test integration test coverage [NRP-429] (#26)

.github/workflows/ci.yml

@@ -0,0 +1,200 @@
+name: Python package
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      run_integration_tests_only:
+        type: boolean
+        description: "Run integration tests only?"
+        required: false
+        default: false
+  schedule:
+    # everyday at 12:00
+    - cron: '0 12 * * *'
+
+jobs:
+
+  version-matrix-integration:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11']
+    steps:
+      - uses: actions/checkout@v3
+      - name: Cache poetry
+        uses: actions/cache@v3.3.1
+        with:
+          path: ~/.cache/pypoetry/virtualenvs
+          key: ${{ runner.os }}-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
+      - name: Set up ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup poetry
+        run: |
+          pip install pip==22.2.1 poetry==1.6.1
+          poetry run pip install --upgrade pip
+      - name: Install dev dependencies
+        run: |
+          poetry install --all-extras
+
+
+  check:
+    name: Check
+    runs-on: ubuntu-latest
+    if: (!inputs.run_integration_tests_only || github.event_name != 'schedule')
+    strategy:
+      matrix:
+        python-version: ['3.11']
+        action: ['lint', 'type', 'format']
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: '0'
+
+      - name: Cache poetry
+        uses: actions/cache@v3.3.1
+        with:
+          path: ~/.cache/pypoetry/virtualenvs
+          key: ${{ runner.os }}-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup poetry
+        run: |
+          pip install pip==22.2.1 poetry==1.6.1
+          poetry run pip install --upgrade pip
+
+      - name: Install dev dependencies
+        run: |
+          poetry install --all-extras
+
+      - name: Check formatting with black
+        run: |
+          poetry run black --check .
+        if: ${{ matrix.action == 'format' }}
+
+      - name: Typecheck with mypy
+        run: |
+          poetry run mypy qnexus/
+          poetry run mypy tests/
+          poetry run mypy integration/
+        if: ${{ matrix.action == 'type' }}
+
+      - name: Lint with pylint
+        run: |
+          poetry run pylint qnexus/
+          poetry run pylint tests/
+          poetry run pylint integration/
+        if: ${{ matrix.action == 'lint' }}
+
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    if: (!inputs.run_integration_tests_only || github.event_name != 'schedule')
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11']
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: '0'
+
+      - name: Cache poetry
+        uses: actions/cache@v3.3.1
+        with:
+          path: ~/.cache/pypoetry/virtualenvs
+          key: ${{ runner.os }}-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup poetry
+        run: |
+          pip install pip==22.2.1 poetry==1.6.1
+          poetry run pip install --upgrade pip
+
+      - name: Install dev dependencies
+        run: |
+          poetry install --all-extras
+
+      - name: Test with pytest
+        run: |
+          poetry run pytest tests/ --doctest-modules --cov=qnexus --cov-report=html --cov-report=term
+
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@master
+        with:
+          name: pytest-results-${{ matrix.python-version }}
+          path: htmlcov/
+
+
+  test-integration:
+    name: Integration
+    needs: [version-matrix-integration]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    env:
+      NEXUS_QA_USER_EMAIL: ${{ secrets.NEXUS_QA_USER_EMAIL }}
+      NEXUS_QA_USER_PASSWORD: ${{ secrets.NEXUS_QA_USER_PASSWORD }}
+      NEXUS_HOST: "staging.myqos.com"
+      STORE_NEXUS_TOKENS: "false"
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: '0'
+
+      - name: Cache poetry
+        uses: actions/cache@v3.3.1
+        with:
+          path: ~/.cache/pypoetry/virtualenvs
+          key: ${{ runner.os }}-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup poetry
+        run: |
+          pip install pip==22.2.1 poetry==1.6.1
+          poetry run pip install --upgrade pip
+
+      - name: Install dev dependencies
+        run: |
+          poetry install --all-extras
+      
+      - name: Set up qnexus login tokens
+        run: |
+          poetry run python integration/setup_tokens.py
+
+      - name: Run integration tests
+        run: |
+          poetry run pytest integration/ --html=integration-results.html --timeout=600 -ra --reruns 3
+
+      - name: Upload integration test results
+        uses: actions/upload-artifact@master
+        with:
+          path: |
+            ./integration-results-*.html
+            ./assets/*.css
+          name: integration-results

