krane 0.0.0

A light-weight bioinformatics package

krane

AWS Scholarship Capstone Project - A light-weight bioinformatics package

Folder structure

krane/
├── src/
│   └── krane/
│       ├── __init__.py         # Package version and top-level imports
│       ├── core/
│       │   ├── __init__.py
│       │   ├── models.py       # Pydantic/data models
│       │   └── sequence.py     # Core sequence analysis logic
│       ├── web/
│       │   ├── __init__.py
│       │   ├── app.py          # FastAPI application setup
│       │   ├── routes/
│       │   │   ├── __init__.py
│       │   │   ├── sequence.py # Sequence-related endpoints
│       │   │   └── utils.py    # Utility endpoints
│       │   ├── schemas/
│       │   │   ├── __init__.py
│       │   │   └── sequence.py # Request/Response models
│       │   └── templates/      # For web interface if needed
│       └── cli/
│           ├── __init__.py
│           └── commands.py     # CLI commands
├── tests/
│   ├── __init__.py
│   ├── test_core.py
│   └── test_web.py
├── pyproject.toml             # Project metadata and dependencies
├── README.md
└── LICENSE

Generate requirements.txt

Install pip-tools

pip install pip-tools

Generate requirements.txt from pyproject.toml

pip-compile pyproject.toml -o requirements.txt

Generate dev requirements (includes test dependencies)

pip-compile pyproject.toml --extra dev --extra test -o requirements-dev.txt

Install package

Dev mode

python3 -m pip install --editable .

How to use krane

pip install krane

Install the package in development mode:

pip install -e .

Run web application

Using the installed command

krane-web

Running directly with uvicorn

uvicorn krane.web.app:app --reload

Use command line

Analyze a sequence

krane analyze ATCG --type DNA --label "Test"

Generate random sequence

krane generate --length 20 --type DNA

Read FASTA file

krane read-fasta sequence.fasta

Automated Test

Install test dependencies

pip install -e ".[test]"

Run all tests

pytest

Run with verbose output

pytest -v

Run with coverage report

pytest --cov=krane

Run all tests together

pytest tests/ -v

Run specific test file

pytest tests/test_web.py
pytest tests/test_core.py

Run tests matching a pattern

pytest -k "test_sequence"

Deployment Process

Deployment to Pypi

• Create PyPI account and get API token
• Add PYPI_API_TOKEN to GitHub repository secrets

For PyPI

# Tag a new version
git tag -a v0.1.0 -m "Release version 0.1.0"
git push origin v0.1.0
# This triggers PyPI workflow

Deployment to GAE

• Create Google Cloud project
• Create service account with App Engine Admin role
• Download JSON key
• Add to GitHub secrets:

• GCP_PROJECT_ID: Your project ID
• GCP_SA_KEY: The entire JSON key content

For Google App Engine:

# Push to main branch
git push origin main

# This triggers GAE workflow

Testing the deployments

After PyPI deployment:

# In a new virtual environment
pip install krane

# Test library
python -c "from krane.core import Sequence; print(Sequence('ATCG', 'DNA').transcription())"

# Test CLI
krane --help

After GAE deployment:

# Your app will be available at
https://<project-id>.appspot.com/