update .github from biocommons.example

.github/workflows/labels.yml

@@ -0,0 +1,26 @@
+name: github
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+jobs:
+  labeler:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Run Labeler
+        uses: crazy-max/ghaction-github-labeler@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          yaml-file: .github/labels.yml
+          exclude: |
+            help*
+            *issue

.github/workflows/python-package.yml

@@ -0,0 +1,108 @@
+name: Python package
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e .[dev]
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Format check with isort
+      run: |
+        isort --check src
+
+    - name: Format check with black
+      run: |
+        black --check src
+
+    - name: Security check with bandit
+      run: |
+        bandit -ll -r src
+
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        make develop
+
+    - name: Test with pytest
+      run: |
+        make test
+        
+  deploy:
+    needs:
+    - cqa
+    - test
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Environment
+      run: |
+        echo "::group::Environment info"
+        echo github.event_name = ${{ github.event_name }}
+        echo refs = ${{ github.ref }}
+        echo tags = ${{ startsWith(github.ref, 'refs/tags') }}
+        echo "::endgroup::"
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: python -m build
+
+    - name: Publish package
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/stale.yml

@@ -0,0 +1,24 @@
+# https://github.com/actions/stale
+
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    - cron: '1 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v8
+        with:
+          days-before-issue-stale: 30
+          days-before-issue-close: 7
+          stale-issue-message: 'This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 7 days with no activity.'
+
+          days-before-pr-stale: 30
+          days-before-pr-close: 7
+          stale-pr-message: 'This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-pr-message: 'This PR was closed because it has been stalled for 7 days with no activity.'
+
+          exempt-all-pr-assignees: true