Project Template

./dev.sh automates common development tasks. Feel free to add new ones! Change NAME and USER at the top of ./dev.sh before use. GPLv3 License included (./LICENSE), keep or change for your project.

External dependencies:

• Anaconda / Mamba (multithreaded Anaconda)
• Docker
• Singluarity (requires docker)

A quick sample:

• ./dev.sh -bc to build conda package
• ./dev.sh -bd to build docker container
• ./dev.sh -bd to run source
• other scripts include uploading to anaconda, running ./src locally, and testing containers

Setting up the environment

./dev.sh -idev

Creates a new conda environement using the base.yml and dev.yml files at ./envs

Running locally

./dev.sh -r

Runs the python package at ./src/* directly

Conda

Requires the development environment and anaconda.org account if uploading. Add dependencies under ./envs/base.yml.

1. bump the version at ./src/<PACKAGE>/version.txt
2. build pip package ./dev.sh -bp
3. build conda package using the pip package ./dev.sh -bc
4. upload to your channel ./dev.sh -uc

Docker / Singularity

1. configure ./Dockerfile
2. build container ./dev.sh -bd
3. upload to quay.io ./dev.sh -ud
4. build singularity from docker ./dev.sh -bs (not dependent on upload)