |
+        # Critical errors, exit on failure
+        flake8 . --count --show-source --statistics --config=.flake8-critical
+        # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
+        flake8 . --exit-zero --statistics
+    - name: Run unit tests ubuntu
+      if: ${{matrix.os == 'ubuntu-20.04'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    - name: Run unit tests windows  
+      if: ${{matrix.os == 'windows-2019'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    - name: Run unit tests MacOS  
+      if: ${{matrix.os == 'macos-11'}}
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    
+  
+  push: # Push to stable "beta" branch on successful build
+
+    runs-on: ubuntu-20.04
+
+    # Only run on "develop" branch if tests pass
+    needs: build
+    if: github.ref == 'refs/heads/develop' && github.event_name == 'push'
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        token: ${{ secrets.PYGSTI_TOKEN }}
+    - name: Merge changes to beta branch
+      run: |
+        git config --global user.name 'PyGSTi'
+        git config --global user.email 'pygsti@noreply.github.com'
+        git checkout beta
+        git merge --ff-only ${GITHUB_SHA} && git push origin beta
+
+
+
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f5361f6c8..c155732ce 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,13 +1,11 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Build and run tests
+name: Build and run tests (no MacOS, all Python versions)
 
 on:
   push:
-    branches-ignore: [ "beta" ]
-  # Hacky way to only run pull requests from forked repositories (assumes : is not used in branch names unless forked)
-  # https://github.community/t/how-to-trigger-an-action-on-push-or-pull-request-but-not-both/16662/10
+    branches: [ "develop", "master" ]
   pull_request:
     branches: [ "**:**" ]
   # Allow running manually from Actions tab
@@ -22,7 +20,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-20.04, windows-2019]
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:

From 708f0c522d42657bfba778099e4b1b2a127fe0d9 Mon Sep 17 00:00:00 2001
From: "Stefan K. Seritan" <sserita@sandia.gov>
Date: Thu, 11 Jan 2024 13:48:09 -0800
Subject: [PATCH 2/4] Update to latest runners.

---
 .github/workflows/extras.yml       | 12 ++++++------
 .github/workflows/main-mac.yml     | 20 ++------------------
 .github/workflows/main-minimal.yml | 21 ++++++---------------
 .github/workflows/main.yml         | 21 ++++++---------------
 .github/workflows/notebook.yml     | 12 ++++++------
 5 files changed, 26 insertions(+), 60 deletions(-)

diff --git a/.github/workflows/extras.yml b/.github/workflows/extras.yml
index 1e7de0c29..6395b642c 100644
--- a/.github/workflows/extras.yml
+++ b/.github/workflows/extras.yml
@@ -21,17 +21,17 @@ jobs:
     strategy:
       fail-fast: false # Finish all tests even if one fails
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.8, 3.9, '3.10', '3.11']
         
     steps:
     - uses: actions/checkout@v2
     - name: Set up installation environment (Ubuntu or Windows)
-      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
     - name: Set up installation environment (MacOS)
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'macos-latest'}}
       run: |
         ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
@@ -51,17 +51,17 @@ jobs:
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
     - name: Run test_packages Ubuntu
-      if: ${{matrix.os == 'ubuntu-20.04'}}
+      if: ${{matrix.os == 'ubuntu-latest'}}
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
         python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages
     - name: Run test_packages Windows
-      if: ${{matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'windows-latest'}}
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
         python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages
     - name: Run test_packages MacOS
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'macos-latest'}}
 
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
diff --git a/.github/workflows/main-mac.yml b/.github/workflows/main-mac.yml
index 44a2a4dca..309827b7a 100644
--- a/.github/workflows/main-mac.yml
+++ b/.github/workflows/main-mac.yml
@@ -19,17 +19,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-11]
+        os: [macos-latest]
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up installation environment (Ubuntu or Windows)
-      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
-      run: |
-        ./.github/ci-scripts/before_install.sh
     - name: Set up installation environment (MacOS)
-      if: ${{matrix.os == 'macos-11'}}
       run: |
         ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,24 +45,13 @@ jobs:
         python setup.py build_ext --inplace
         # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
-      if: ${{matrix.os != 'windows-2019'}}
       run: |
         # Critical errors, exit on failure
         flake8 . --count --show-source --statistics --config=.flake8-critical
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
-    - name: Run unit tests ubuntu
-      if: ${{matrix.os == 'ubuntu-20.04'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    - name: Run unit tests windows  
-      if: ${{matrix.os == 'windows-2019'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
     - name: Run unit tests MacOS  
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'macos-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
diff --git a/.github/workflows/main-minimal.yml b/.github/workflows/main-minimal.yml
index 752d41982..242443ad3 100644
--- a/.github/workflows/main-minimal.yml
+++ b/.github/workflows/main-minimal.yml
@@ -23,19 +23,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019]
+        os: [ubuntu-latest, windows-latest]
         python-version: [3.8,'3.11']
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up installation environment (Ubuntu or Windows)
-      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
-    - name: Set up installation environment (MacOS)
-      if: ${{matrix.os == 'macos-11'}}
-      run: |
-        ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
@@ -54,24 +50,19 @@ jobs:
         python setup.py build_ext --inplace
         # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
-      if: ${{matrix.os != 'windows-2019'}}
+      if: ${{matrix.os != 'windows-latest'}}
       run: |
         # Critical errors, exit on failure
         flake8 . --count --show-source --statistics --config=.flake8-critical
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
     - name: Run unit tests ubuntu
-      if: ${{matrix.os == 'ubuntu-20.04'}}
+      if: ${{matrix.os == 'ubuntu-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
     - name: Run unit tests windows  
-      if: ${{matrix.os == 'windows-2019'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    - name: Run unit tests MacOS  
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'windows-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
@@ -79,7 +70,7 @@ jobs:
   
