Merge pull request #1 from TheJacksonLaboratory/G3-58-set-up-cicd-for…

…-geneweaver-api

G3 58 set up cicd for geneweaver api

.github/workflows/_check-coverage-action.yml

@@ -0,0 +1,65 @@
+name: 'Test Coverage Definition'
+on:
+  workflow_call:
+    inputs:
+      coverage-module:
+        description: "Module to test coverage for"
+        type: string
+        required: true
+      python-version:
+        description: Python version to set up'
+        default: '3.11'
+        type: string
+      runner-os:
+        description: 'Runner OS'
+        default: 'ubuntu-latest'
+        type: string
+      upload-coverage:
+        description: 'Upload coverage results'
+        default: true
+        type: boolean
+      required-coverage:
+        description: 'Required coverage percentage'
+        default: 100
+        type: string
+      show-test-traceback:
+        description: "Show traceback for failed tests"
+        type: string
+        default: "no"
+jobs:
+  run-tests:
+    runs-on: ${{ inputs.runner-os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ inputs.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            echo "/Users/runner/.local/bin:$PATH" >> $GITHUB_PATH
+          fi
+      - name: Configure Poetry
+        run: poetry config virtualenvs.create false
+      - name: Install dependencies with Poetry
+        run: poetry install
+      - name: Test with pytest
+        run: |
+          poetry run pytest tests \
+          --tb=${{ inputs.show-test-traceback }} \
+          --cov=${{ inputs.coverage-module }} \
+          --cov-report=term \
+          --cov-report=html \
+          --cov-fail-under=${{ inputs.required-coverage }} > coverage_report.txt
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-report
+          path: coverage_report.txt
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-report-html
+          path: htmlcov

.github/workflows/_format-lint-action.yml

@@ -0,0 +1,24 @@
+name: 'Lint Code Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: 'Python version to set up'
+        required: true
+        default: '3.9'
+        type: string
+jobs:
+  format-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+      - name: Install Black and Ruff
+        run: pip install black ruff
+      - name: Run Ruff Linter
+        run: ruff src/ tests/
+      - name: Run Black Formatter
+        run: black src/ tests/

.github/workflows/_run-tests-action.yml

@@ -0,0 +1,44 @@
+name: 'Python Tests Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: Python version to set up'
+        required: true
+        default: '3.9'
+        type: string
+      runner-os:
+        description: 'Runner OS'
+        required: true
+        default: 'ubuntu-latest'
+        type: string
+      upload-coverage:
+        description: 'Upload coverage results'
+        default: true
+        type: boolean
+      required-coverage:
+        description: 'Required coverage percentage'
+        default: 75
+        type: string
+jobs:
+  run-tests:
+    runs-on: ${{ inputs.runner-os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ inputs.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            echo "/Users/runner/.local/bin:$PATH" >> $GITHUB_PATH
+          fi
+      - name: Configure Poetry
+        run: poetry config virtualenvs.create false
+      - name: Install dependencies with Poetry
+        run: poetry install
+      - name: Test with pytest
+        run: |
+          poetry run pytest tests

.github/workflows/coverage.yml

@@ -0,0 +1,49 @@
+name: Coverage
+on:
+  pull_request:
+    branches:
+      - 'main'
+  push:
+    branches:
+      - 'main'
+jobs:
+  check-coverage:
+    uses: ./.github/workflows/_check-coverage-action.yml
+    with:
+      required-coverage: ${{ vars.REQUIRED_COVERAGE }}
+      coverage-module: "geneweaver.api"
+  comment-coverage-report:
+    needs: [ check-coverage ]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Download coverage report artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage-report
+      - name: Read coverage report
+        id: read-coverage
+        run: |
+          echo "COVERAGE_REPORT<<EOF" >> $GITHUB_ENV
+          cat coverage_report.txt >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
+      - name: Find Comment
+        uses: peter-evans/find-comment@v2
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: '### Test Coverage Report'
+      - name: Create or update comment
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          edit-mode: replace
+          body: |
+            ### Test Coverage Report
+            ```
+            ${{ env.COVERAGE_REPORT }}
+            ```

.github/workflows/release.yml

@@ -0,0 +1,76 @@
+name: Release to PyPI
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - 'pyproject.toml'
+
+permissions:
+  contents: write
+
+jobs:
+  format-lint:
+    uses: ./.github/workflows/_format-lint-action.yml
+    with:
+      python-version: '3.9'
+  test:
+    needs: format-lint
+    uses: ./.github/workflows/_run-tests-action.yml
+    with:
+      python-version: '3.9'
+      runner-os: 'ubuntu-latest'
+      upload-coverage: false
+      required-coverage: ${{ vars.REQUIRED_COVERAGE }}
+  release:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'z
+
+    - name: Install dependencies
+      run: |
+        pip install toml
+
+    - name: Check for version change
+      id: version_check
+      run: |
+        # Extract version from pyproject.toml
+        version=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
+        echo "Version=$version"
+        echo "version=$version" >> $GITHUB_OUTPUT
+
+        # Check if this version tag already exists
+        if git rev-parse "v$version" >/dev/null 2>&1; then
+            echo "Version already released"
+            echo "should_release=true" >> $GITHUB_OUTPUT
+        else
+            echo "New version detected"
+            echo "should_release=false" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Determine Release Type
+      id: release_type
+      run: |
+        version=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
+        if [[ $version =~ [a-zA-Z] ]]; then
+          echo "Pre-release version detected"
+          echo "prerelease=true" >> $GITHUB_OUTPUT
+        else
+          echo "Full release version detected"
+          echo "prerelease=false" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Install Poetry
+      if: ${{ steps.version_check.outputs.should_release }} == 'true'
+      run: |
+        curl -sSL https://install.python-poetry.org | python3 -
+
+    # TODO: Add deploy to kubernetes step

.github/workflows/style.yml

@@ -0,0 +1,13 @@
+name: Style
+on:
+  pull_request:
+    branches:
+      - 'main'
+  push:
+    branches:
+      - 'main'
+jobs:
+  format-lint:
+    uses: ./.github/workflows/_format-lint-action.yml
+    with:
+      python-version: '3.9'

.github/workflows/tests.yml

@@ -0,0 +1,19 @@
+name: Tests
+on:
+  pull_request:
+    branches:
+      - 'main'
+  push:
+    branches:
+      - 'main'
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11']
+    uses: ./.github/workflows/_run-tests-action.yml
+    with:
+      runner-os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      required-coverage: ${{ vars.REQUIRED_COVERAGE }}

README.MD

@@ -1,7 +1,26 @@
-## Project Name: geneweaver-api
+# Geneweaver 3 API
 
-Description: description
+Description: The API for the Geneweaver v3 application ecosystem.
 
-App: geneweaver_api
+## Setup
 
-To run the app execute `uvicorn geneweaver_api.main:app --reload`
+### Local
+
+#### Requirements
+
+- Python Poetry
+- Python 3.9 or higher
+- A connection to a copy of the Geneweaver Database
+
+#### Setup
+
+1. Clone the repository
+2. Run `poetry install` in project root to install dependencies
+3. Configure environment settings with environment variables or a `.env` file.
+4. Run the application
+
+To run the app execute either `uvicorn geneweaver.api.main:app --reload` with the poetry
+virtualenv activated, or just run `poetry run uvicorn geneweaver.api.main:app --reload`.
+
+This will host the application on `http://127.0.0.1:8000/` which means the swagger docs
+page is available at `http://127.0.0.1:8000/docs`.