feat: update lint and test workflows

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+<!--
+Thank you for contributing! Please fill out the sections below to help maintainers review your change faster.
+Delete any sections that don't apply.
+-->
+
+# Pull Request
+
+## Summary
+[SBP-XXX](https://biocloud.atlassian.net/browse/SBP-XXX) <Provide a short description of the changes in this pull request and the motivation behind them.>
+
+## Changes
+- <What changed? (files, components, behavior)>
+- <Any migration or backwards-incompatible changes?>
+
+## How to Test
+<Provide step-by-step instructions for testing the changes locally. Include any setup, commands, or screenshots where helpful.>
+
+## Type of change
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+- [ ] Documentation update
+
+## Checklist
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] I have added or updated documentation where necessary
+- [ ] I have run linting and unit tests locally
+- [ ] The code follows the project's style guidelines

.github/workflows/lint.yml

@@ -0,0 +1,37 @@
+name: Lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras
+
+      - name: Run Ruff
+        run: uv run ruff check app tests
+
+      - name: Run Black
+        run: uv run black --check app tests
+
+      - name: Run MyPy
+        run: uv run mypy app --ignore-missing-imports

.github/workflows/test-coverage.yml

@@ -0,0 +1,60 @@
+name: Coverage
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras
+
+      - name: Run tests with coverage
+        env:
+          ALLOWED_ORIGINS: http://localhost
+          SEQERA_API_URL: https://example.com/api
+          SEQERA_ACCESS_TOKEN: test-token
+          WORK_SPACE: demo-workspace
+          COMPUTE_ID: compute-123
+          WORK_DIR: /tmp/work
+        run: |
+          uv run pytest --cov=app --cov-report=xml --cov-report=term-missing --cov-report=html -v
+
+      - name: Check coverage threshold (90%)
+        run: |
+          uv run coverage report --fail-under=90
+
+      - name: Coverage summary
+        uses: irongut/CodeCoverageSummary@v1.3.0
+        with:
+          filename: coverage.xml
+          badge: true
+          fail_below_min: true
+          format: markdown
+          hide_branch_rate: false
+          hide_complexity: true
+          indicators: true
+          thresholds: "90 90"
+          output: both

.gitignore

@@ -1,8 +1,41 @@
+# Python
 .venv/
+venv/
+env/
 __pycache__/
 *.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+*.whl
+
+# Environment
 .env
-*.log
+.env.local
+.env.*.local
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.hypothesis/
+
+# IDE
 .DS_Store
 .idea/
 .vscode/
+*.swp
+*.swo
+*~
+
+# Logs
+*.log
+logs/
+
+# UV
+# Note: uv.lock is tracked for reproducibility
+# .python-version is tracked if using specific Python version

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+# Pre-commit hooks configuration
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.10
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        language_version: python3.11
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-httpx]
+        args: [--ignore-missing-imports]

Dockerfile

@@ -2,17 +2,21 @@
 FROM python:3.11-slim AS base
 
 ENV PYTHONDONTWRITEBYTECODE=1 \
-    PYTHONUNBUFFERED=1 \
-    PIP_NO_CACHE_DIR=1
+    PYTHONUNBUFFERED=1
 
 WORKDIR /app
 
-COPY requirements.txt ./
-RUN pip install --upgrade pip && \
-    pip install --no-cache-dir -r requirements.txt
+# Install UV
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Copy dependency files
+COPY pyproject.toml uv.lock ./
+
+# Install dependencies
+RUN uv sync --frozen --no-dev
 
 COPY app ./app
 
 EXPOSE 3000
 
-CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "3000"]
+CMD ["uv", "run", "uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "3000"]

README.md

@@ -1,25 +1,32 @@
 # SBP Portal Backend Server
 
+![Lint](https://github.com/AustralianBioCommons/sbp-backend/actions/workflows/lint.yml/badge.svg)
+![Coverage](https://github.com/AustralianBioCommons/sbp-backend/actions/workflows/test-coverage.yml/badge.svg)
+[![codecov](https://codecov.io/gh/AustralianBioCommons/sbp-backend/branch/main/graph/badge.svg)](https://codecov.io/gh/AustralianBioCommons/sbp-backend)
+
 FastAPI backend for handling Seqera Platform workflow launches.
 
 ## Prerequisites
 
-- Python 3.9+ (matching the version used by your deployment target)
-- [uvicorn](https://www.uvicorn.org/) and other dependencies listed in `requirements.txt`
+- Python 3.10+
+- [UV](https://docs.astral.sh/uv/) package manager
 
 ## Setup
 
-1. Create a virtual environment (recommended):
+1. Install UV (if not already installed):
 
    ```bash
-   python3 -m venv .venv
-   source .venv/bin/activate
+   # macOS/Linux
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+
+   # Windows
+   powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
    ```
 
 2. Install dependencies:
 
    ```bash
-   pip install -r requirements.txt
+   uv sync --all-extras
    ```
 
 3. Configure environment variables:
@@ -32,8 +39,7 @@ FastAPI backend for handling Seqera Platform workflow launches.
 4. Run the API locally:
 
    ```bash
-   uvicorn app.main:app --reload --host 0.0.0.0 --port 3000
-   # or: python -m app.main  (uses PORT/UVICORN_RELOAD variables)
+   uv run uvicorn app.main:app --reload --host 0.0.0.0 --port 3000
    ```
 
 ## API Endpoints
@@ -46,6 +52,51 @@ FastAPI backend for handling Seqera Platform workflow launches.
 - `GET /api/workflows/{runId}/details` — Placeholder details endpoint
 - `POST /api/workflows/datasets/upload` — Create a Seqera dataset and upload submitted form data as a CSV
 
+## Testing
+
+Run the test suite with coverage:
+
+```bash
+# Run all tests with coverage report
+uv run pytest --cov=app --cov-report=term-missing --cov-report=html
+
+# Run tests with verbose output
+uv run pytest -v
+
+# Run specific test file
+uv run pytest tests/test_main.py
+
+# Check coverage threshold (90%)
+uv run coverage report --fail-under=90
+```
+
+View HTML coverage report:
+
+```bash
+open htmlcov/index.html  # macOS
+xdg-open htmlcov/index.html  # Linux
+start htmlcov/index.html  # Windows (Command Prompt / PowerShell)
+```
+
+## Linting and Code Quality
+
+```bash
+# Run ruff linter
+uv run ruff check app tests
+
+# Run black formatter
+uv run black app tests
+
+# Run type checking with mypy
+uv run mypy app --ignore-missing-imports
+
+# Install pre-commit hooks
+uv run pre-commit install
+
+# Run pre-commit on all files
+pre-commit run --all-files
+```
+
 ## Environment Variables
 
 Required entries in `.env`:

app/main.py

@@ -1,4 +1,5 @@
 """FastAPI application entry point for the SBP Portal backend."""
+
 from __future__ import annotations
 
 import logging
@@ -29,7 +30,9 @@ def create_app() -> FastAPI:
     if not allowed_origins_env:
         raise RuntimeError("ALLOWED_ORIGINS environment variable is required but not set")
 
-    allowed_origins = [origin.strip() for origin in allowed_origins_env.split(",") if origin.strip()]
+    allowed_origins = [
+        origin.strip() for origin in allowed_origins_env.split(",") if origin.strip()
+    ]
 
     app.add_middleware(
         CORSMiddleware,