   push: # Push to stable "beta" branch on successful build
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     # Only run on "develop" branch if tests pass
     needs: build
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c155732ce..48074da81 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,19 +20,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019]
+        os: [ubuntu-latest, windows-latest]
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up installation environment (Ubuntu or Windows)
-      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
-    - name: Set up installation environment (MacOS)
-      if: ${{matrix.os == 'macos-11'}}
-      run: |
-        ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
@@ -51,24 +47,19 @@ jobs:
         python setup.py build_ext --inplace
         # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
-      if: ${{matrix.os != 'windows-2019'}}
+      if: ${{matrix.os != 'windows-latest'}}
       run: |
         # Critical errors, exit on failure
         flake8 . --count --show-source --statistics --config=.flake8-critical
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
     - name: Run unit tests ubuntu
-      if: ${{matrix.os == 'ubuntu-20.04'}}
+      if: ${{matrix.os == 'ubuntu-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
     - name: Run unit tests windows  
-      if: ${{matrix.os == 'windows-2019'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    - name: Run unit tests MacOS  
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'windows-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
@@ -76,7 +67,7 @@ jobs:
   
   push: # Push to stable "beta" branch on successful build
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     # Only run on "develop" branch if tests pass
     needs: build
diff --git a/.github/workflows/notebook.yml b/.github/workflows/notebook.yml
index c3b3e3204..30d52de1b 100644
--- a/.github/workflows/notebook.yml
+++ b/.github/workflows/notebook.yml
@@ -19,13 +19,13 @@ jobs:
     strategy:
       fail-fast: false # Finish all tests even if one fails
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.8, 3.9, '3.10', '3.11']
         
     steps:
     - uses: actions/checkout@v2
     - name: Set up installation environment (Ubuntu or Windows)
-      if: ${{matrix.os == 'ubuntu-20.04' || matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
         #download chp source code
@@ -33,7 +33,7 @@ jobs:
         #compile chp
         gcc -o ./jupyter_notebooks/Tutorials/algorithms/advanced/chp ./jupyter_notebooks/Tutorials/algorithms/advanced/chp.c 
     - name: Set up installation environment (MacOS)
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'macos-latest'}}
       run: |
         ./.github/ci-scripts/before_install_macos.sh
         #download chp source code
@@ -57,17 +57,17 @@ jobs:
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
     - name: Run notebook regression ubuntu
-      if: ${{matrix.os == 'ubuntu-20.04'}}
+      if: ${{matrix.os == 'ubuntu-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks
     - name: Run notebook regression windows 
-      if: ${{matrix.os == 'windows-2019'}}
+      if: ${{matrix.os == 'windows-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks
     - name: Run notebook regression MacOS  
-      if: ${{matrix.os == 'macos-11'}}
+      if: ${{matrix.os == 'macos-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks

From e228dbad1b4a1e567a91ac223268c0c18a3a8083 Mon Sep 17 00:00:00 2001
From: "Stefan K. Seritan" <sserita@sandia.gov>
Date: Thu, 11 Jan 2024 13:57:57 -0800
Subject: [PATCH 3/4] Revert name for main workflow.

Should keep the README badges working still,
and have better continuity in the Actions tab on GitHub.
---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 48074da81..68094fc8a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Build and run tests (no MacOS, all Python versions)
+name: Build and run tests
 
 on:
   push:

From 1f4eaabab4e319d56e7bf0fafea915835b2de250 Mon Sep 17 00:00:00 2001
From: "Stefan K. Seritan" <sserita@sandia.gov>
Date: Thu, 11 Jan 2024 14:33:17 -0800
Subject: [PATCH 4/4] Upgrade GitHub Actions for node12 deprecation.

