Merge branch 'beta' into master (will become v0.9.10 soon)

.flake8

@@ -20,12 +20,24 @@
 # F401: module imported but unused
 # F403: 'from module import *' used; unable to detect undefined names
 # F405: name may be undefined, or defined from star imports: module
-ignore=E265,E266,E402,E701,E702,E704,E722,E741,W503,W605,F401,F403,F405
+# N806: variable in function should be lowercase 
+ignore=E265,E266,E402,E701,E702,E704,E722,E741,W503,W605,F401,F403,F405,N806
 
 exclude=
     # automatically generated
     pygsti/io/parsetab_string.py
     pygsti/modelpacks/smq*.py
+    pygsti/modelpacks/legacy/std*.py
+
+#Allow legacyio to have names like 'GateString_setstate' and classes like 'dummy_GateString'
+#Also allow report sections to have figure-factory methods whose first arg is 'workspace', not 'self'
+# N801 : class name should not be mixed case
+# N802 : function name should be lowercase
+# N805 : first argument to method should be called 'self'
+per-file-ignores =
+    pygsti/io/legacyio.py:N801,N802
+    pygsti/objects/replib/slowreplib.py:N802
+    pygsti/report/section/*.py:N805
 
 # 120 characters is a more agreeable max line length for modern displays
 max-line-length=120

.flake8-critical

@@ -10,7 +10,21 @@
 [flake8]
 # ONLY check for these linting errors:
 # E9**: Runtime errors
+# F63*: Invalid tests and comparisons
 # F7**: Flake8 syntax errors
 # F82*: Undefined names
 # This list may be expanded in the future
-select=E9,F7,F82
+select=E9,F63,F7,F82
+
+exclude=
+	# Known issues with rb tests. Currently skipped, but technically have F821 errors
+	test/unit/extras/rb/test_analysis.py
+	test/unit/extras/rb/test_group.py
+	test/unit/extras/rb/test_sample.py
+	test/unit/extras/rb/test_theory.py
+	test/unit/tools/test_internalgates.py
+	test/test_packages/extras/test_rb.py
+	# F821 error. Should nPossible be nLocal?
+	test/test_packages/drivers/nqubitconstruction.py
+	# F821 error. Likely results existed in a deleted cell
+	scripts/profiling/gaugeopt/3Q_example.py

.github/ci-scripts/before_install.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+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
+cmake --version
+gcc --version

.github/ci-scripts/merge.sh

@@ -0,0 +1,63 @@
+#! /usr/bin/env bash
+# This script is run by a GitHub Action
+# This merges passing builds on the `deploy' branch to `beta'
+
+GIT_USER="GitHub Action"
+GIT_EMAIL="[email protected]"
+
+# we should only be run during Action
+if [ -z "$GITHUB_ACTIONS" ]; then
+    echo "This script is run automatically by GitHub Actions."
+    echo "Please don't run it manually!"
+    echo '... But if you really have to, set $GITHUB_ACTIONS to "true" to bypass this safety check.'
+    exit 1
+fi
+
+# trigger only on `develop' by default (configurable)
+if [ -z "$TRIGGER_REF" ]; then
+    TRIGGER_REF="/refs/heads/develop"
+fi
+
+# push to `beta' by default (configurable)
+if [ -z "$MERGE_BRANCH" ]; then
+    MERGE_BRANCH="beta"
+fi
+
+echo "GITHUB_REPOSITORY = $GITHUB_REPOSITORY"
+echo "GITHUB_REF = $GITHUB_REF"
+echo "TRIGGER_REF = $TRIGGER_REF"
+echo "MERGE_BRANCH = $MERGE_BRANCH"
+
+# Following should only be set for pull requests
+PULL_REQUEST=false
+if [ -z "$GITHUB_HEAD_REF" ] || [ -z "$GITHUB_BASE_REF" ]; then
+    PULL_REQUEST=true
+fi
+echo "PULL_REQUEST = $PULL_REQUEST"
+
+if [ "$GITHUB_REF" = "$TRIGGER_REF" ] && [ "$PULL_REQUEST" = "false" ]; then
+    # setup git user
+    git config user.email "$GIT_EMAIL"
+    git config user.name "$GIT_USER"
+
+    # branch develop head to beta
+    git checkout -b "$MERGE_BRANCH"
+
+    # if branch exists upstream, apply it on top of this one
+    UPSTREAM_URI="[email protected]:$GITHUB_REPOSITORY.git"
+    UPSTREAM_BRANCH=$(git ls-remote --heads "$UPSTREAM_URI" "$MERGE_BRANCH")
+    if [ "$?" -eq 0 ] && [ -n "$UPSTREAM_BRANCH" ]; then
+        git pull --ff-only "$UPSTREAM_URI" "$MERGE_BRANCH"
+        if [ "$?" -eq 0 ]; then
+            echo "Fast-forwarded $MERGE_BRANCH to $TRIGGER_REF."
+        else
+            echo "ERROR: couldn't fast-forward $MERGE_BRANCH to $TRIGGER_REF!"
+            echo "These branches must be merged manually."
+            echo "hint: If you wish to merge these branches automatically in the future,"
+            echo "hint: add the conflicting refs from $PUSH BRANCH to $DEVELOP BRANCH."
+            exit 2
+        fi
+    fi
+else
+    echo "Not triggering pull: GITHUB_REF != TRIGGER_REF or PULL_REQUEST != false"
+fi

