feat: update lint and test workflows #1

vtnphan · 2025-12-17T04:27:49Z

Pull Request

SBP-232 Enable BindFlow Workflow Execution from Input Workflow Page

Summary

This PR introduces comprehensive testing infrastructure and automated quality checks to the SBP Portal Backend, establishing a solid foundation for maintainability and code quality. The changes include 93% test coverage (exceeding the 90% requirement), modern Python 3.10+ type hints, and CI/CD pipelines for automated testing and linting.

Changes

Testing Infrastructure (70 tests, 93.14% coverage)

Added comprehensive test suite covering all service layers:
- test_main.py - FastAPI app initialization, CORS, health endpoints (8 tests)
- test_schemas.py - Pydantic schema validation and transformations (17 tests)
- test_routes_workflows.py - API endpoint integration tests (12 tests)
- test_services_seqera.py - Seqera Platform API integration (11 tests)
- test_services_datasets.py - Dataset creation/upload service (20 tests)
- test_additional_coverage.py - Edge case coverage (2 tests)
Test configuration:
- conftest.py - Shared fixtures, mock clients, environment setup
- pytest.ini - Pytest configuration with async mode
- requirements-dev.txt - Development dependencies (pytest, coverage, mocking)

CI/CD Workflows

test-coverage.yml:
- Runs tests on Python 3.10, 3.11, 3.12
- Enforces 90% coverage threshold (currently at 93.14%)
- Uploads coverage reports to Codecov
- Generates coverage summary with badges
lint.yml:
- Runs ruff (linter), black (formatter), mypy (type checker)
- Ensures code quality and consistency
release.yml & release-simple.yml:
- Automated release creation on version tags
- Optional changelog generation

Project Configuration

pyproject.toml:
- Coverage configuration (90% threshold, branch coverage)
- Ruff linting rules and exclusions
- Black formatting settings (line-length 100, Python 3.10-3.12)
- MyPy type checking configuration
.pre-commit-config.yaml:
- Pre-commit hooks for ruff, black, and mypy
- Automated code quality checks before commits
README.md:
- Added CI/CD badges (Coverage, Lint, Tests)
- Updated Python version requirement to >=3.10
- Documented testing and linting procedures

Coverage by Module

main.py: 93.94%
workflows.py: 97.92%
datasets.py: 94.92%
seqera.py: 100%
workflows.py: 75.38%
Overall: 93.14%

How to Test

Running Tests Locally

# Install development dependencies
pip install -r requirements-dev.txt

# Run all tests with coverage
pytest --cov=app --cov-report=term-missing

# Run specific test file
pytest tests/test_services_seqera.py -v

# Generate HTML coverage report
pytest --cov=app --cov-report=html
open htmlcov/index.html

Running Linters

# Run all linters
ruff check app tests
black --check app tests
mypy app --ignore-missing-imports

# Auto-fix linting issues
ruff check app tests --fix
black app tests

Pre-commit Hooks

# Install pre-commit hooks
pip install pre-commit
pre-commit install

# Run manually
pre-commit run --all-files

CI/CD Validation

Push to branch triggers:
- Test coverage workflow (Python 3.10, 3.11, 3.12)
- Lint workflow (ruff, black, mypy)
Both workflows must pass before merge

Type of change

New feature (non-breaking change which adds functionality)
Documentation update

Checklist

I have added tests that prove my fix is effective or that my feature works (70 tests, 93% coverage)
I have added or updated documentation where necessary (README.md, inline docstrings)
I have run linting and unit tests locally (all passing)
The code follows the project's style guidelines (ruff + black + mypy compliant)

Copilot

Pull request overview

This PR introduces comprehensive testing infrastructure and linting workflows to the SBP Portal Backend. The changes modernize the codebase with Python 3.10+ type hints, add extensive test coverage across all service layers, and establish CI/CD pipelines for automated quality checks.

Key Changes:

Added comprehensive test suite with 90% coverage requirement across services, routes, schemas, and main application
Introduced GitHub Actions workflows for linting (ruff, black, mypy) and test coverage with Codecov integration
Modernized type hints from Optional[X], Dict, List to Python 3.10+ syntax (X | None, dict, list)

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
tests/conftest.py	Adds shared test fixtures including mock clients, sample data, and environment setup for all tests
tests/test_main.py	Tests FastAPI app creation, health endpoint, CORS configuration, and router inclusion
tests/test_schemas.py	Validates Pydantic schema validation, field requirements, and data transformations
tests/test_services_seqera.py	Tests Seqera Platform integration including workflow launches, error handling, and API interactions
tests/test_services_datasets.py	Tests dataset creation, upload, CSV conversion, and form data handling
tests/test_routes_workflows.py	Tests workflow API endpoints including launch, cancel, list, logs, and details
tests/test_additional_coverage.py	Provides additional tests to meet coverage thresholds for edge cases
tests/init.py	Marks the tests directory as a Python package
pytest.ini	Configures pytest with async mode, test paths, and marker definitions
pyproject.toml	Defines project metadata and configuration for coverage, ruff, black, and mypy
requirements-dev.txt	Specifies development dependencies for testing and linting
.pre-commit-config.yaml	Configures pre-commit hooks for automated code quality checks
.github/workflows/lint.yml	CI workflow for running ruff, black, and mypy linters
.github/workflows/test-coverage.yml	CI workflow for running tests with coverage reporting to Codecov
.github/PULL_REQUEST_TEMPLATE.md	Template to standardize pull request descriptions
app/main.py	Updates type hints to modern Python 3.10+ syntax
app/services/seqera.py	Modernizes type hints and improves code formatting consistency
app/services/datasets.py	Updates type hints to Python 3.10+ syntax and improves readability
app/schemas/workflows.py	Converts all type hints to modern syntax (pipe union notation)
app/routes/workflows.py	Updates type hints and adds proper exception chaining with `from exc`
README.md	Adds CI badges, updates Python version requirement, and documents testing/linting procedures

