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 +1,36 @@
+name: Lint
+
+on:
+  push:
+    branches: [main, workflows]
+  pull_request:
+    branches: [main, workflows]
+
+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"
+          cache: "pip"
+          cache-dependency-path: requirements.txt
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt
+          python -m pip install ruff black mypy
+
+      - name: Run Ruff
+        run: ruff check app tests
+
+      - name: Run Black
+        run: black --check app tests
+
+      - name: Run MyPy
+        run: mypy app --ignore-missing-imports

.github/workflows/test-coverage.yml

@@ -0,0 +1,69 @@
+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 }}
+          cache: "pip"
+          cache-dependency-path: requirements.txt
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt
+          python -m pip install -r requirements-dev.txt
+
+      - 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: |
+          pytest --cov=app --cov-report=xml --cov-report=term-missing --cov-report=html -v
+
+      - name: Check coverage threshold (90%)
+        run: |
+          coverage report --fail-under=90
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.11'
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+      - name: Coverage summary
+        uses: irongut/[email protected]
+        if: matrix.python-version == '3.11'
+        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

.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: v0.1.15
+    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]

README.md

@@ -1,10 +1,14 @@
 # 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)
+- Python 3.10+ (matching the version used by your deployment target)
 - [uvicorn](https://www.uvicorn.org/) and other dependencies listed in `requirements.txt`
 
 ## Setup
@@ -22,7 +26,13 @@ FastAPI backend for handling Seqera Platform workflow launches.
    pip install -r requirements.txt
    ```
 
-3. Configure environment variables:
+3. Install development dependencies (for testing and linting):
+
+   ```bash
+   pip install -r requirements-dev.txt
+   ```
+
+4. Configure environment variables:
 
    ```bash
    cp .env.example .env
@@ -46,6 +56,52 @@ 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
+pytest --cov=app --cov-report=term-missing --cov-report=html
+
+# Run tests with verbose output
+pytest -v
+
+# Run specific test file
+pytest tests/test_main.py
+
+# Check coverage threshold (90%)
+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
+ruff check app tests
+
+# Run black formatter
+black app tests
+
+# Run type checking with mypy
+mypy app --ignore-missing-imports
+
+# Install pre-commit hooks
+pip install pre-commit
+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,

app/routes/workflows.py

@@ -1,9 +1,9 @@
 """Workflow-related HTTP routes."""
+
 from __future__ import annotations
 
 import asyncio
 from datetime import datetime, timezone
-from typing import Optional
 
 from fastapi import APIRouter, HTTPException, Query, status
 
@@ -36,26 +36,23 @@ async def launch_workflow(payload: WorkflowLaunchPayload) -> WorkflowLaunchRespo
     """Launch a workflow on the Seqera Platform."""
     try:
         dataset_id = payload.datasetId
-        
+
         # If formData is provided, create and upload dataset
         if payload.formData:
             dataset_result = await create_seqera_dataset(
                 name=payload.launch.runName or "workflow-dataset"
             )
             dataset_id = dataset_result.dataset_id
-
-            await upload_dataset_to_seqera(
-                dataset_id=dataset_id,
-                form_data=payload.formData
-            )
-
-        result: SeqeraLaunchResult = await launch_seqera_workflow(
-            payload.launch, dataset_id
-        )
+
+            await upload_dataset_to_seqera(dataset_id=dataset_id, form_data=payload.formData)
+
+        result: SeqeraLaunchResult = await launch_seqera_workflow(payload.launch, dataset_id)
     except SeqeraConfigurationError as exc:
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc))
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
+        ) from exc
     except SeqeraServiceError as exc:
-        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc))
+        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc)) from exc
 
     return WorkflowLaunchResponse(
         message="Workflow launched successfully",
@@ -77,8 +74,8 @@ async def cancel_workflow(run_id: str) -> CancelWorkflowResponse:
 
 @router.get("/runs", response_model=ListRunsResponse)
 async def list_runs(
-    status_filter: Optional[str] = Query(None, alias="status"),
-    workspace: Optional[str] = Query(None),
+    status_filter: str | None = Query(None, alias="status"),
+    workspace: str | None = Query(None),
     limit: int = Query(50, ge=1, le=200),
     offset: int = Query(0, ge=0),
 ) -> ListRunsResponse:
@@ -143,23 +140,23 @@ async def upload_dataset(payload: DatasetUploadRequest) -> DatasetUploadResponse
     except SeqeraConfigurationError as exc:
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
-        )
+        ) from exc
     except SeqeraServiceError as exc:
-        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc))
+        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc)) from exc
 
     # Allow Seqera time to finish dataset initialization before uploading
     await asyncio.sleep(2)
 
     try:
         upload_result = await upload_dataset_to_seqera(dataset.dataset_id, payload.formData)
     except ValueError as exc:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc)) from exc
     except SeqeraConfigurationError as exc:
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
-        )
+        ) from exc
     except SeqeraServiceError as exc:
-        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc))
+        raise HTTPException(status_code=status.HTTP_502_BAD_GATEWAY, detail=str(exc)) from exc
 
     return DatasetUploadResponse(
         message="Dataset created and uploaded successfully",