Merge branch 'master' of https://github.com/sandialabs/pyGSTi into fe…

…ature-crosstalk-free-gst

.github/CODEOWNERS

@@ -0,0 +1,92 @@
+## Global owners (default to pyGSTi maintainers) ##
+# These will also be owners for everything below
+# so they can approve minor PRs without adding
+# undue burden on volunteer code owners
+*       @sandialabs/pygsti-maintainers @sandialabs/pygsti-gatekeepers
+
+
+## Drift analysis ##
+pygsti/protocols/stability.py @tjproct @sandialabs/pygsti-gatekeepers
+pygsti/report/section/drift.py @tjproct @sandialabs/pygsti-gatekeepers
+pygsti/report/templates/drift_html_report/ @tjproct @sandialabs/pygsti-gatekeepers
+
+## Forward simulators ##
+pygsti/forwardsims @rileyjmurray @sandialabs/pygsti-gatekeepers
+pygsti/forwardsims/termforwardsim* @adhumu @sandialabs/pygsti-gatekeepers
+
+## IBMQ interface ##
+pygsti/extras/devices @sandialabs/pygsti-ibmq @sandialabs/pygsti-gatekeepers
+pygsti/extras/ibmq @sandialabs/pygsti-ibmq @sandialabs/pygsti-gatekeepers
+
+## Interpygate ##
+pygsti/extras/interpygate/ @kevincyoung @sandialabs/pygsti-gatekeepers
+
+## Modelmembers ##
+pygsti/modelmembers/ @rileyjmurray @sandialabs/pygsti-gatekeepers
+pygsti/modelmembers/instruments/ @sandialabs/pygsti-mcm @sandialabs/pygsti-gatekeepers
+
+## Modelpack owners ##
+pygsti/modelpacks/ @kmrudin @sandialabs/pygsti-gatekeepers
+
+## Optimizer owners ##
+pygsti/objectivefns @rileyjmurray @sandialabs/pygsti-gatekeepers
+pygsti/optimize @rileyjmurray @sandialabs/pygsti-gatekeepers
+
+## RB owners ##
+pygsti/algorithms/compilers.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/algorithms/mirroring.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/algorithms/randomcircuit.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/algorithms/rbfit.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/protocols/rb.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/tools/rbtheory.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/tools/rbtools.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+pygsti/tools/symplectic.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+
+## RPE owners ##
+pygsti/extras/rpe @kmrudin @sandialabs/pygsti-gatekeepers
+pygsti/models/rpemodel.py @kmrudin @sandialabs/pygsti-gatekeepers
+pygsti/protocols/rpe.py @kmrudin @sandialabs/pygsti-gatekeepers
+
+## Reporting owners ##
+# Specifically just for workspace plots/tables
+pygsti/report/workspace*.py @pcwysoc @sandialabs/pygsti-gatekeepers
+
+
+
+## Tutorial owners ##
+# In addition to general tutorial owners,
+# we will also have specific tutorials be owned
+# by topics owners are responsible for above
+jupyter_notebooks/ @sandialabs/pygsti-tutorials @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/**/*RB-*.ipynb @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Examples/1QGST-InterpolatedOps.ipynb @kevincyoung @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/algorithms/DriftCharacterization.ipynb @tjproct @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/algorithms/MirrorCircuitBenchmarks.ipynb @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/algorithms/RobustPhaseEstimation.ipynb @kmrudin @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/objects/advanced/IBMQExperiment.ipynb @sandialabs/pygsti-ibmq @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/objects/advanced/Instruments.ipynb @sandialabs/pygsti-mcm @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/objects/advanced/InterpolatedOperators.ipynb @kevincyoung @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/objects/advanced/ModelPacks.ipynb @kmrudin @sandialabs/pygsti-gatekeepers
+jupyter_notebooks/Tutorials/reporting/ @pcwysoc @sandialabs/pygsti-gatekeepers
+
+## Test owners ##
+test/ @rileyjmurray @sandialabs/pygsti-gatekeepers
+test/test_packages/extras/test_drift.py @tjproct @sandialabs/pygsti-gatekeepers
+test/test_packages/extras/test_interpygate.py @kevincyoung @sandialabs/pygsti-gatekeepers
+test/test_packages/extras/test_rb.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+test/test_packages/extras/test_rpe.py @kmrudin @sandialabs/pygsti-gatekeepers
+test/test_packages/extras/test_rpeobjects.py @kmrudin @sandialabs/pygsti-gatekeepers
+test/test_packages/objects/test_instruments.py @sandialabs/pygsti-mcm @sandialabs/pygsti-gatekeepers
+test/test_packages/report/ @pcwysoc @sandialabs/pygsti-gatekeepers
+test/test_packages/reportb/ @pcwysoc @sandialabs/pygsti-gatekeepers
+test/unit/algorithms/test_randomcircuit.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+test/unit/extras/interpygate @kevincyoung @sandialabs/pygsti-gatekeepers
+test/unit/extras/rb/ @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+test/unit/extras/rpe/ @kmrudin @sandialabs/pygsti-gatekeepers
+test/unit/modelpacks/ @kmrudin @sandialabs/pygsti-gatekeepers
+test/unit/objects/test_instrument.py @sandialabs/pygsti-mcm @sandialabs/pygsti-gatekeepers
+test/unit/protocols/test_rb.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+test/unit/report/ @pcwysoc @sandialabs/pygsti-gatekeepers
+test/unit/tools/test_symplectic.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers
+
+