.github/workflows/deploy.yml

@@ -0,0 +1,80 @@
+# 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:
+  push:
+    branches: [ "master" ]
+
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # to fetch all branches and *tags* (needed to get version number correctly)
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Build sdist
+        run: python setup.py sdist
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    # upload to PyPI on every tag starting with 'v'
+    if: github.event_name == 'push' && startsWith(github.event.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'
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish package on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          verbose: true

.github/workflows/extras.yml

@@ -0,0 +1,70 @@
+# 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 test extras
+
+on:
+  push:
+    branches: [ "beta" ]
+  #pull_requests
+  #  branches: [ "master", "develop", "beta" ]
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+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
+
+    runs-on: ubuntu-18.04
+    strategy:
+      fail-fast: false # Finish all tests even if one fails
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        nose-tests:
+        - "algorithms algorithmsb"
+        - "report reportb"
+        - "drivers objects tools iotest optimize construction extras"
+        # - "mpi" # Fails in GitHub Actions, passes locally but doesn't terminate threads properly
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up installation environment
+      run: |
+        ./.github/ci-scripts/before_install.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
+        # Installing with -e to keep installation local (for NOSE_NOPATH)
+        # but still compile Cython extensions
+        python -m pip install -e .[testing]
+    - name: Run test_packages ${{ matrix.nose-tests }}
+      env:
+        NOSETESTS: ${{ matrix.nose-tests }}
+      run: |
+        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+        echo "nosetests: $NOSETESTS"
+        nosetests $NOSETESTS
+
+
+

.github/workflows/main.yml

@@ -0,0 +1,90 @@
+# 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
+
+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
+  pull_request:
+    branches: [ "**:**" ]
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+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: 1 # use installed package, not source tree under CWD
+  NOSE_PROCESS_TIMEOUT: 2400
+  NOSE_WHERE: "test/unit/"
+
+jobs:
+  build: # Main build + unit test check
+
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up installation environment
+      run: |
+        ./.github/ci-scripts/before_install.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 flake8
+        python -m pip install .[testing]
+        # 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      
+      run: |
+        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+        echo "nosetests: $NOSETESTS"  
+        nosetests $NOSETESTS
+  
+  push: # Push to stable "beta" branch on successful build
+
+    runs-on: ubuntu-18.04
+
+    # 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 '[email protected]'
+        git checkout beta
+        git merge --ff-only ${GITHUB_SHA} && git push origin beta
+
+
+