Merge branch 'develop' into feature-cloudnoise-experimental

.github/CODEOWNERS

@@ -0,0 +1,93 @@
+## 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/extras/rb.py @sandialabs/pygsti-rb @sandialabs/pygsti-gatekeepers # Should this just be deprecated and removed?
+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/ci-scripts/before_install.sh

@@ -3,6 +3,6 @@
 sudo apt-get update -qq -y && \
 sudo apt-get install -qq -y \
 gfortran libblas-dev liblapack-dev openmpi-bin openmpi-common openssh-client \
-openssh-server libopenmpi2 libopenmpi-dev libsuitesparse-dev
+openssh-server libopenmpi3 libopenmpi-dev libsuitesparse-dev
 cmake --version
 gcc --version

.github/ci-scripts/before_install_macos.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+brew update && \
+brew install \
+gfortran openblas lapack openmpi \
+openssh suite-sparse
+cmake --version
+gcc --version

.github/workflows/autodeploy.yml

@@ -6,9 +6,9 @@ name: Deploy new version on pypi.org
 on:
   push:
     branches: [ "master" ]
-    # Pattern matched against refs/tags
-    tags:        
-      - '*'           # Push events to every tag not containing '/' (use '**' for hierarchical tags)
+  release:
+    types:
+      - published
 
   # Dont allow running manually from Actions tab -- use manualdeploy for this
   #workflow_dispatch:
@@ -17,30 +17,30 @@ 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]
     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/cibuildwheel@v2.1.2
         env:
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
           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:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
@@ -49,38 +49,38 @@ 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/extras.yml

@@ -13,16 +13,6 @@ on:
 
 env:
   SKIP_DEAP: 1
-  NOSE_VERBOSE: 2
-  NOSE_WITH_TIMER: 1
-  NOSE_WITH_ID: 1
-  NOSE_REDNOSE: 1
-  NOSE_WITH_COVERAGE: 1
-  NOSE_COVER_PACKAGE: "pygsti"
-  #NOSE_PROCESSES: -1
-  NOSE_NOPATH: ""
-  NOSE_PROCESS_TIMEOUT: 2400
-  NOSE_WHERE: "test/test_packages/"
 
 jobs:
   test_extras: # On stable branches, run extended tests
@@ -31,59 +21,51 @@ jobs:
     strategy:
       fail-fast: false # Finish all tests even if one fails
       matrix:
-        os: [ubuntu-18.04, windows-2019]
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        nose-tests:
-        - "algorithms"
-        - "algorithmsb"
-        - "report"
-        - "reportb"
-        - "report"
-        - "objects"
-        - "tools"
-        - "iotest"
-        - "drivers"
-        - "optimize"
-        - "construction"
-        - "extras"
-        # - "mpi" # Fails in GitHub Actions, passes locally but doesn't terminate threads properly
-
+        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
+    - 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 installation environment (MacOS)
+      if: ${{matrix.os == 'macos-latest'}}
+      run: |
+        ./.github/ci-scripts/before_install_macos.sh
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip packages
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        # Installing with -e to keep installation local (for NOSE_NOPATH)
+        # Installing with -e to keep installation local
         # but still compile Cython extensions
         python -m pip install -e .[testing]
-    - name: Run test_packages Ubuntu ${{ matrix.nose-tests }}
-      if: ${{matrix.os == 'ubuntu-18.04'}}
-      env:
-        NOSETESTS: ${{ matrix.nose-tests }}
+        python setup.py build_ext --inplace
+    - name: Run test_packages Ubuntu
+      if: ${{matrix.os == 'ubuntu-latest'}}
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-        echo "nosetests: $NOSETESTS"
-        nosetests $NOSETESTS
-    - name: Run test_packages Windows ${{ matrix.nose-tests }}
-      if: ${{matrix.os == 'windows-2019'}}
-      env:
-        NOSETESTS: ${{ matrix.nose-tests }}
+        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-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-latest'}}
+
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-        echo "nosetests: $Env:NOSETESTS"
-        nosetests --traverse-namespace $Env:NOSETESTS
+        python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages
 
 
 

.github/workflows/main-mac.yml

@@ -0,0 +1,61 @@
+# 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-latest]
+        python-version: [3.8, 3.9, '3.10', '3.11']
+
+    steps:
+    - 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@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip packages
+      uses: actions/cache@v4
+      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
+      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 MacOS  
+      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
+
+
+
+