.github/workflows/autodeploy.yml

@@ -4,43 +4,40 @@
 name: Deploy new version on pypi.org
 
 on:
-  push:
-    branches: [ "master" ]
-    # Pattern matched against refs/tags
-    tags:        
-      - 'v*'           # Push events to every tag not containing '/' (use '**' for hierarchical tags)
-
-  # Dont allow running manually from Actions tab -- use manualdeploy for this
-  #workflow_dispatch:
+  release:
+    types:
+      - published
+  workflow_dispatch:
 
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
-    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')  # doesn't work -- try using tags: above
 
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-13, 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@v5
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.10'
 
       - name: Build wheels
         uses: pypa/[email protected]
         env:
-          CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
+          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
+          CIBW_BEFORE_ALL_MACOS: ./.github/ci-scripts/before_install_macos.sh
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
@@ -49,38 +46,38 @@ 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@v5
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.10'
 
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
-    # upload to PyPI on every tag starting with 'v' --  doesn't work -> try using tags: above
-    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-    # alternatively, to publish when a GitHub Release is created, use the following rule:
-    # if: github.event_name == 'release' && github.event.action == 'published'
+    if: github.event_name == 'release' && github.event.action == 'published'
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: cibw-*
           path: dist
+          merge-multiple: true
 
       - name: Publish package on PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          verbose: true
+        # With the use of OIDC, API tokens are no longer needed
+        # See https://docs.pypi.org/trusted-publishers/using-a-publisher/ for more info

.github/workflows/beta-master.yml

@@ -0,0 +1,33 @@
+# This workflow runs a full test suite on beta and master
+# This includes all versions of supported Python, all OSes, and all test subsets
+
+name: Build and run tests (beta & master)
+
+on:
+  push:
+    branches: [ "beta", "master" ]
+  workflow_dispatch: # Allow manual running from GitHub
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-13, ubuntu-latest, windows-latest] # TODO: Unpin mac version when cvxopt or Python 3.8 dropped
+        python-version: [3.8, 3.9, '3.10', '3.11']
+        use-cython: ['true', 'false']
+    uses: ./.github/workflows/reuseable-main.yml
+    name: Run pyGSTi tests
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      use-cython: ${{ matrix.use-cython }}
+      run-unit-tests: 'true'
+      run-extra-tests: 'true'
+      run-notebook-tests: 'false' # TODO: Turn off failing notebook tests for runner failures starting end of May 2024
+
+
+
+
+
+

.github/workflows/develop.yml

@@ -0,0 +1,52 @@
+# This workflow runs a moderate test suite on develop
+# This includes all versions of supported Python, no MacOS, only unit tests,
+# and only tests environments with Cython in them
+
+name: Build and run tests (develop)
+
+on:
+  push:
+    branches: [ "develop" ]
+  workflow_dispatch: # Allow manual running from GitHub
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest] # No Mac
+        python-version: [3.8, 3.9, '3.10', '3.11']
+        use-cython: ['true', 'false']
+    uses: ./.github/workflows/reuseable-main.yml
+    name: Run pyGSTi tests
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      use-cython: 'true' # Cython only
+      run-unit-tests: 'true'
+      run-extra-tests: 'false' # No integration tests
+      run-notebook-tests: 'false' # No notebook tests 
+
+  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@v4
+      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 '[email protected]'
+        git checkout beta
+        git merge --ff-only ${GITHUB_SHA} && git push origin beta
+
+
+
+
+

.github/workflows/feature-branches.yml

@@ -0,0 +1,37 @@
+# This workflow runs a light test suite on all non-main branches
+# This includes only least/most supported Python version, no MacOS, only unit tests,
+# and only tests environments with Cython in them
+
+name: Build and run tests (feature branches)
+
+on:
+  push:
+    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: [ "**:**" ]
+  workflow_dispatch: # Allow manual running from GitHub
+
+jobs:
+  build:
+    strategy:
+      # fail-fast: true is OK here
+      matrix:
+        os: [ubuntu-latest, windows-latest] # No Mac
+        python-version: [3.8, '3.11'] # Only extremal Python versions
+    uses: ./.github/workflows/reuseable-main.yml
+    name: Run pyGSTi tests
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      use-cython: 'true' # Only test environment with Cython
+      run-unit-tests: 'true'
+      run-extra-tests: 'false' # No integration tests
+      run-notebook-tests: 'false' # No notebook tests 
+
+
+
+
+
+