.github/workflows/pr-title.yml

@@ -0,0 +1,159 @@
+name: Check Conventional Commits format
+# Cribbed from https://github.com/CQCL/hugr/blob/main/.github/workflows/pr-title.yml
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    types:
+      - opened
+      - edited
+      - synchronize
+      - labeled
+      - unlabeled
+  merge_group:
+    types: [checks_requested]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  main:
+    name: Validate Conventional Commit PR title
+    runs-on: ubuntu-latest
+    # The action does not support running on merge_group events,
+    # but if the check succeeds in the PR there is no need to check it again.
+    if: github.event_name == 'pull_request_target'
+    outputs:
+      # Whether the PR title indicates a breaking change.
+      breaking: ${{ steps.breaking.outputs.breaking }}
+      # Whether the PR body contains a "BREAKING CHANGE:" footer describing the breaking change.
+      has_breaking_footer: ${{ steps.breaking.outputs.has_breaking_footer }}
+    steps:
+      - name: Validate the PR title format
+        uses: amannn/action-semantic-pull-request@v5
+        id: lint_pr_title
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          # Configure which types are allowed (newline-delimited).
+          # Default: https://github.com/commitizen/conventional-commit-types
+          types: |
+            feat
+            fix
+            docs
+            style
+            refactor
+            perf
+            test
+            ci
+            chore
+            revert
+            infra
+          # Configure which scopes are allowed (newline-delimited).
+          # These are regex patterns auto-wrapped in `^ $`.
+          #scopes: |
+          #  .*
+          # Configure that a scope must always be provided.
+          requireScope: false
+          # Configure which scopes are disallowed in PR titles (newline-delimited).
+          # For instance by setting the value below, `chore(release): ...` (lowercase)
+          # and `ci(e2e,release): ...` (unknown scope) will be rejected.
+          # These are regex patterns auto-wrapped in `^ $`.
+          #disallowScopes: |
+          #  release
+          #  [A-Z]+
+          # Configure additional validation for the subject based on a regex.
+          # This example ensures the subject doesn't start with an uppercase character.
+          #subjectPattern: ^(?![A-Z]).+$
+          # If `subjectPattern` is configured, you can use this property to override
+          # the default error message that is shown when the pattern doesn't match.
+          # The variables `subject` and `title` can be used within the message.
+          #subjectPatternError: |
+          #  The subject "{subject}" found in the pull request title "{title}"
+          #  didn't match the configured pattern. Please ensure that the subject
+          #  doesn't start with an uppercase character.
+          # If the PR contains one of these newline-delimited labels, the
+          # validation is skipped. If you want to rerun the validation when
+          # labels change, you might want to use the `labeled` and `unlabeled`
+          # event triggers in your workflow.
+          ignoreLabels: |
+            ignore-semantic-pull-request
+
+      # `action-semantic-pull-request` does not parse the title, so it cannot
+      # detect if it is marked as a breaking change.
+      #
+      # Since at this point we know the PR title is a valid conventional commit,
+      # we can use a simple regex that looks for a '!:' sequence. It could be
+      # more complex, but we don't care about false positives.
+      - name: Check for breaking change flag
+        id: breaking
+        run: |
+          if [[ "${{ github.event.pull_request.title }}" =~ ^.*\!:.*$ ]]; then
+            echo "breaking=true" >> $GITHUB_OUTPUT
+          else
+            echo "breaking=false" >> $GITHUB_OUTPUT
+          fi
+
+          # Check if the PR comment has a "BREAKING CHANGE:" footer describing
+          # the breaking change.
+          if [[ "${{ github.event.pull_request.body }}" != *"BREAKING CHANGE:"* ]]; then
+            echo "has_breaking_footer=false" >> $GITHUB_OUTPUT
+          else
+            echo "has_breaking_footer=true" >> $GITHUB_OUTPUT
+          fi
+
+      # Post a help comment if the PR title indicates a breaking change but does
+      # not contain a "BREAKING CHANGE:" footer.
+      - name: Require "BREAKING CHANGE:" footer for breaking changes
+        id: breaking-comment
+        if: ${{ steps.breaking.outputs.breaking == 'true' && steps.breaking.outputs.has_breaking_footer == 'false' }}
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: pr-title-lint-error
+          message: |
+            Hey there and thank you for opening this pull request! 👋🏼
+
+            It looks like your proposed title indicates a breaking change. If that's the case,
+            please make sure to include a "BREAKING CHANGE:" footer in the body of the pull request
+            describing the breaking change and any migration instructions.
+      - name: Fail if the footer is required but missing
+        if: ${{ steps.breaking.outputs.breaking == 'true' && steps.breaking.outputs.has_breaking_footer == 'false' }}
+        run: exit 1
+
+      - name: Post a comment if the PR badly formatted
+        uses: marocchino/sticky-pull-request-comment@v2
+        # When the previous steps fails, the workflow would stop. By adding this
+        # condition you can continue the execution with the populated error message.
+        if: always() && (steps.lint_pr_title.outputs.error_message != null)
+        with:
+          header: pr-title-lint-error
+          message: |
+            Hey there and thank you for opening this pull request! 👋🏼
+
+            We require pull request titles to follow the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/)
+            and it looks like your proposed title needs to be adjusted.
+
+            Your title should look like this. The scope field is optional.
+            ```
+            <type>(<scope>): <description>
+            ```
+
+            If the PR includes a breaking change, mark it with an exclamation mark:
+            ```
+            <type>!: <description>
+            ```
+            and include a "BREAKING CHANGE:" footer in the body of the pull request.
+
+            Details:
+            ```
+            ${{ steps.lint_pr_title.outputs.error_message }}
+            ```
+
+      # Delete previous comments when the issues have been resolved
+      # This step doesn't run if any of the previous checks fails.
+      - name: Delete previous comments
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: pr-title-lint-error
+          delete: true

.gitignore

@@ -13,6 +13,7 @@ __pycache__/
 .env
 
 dist/
+docs/_build
 
 # IPython
 .ipynb_checkpoints

.pylintrc

@@ -435,6 +435,7 @@ disable=raw-checker-failed,
         duplicate-code,
         too-many-arguments,
         too-many-instance-attributes,
+        fixme,
 
 
 # Enable the message, report, category or checker with the given id(s). You can