---
 .github/workflows/autodeploy.yml   | 14 +++++++-------
 .github/workflows/extras.yml       |  6 +++---
 .github/workflows/main-mac.yml     |  6 +++---
 .github/workflows/main-minimal.yml | 26 +++-----------------------
 .github/workflows/main.yml         |  8 ++++----
 .github/workflows/manualdeploy.yml | 14 +++++++-------
 .github/workflows/notebook.yml     |  6 +++---
 .github/workflows/testdeploy.yml   | 14 +++++++-------
 8 files changed, 37 insertions(+), 57 deletions(-)

diff --git a/.github/workflows/autodeploy.yml b/.github/workflows/autodeploy.yml
index 5ad63e206..2d44439ab 100644
--- a/.github/workflows/autodeploy.yml
+++ b/.github/workflows/autodeploy.yml
@@ -23,11 +23,11 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
   
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -39,7 +39,7 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
 
@@ -49,11 +49,11 @@ jobs:
     #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')   # doesn't work -- try using tags: above
     
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -61,7 +61,7 @@ jobs:
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -73,7 +73,7 @@ jobs:
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
diff --git a/.github/workflows/extras.yml b/.github/workflows/extras.yml
index 6395b642c..d078237af 100644
--- a/.github/workflows/extras.yml
+++ b/.github/workflows/extras.yml
@@ -25,7 +25,7 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
         
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up installation environment (Ubuntu or Windows)
       if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
@@ -35,11 +35,11 @@ jobs:
       run: |
         ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
diff --git a/.github/workflows/main-mac.yml b/.github/workflows/main-mac.yml
index 309827b7a..9e4b0290f 100644
--- a/.github/workflows/main-mac.yml
+++ b/.github/workflows/main-mac.yml
@@ -23,16 +23,16 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up installation environment (MacOS)
       run: |
         ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
diff --git a/.github/workflows/main-minimal.yml b/.github/workflows/main-minimal.yml
index 242443ad3..6760a49a1 100644
--- a/.github/workflows/main-minimal.yml
+++ b/.github/workflows/main-minimal.yml
@@ -27,17 +27,17 @@ jobs:
         python-version: [3.8,'3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up installation environment (Ubuntu or Windows)
       if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
@@ -66,27 +66,7 @@ jobs:
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    
-  
-  push: # Push to stable "beta" branch on successful build
 
-    runs-on: ubuntu-latest
-
-    # Only run on "develop" branch if tests pass
-    needs: build
-    if: github.ref == 'refs/heads/develop' && github.event_name == 'push'
-
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-        token: ${{ secrets.PYGSTI_TOKEN }}
-    - name: Merge changes to beta branch
-      run: |
-        git config --global user.name 'PyGSTi'
-        git config --global user.email 'pygsti@noreply.github.com'
-        git checkout beta
-        git merge --ff-only ${GITHUB_SHA} && git push origin beta
 
 
 
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 68094fc8a..d7134c893 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,17 +24,17 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up installation environment (Ubuntu or Windows)
       if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
         ./.github/ci-scripts/before_install.sh
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
@@ -74,7 +74,7 @@ jobs:
     if: github.ref == 'refs/heads/develop' && github.event_name == 'push'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         token: ${{ secrets.PYGSTI_TOKEN }}
diff --git a/.github/workflows/manualdeploy.yml b/.github/workflows/manualdeploy.yml
index b54972b15..15519b59f 100644
--- a/.github/workflows/manualdeploy.yml
+++ b/.github/workflows/manualdeploy.yml
@@ -16,11 +16,11 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
   
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -32,7 +32,7 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
 
@@ -41,11 +41,11 @@ jobs:
     runs-on: ubuntu-latest
     
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -53,7 +53,7 @@ jobs:
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -61,7 +61,7 @@ jobs:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
diff --git a/.github/workflows/notebook.yml b/.github/workflows/notebook.yml
index 30d52de1b..ac7dc36be 100644
--- a/.github/workflows/notebook.yml
+++ b/.github/workflows/notebook.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
         
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up installation environment (Ubuntu or Windows)
       if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
       run: |
@@ -41,11 +41,11 @@ jobs:
         #compile chp source code
         gcc -o ./jupyter_notebooks/Tutorials/algorithms/advanced/chp ./jupyter_notebooks/Tutorials/algorithms/advanced/chp.c 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
diff --git a/.github/workflows/testdeploy.yml b/.github/workflows/testdeploy.yml
index 2926f62eb..48badd5e9 100644
--- a/.github/workflows/testdeploy.yml
+++ b/.github/workflows/testdeploy.yml
@@ -19,11 +19,11 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
   
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -41,7 +41,7 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
 
@@ -49,11 +49,11 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.10'
@@ -61,7 +61,7 @@ jobs:
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -73,7 +73,7 @@ jobs:
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist