krane 0.1.2

A light-weight bioinformatics package

krane

AWS Scholarship Capstone Project - A light-weight bioinformatics package

Folder structure

krane/
├── LICENSE
├── MANIFEST.in
├── README.md
├── dispatch.yaml                   # For GAE domain mapping
├── gae-deploy-flow.yml             # For GAE workflow (move to workflow)
├── krane.app.yaml                  # For GAE gloud deployment
├── pyproject.toml
├── requirements-dev.txt
├── requirements.txt
├── src
│   └── krane
│       ├── README.md
│       ├── __init__.py             # Package version and top-level imports
│       ├── cli
│       │   ├── __init__.py
│       │   └── commands.py         # CLI commands
│       ├── core
│       │   ├── __init__.py
│       │   ├── models.py           # Pydantic/data models
│       │   ├── sequence.py         # Core sequence analysis logic
│       │   └── utils.py
│       └── web
│           ├── __init__.py
│           ├── app.py              # FastAPI application setup
│           ├── documentation.md    # Markdown documentation
│           ├── index.md            # Markdown home description
│           ├── routes
│           │   ├── __init__.py
│           │   ├── sequence.py     # Sequence-related endpoints
│           │   └── utils.py        # Utility endpoints
│           ├── schemas
│           │   ├── __init__.py
│           │   └── sequence.py     # Request/Response models
│           ├── static
│           │   ├── css
│           │   ├── img
│           │   └── js
│           └── templates           # For web interface
│               ├── demo.html
│               ├── help.html
│               └── index.html
├── tests                           # For automated tests
│   ├── __init__.py
│   ├── test_cli.py
│   ├── test_core.py
│   └── test_web.py
└── tox.ini

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 by creating annotated tags
# git tag -a v0.1.0 -m "Release version v0.1.0" 
# git tag -a v0.1.0 -m "Version 0.1.0" # setuptools_scm does not recognize lightweight tags
git tag -a v0.1.0 -m "Release version 0.1.0" # setuptools_scm does not recognize lightweight tags
# Push the Specific Tag to Remote
git push origin v0.1.0
# Push all tags to the remote
git push --tags --force  # Push updated tags to remote
# This triggers PyPI workflow

Debug tag

git ls-remote --tags origin
git push origin --delete v0.1.0 # Deletes a tag named v0.1.0 from the remote repository named origin
git fetch --prune origin # Removes any remote-tracking references in local that no longer exist in the remote.
git tag
git tag -l | xargs git tag -d # Removes local tag
git show v0.1.0
git tag -d v0.1.1 v0.1.0

Force update tag locally first:

git tag -f v0.1.0 <local-commit-hash>
git push -f origin v0.1.0

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://krane.barestripe.com/