pyGSTi 0.9.12.1__tar.gz → 0.9.13__tar.gz

pyGSTi-0.9.13/.github/CODEOWNERS

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+## 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
+
+

pyGSTi-0.9.13/.github/workflows/autodeploy.yml

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+# 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: Deploy new version on pypi.org
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
+  
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.10'
+          
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.1.2
+        env:
+          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
+          CIBW_BEFORE_ALL_MACOS: ./.github/ci-scripts/before_install_macos.sh
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')   # doesn't work -- try using tags: above
+    
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
+
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Build sdist
+        run: python setup.py sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    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@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Publish package on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        # With the use of OIDC, API tokens are no longer needed
+        # See https://docs.pypi.org/trusted-publishers/using-a-publisher/ for more info

pyGSTi-0.9.13/.github/workflows/beta-master.yml

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+# 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
+
+
+
+
+
+

pyGSTi-0.9.13/.github/workflows/develop.yml

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+# 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 'pygsti@noreply.github.com'
+        git checkout beta
+        git merge --ff-only ${GITHUB_SHA} && git push origin beta
+
+
+
+
+

pyGSTi-0.9.13/.github/workflows/feature-branches.yml

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+# 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 
+
+
+
+
+
+

pyGSTi-0.9.13/.github/workflows/reuseable-main.yml

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+# This is the core workflow for running pyGSTi linting and unit tests
+# This is used by other workflows to call this on a variety of OS/Python/environment options
+# By doing it this way, we can quickly call different matrix jobs on different branches
+
+name: Core pyGSTi build and run tests
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        required: true
+        type: string
+      python-version:
+        required: true
+        type: string
+      use-cython:
+        required: true
+        type: string
+      run-unit-tests:
+        required: true
+        type: string
+      run-extra-tests:
+        required: true
+        type: string
+      run-notebook-tests:
+        required: true
+        type: string
+
+env:
+  SKIP_DEAP: 1
+
+jobs:
+  build-and-test:
+    runs-on: ${{ inputs.os }}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up installation environment (Linux and Windows)
+      if: ${{ inputs.os != 'macos-13' }}
+      run: |
+        ./.github/ci-scripts/before_install.sh
+    - name: Set up installation environment (MacOS)
+      if: ${{ inputs.os == 'macos-13' }}
+      run: |
+        ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.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 pip packages
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install flake8
+    - name: Install package (Cython)
+      if: ${{ inputs.use-cython == 'true' }}
+      run: |
+        python -m pip install -e .[testing]
+        python setup.py build_ext --inplace
+    - name: Install package (No Cython)
+      if: ${{ inputs.use-cython != 'true' }}
+      run: |
+        python -m pip install -e .[testing_no_cython]
+    - name: Lint with flake8 (Linux only)
+      if: ${{ inputs.os == 'ubuntu-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
+      if: ${{ inputs.run-unit-tests == 'true' }}
+      run: |
+        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
+    - name: Run test_packages
+      if: ${{ inputs.run-extra-tests == 'true' }}
+      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 notebook regression
+      if: ${{ inputs.run-notebook-tests == 'true' }}
+      run: |
+        # If we are running notebooks, we also need to download and compile CHP
+        curl -o ./jupyter_notebooks/Tutorials/algorithms/advanced/chp.c https://www.scottaaronson.com/chp/chp.c
+        gcc -o ./jupyter_notebooks/Tutorials/algorithms/advanced/chp ./jupyter_notebooks/Tutorials/algorithms/advanced/chp.c
+
+        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+        python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks

pyGSTi-0.9.13/.gitignore

@@ -0,0 +1,147 @@
+*~
+*.tmp
+*.bak
+*.swp
+*.pkl
+*.out
+*.coverage*
+*.serial
+*.cache
+*.pyd
+.ipynb_checkpoints
+test/test_packages/temp_test_files/*
+*_checkpoints/
+jupyter_notebooks/**/offline
+test/test_packages/offline
+hooks/etc/permissions.yml
+*comm_output*.txt
+*.lprof
+*.cache
+/.eggs/
+.ropeproject
+.vscode
+doc/_autosummary
+doc/autoapi
+doc/build
+.venv*
+*.pyc*
+
+# Protocol Checkpointing #
+##########################
+*gst_checkpoints*
+*model_test_checkpoints*
+*standard_gst_checkpoints*
+*ibmqexperiment_checkpoint*
+
+# Serialization Testing Artifacts #
+###################################
+*LinearGateSetTomography_serialization*
+
+# Test Metadata #
+#################
+test/output/*
+test/output/pylint/*
+test/output/individual_coverage/*/*
+test/test_packages/cmp_chk_files/Fake_Dataset_none.txt.cache
+**.noseids
+**test_ibmq**
+
+# Tutorial Notebook Untracked Files #
+####################################
+jupyter_notebooks/Tutorials/tutorial_files/modeltest_report
+jupyter_notebooks/Tutorials/tutorial_files/gettingStartedReport
+jupyter_notebooks/Examples/example_files/*.pkl
+jupyter_notebooks/Examples/example_files/*.json
+jupyter_notebooks/Examples/example_files/leakage_*
+jupyter_notebooks/Tutorials/tutorial_files/exampleReport
+jupyter_notebooks/Tutorials/tutorial_files/exampleStdReport
+jupyter_notebooks/Tutorials/tutorial_files/exampleMultiEstimateReport
+jupyter_notebooks/Tutorials/tutorial_files/exampleMultiEstimateReport2
+jupyter_notebooks/Tutorials/tutorial_files/exampleMultiDataSetReport
+jupyter_notebooks/Tutorials/tutorial_files/exampleBriefReport
+jupyter_notebooks/Tutorials/tutorial_files/*.ipynb
+jupyter_notebooks/Tutorials/tutorial_files/tempTest
+jupyter_notebooks/Tutorials/tutorial_files/*checkpoints
+jupyter_notebooks/Tutorials/tutorial_files/test_mirror_benchmark
+
+
+
+# Compiled source #
+###################
+*.c
+*.cpp
+*.pyc
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.aux
+*.dvi
+*.toc
+build/*
+dist/*
+/pygsti.egg-info
+/pyGSTi.egg-info
+parsetab_string.py
+*.pyd
+
+# These are handwritten, not generated by cython, and should not be ignored
+!/pygsti/objects/replib/fastreps.cpp
+!/pygsti/objects/replib/fastreps.h
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+ehthumbs.db
+Icon?
+Thumbs.db
+.idea/
+HighImpactPaper1/texFiles/.DS_Store
+
+# Generated documentation #
+###########################
+doc/html/*
+doc/_auto
+doc/_build
+
+# Customer Data #
+#################
+scripts/profiling/report/*.ipynb
+scripts/profiling/report/Analyze+2Q+data.py
+scripts/profiling/report/*.html
+scripts/profiling/*.html
+scripts/profiling/report/standard_report.py
+scripts/profiling/report/tp_report.py
+scripts/profiling/report/rigetti_nocache.py
+
+# Profiling data #
+#################
+scripts/profiling/output
+scripts/profiling/data
+
+# Other Local-only Files #
+############################
+local
+pygsti/_version.py