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.pre-commit-config.yaml

requirements-dev.txt

README.md

.pre-commit-config.yaml

requirements-dev.txt

tests/test_services_seqera.py

.github/workflows/test-coverage.yml

Co-authored-by: Copilot <[email protected]>

marius-mather

The tests and CI checks look great, just a few suggestions on project and testing setup that will hopefully make things easier down the line.

You don't have to use the testing/mocking libraries like respx or polyfactory - just wanted to point them out as I find them useful for my own testing.

marius-mather · 2025-12-18T22:56:28Z

.github/workflows/lint.yml

+    branches: [main, workflows]
+  pull_request:
+    branches: [main, workflows]


This is right - you generally only need CI to run on pushes or pull requests to main

marius-mather · 2025-12-18T23:00:09Z

.github/workflows/lint.yml

+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt
+          python -m pip install ruff black mypy


These types of requirements should be in requirements-dev.txt so you can run the same checks locally (or in pyproject.toml as discussed below)

marius-mather · 2025-12-18T23:13:41Z

requirements-dev.txt

@@ -0,0 +1,7 @@
+# Development dependencies
+pytest==8.3.3


I'd encourage you to look at uv for managing dependencies, instead of just using pip and requirements.txt. You can have dev dependencies as a dependency group.

A couple of tips:

Add any dependencies required for dev/testing with uv add --dev pytest

Don't pin exact versions, allow minor version upgrades by using version specifiers like pytest ~= 8.3. I find that if you pin dependencies to exact versions, it just creates a lot of work later when you need to update something, as you have to figure out which other versions need to be updated. Also, you want to regularly update packages for security updates.

marius-mather · 2025-12-18T23:15:35Z

tests/conftest.py

+
+
+@pytest.fixture
+def mock_httpx_response():


Have a look at the respx library for mocking httpx - it will handle a lot of this for you

marius-mather · 2025-12-18T23:21:22Z

tests/conftest.py

+
+
+@pytest.fixture
+def sample_form_data():


Also have a look at polyfactory for generating mock responses automatically from schemas - can save time if you need to specify some fields in a schema for a test but don't care about the rest.

marius-mather · 2025-12-18T23:28:04Z

tests/test_additional_coverage.py

+from app.services.datasets import DatasetUploadResult
+
+
+class TestUploadDataset:


I generally don't use test classes when using pytest - you can just use individual test functions and use fixtures for any setup that's required.

vtnphan added 5 commits December 17, 2025 15:07

feat: update lint and test workflows

21ae3aa

feat: add tests

a97be3f

feat: update CI

f9bdf91

fix: improve lint

8abc251

fix: improve lint

367763c

vtnphan marked this pull request as ready for review December 18, 2025 03:42

vtnphan requested a review from Copilot December 18, 2025 03:42

Copilot started reviewing on behalf of vtnphan December 18, 2025 03:43 View session

Copilot AI reviewed Dec 18, 2025

View reviewed changes

vtnphan and others added 5 commits December 18, 2025 14:55

fix: update requirements-dev.txt

ddb6e04

Co-authored-by: Copilot <[email protected]>

fix: update .pre-commit-config.yaml

a0bb969

Co-authored-by: Copilot <[email protected]>

fix: update requirements-dev.txt

d6fa9f2

Co-authored-by: Copilot <[email protected]>

fix: update readme

a51ac2d

Co-authored-by: Copilot <[email protected]>

fix: update .github/workflows/test-coverage.yml

b8c573f

Co-authored-by: Copilot <[email protected]>

vtnphan requested review from amandazhuyilan and marius-mather and removed request for amandazhuyilan and marius-mather December 18, 2025 04:13

marius-mather requested changes Dec 18, 2025

View reviewed changes

		from app.services.datasets import DatasetUploadResult


		class TestUploadDataset:



		@pytest.fixture
		def mock_httpx_response():



		@pytest.fixture
		def sample_form_data():

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Pull Request

Summary

Changes

Testing Infrastructure (70 tests, 93.14% coverage)

CI/CD Workflows

Project Configuration

Coverage by Module

How to Test

Running Tests Locally

Running Linters

Pre-commit Hooks

CI/CD Validation

Type of change

Checklist

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Reviewed changes

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vtnphan commented Dec 17, 2025 •

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