snakemake-kubernetes-api

This project contains a simple API to interact with the Kubernetes API from Snakemake.

Setup

This project uses Pixi to manage packages and the environment.

# linux / mac os
curl -fsSL https://pixi.sh/install.sh | bash

To install the dependencies, run the following command:

pixi install

What this does is create a virtual environment and install the dependencies listed in the pyproject.toml file. By starting command line commands with pixi run, you can run the commands in the specific environment.

This ensures that any other packages or dependencies can be synchronized across different environments, systems, and developers.

Quick start with the project and Pixi

There is a simple test function implemented in src/common/logging/logging.py called test_function that is called from the src/core/snakemake/main.py file. This function is used to test the logging functionality.

To run using the environment managed by pixi, run the following command in the root directory of the project:

pixi run python -m src.core.snakemake.main

A feature of pixi is that it can be used to run common tasks. For example, the above command has been implemented as a pixi task in the pyproject.toml file.

To run the task, use the following command:

pixi run hello

TODO:: as development progresses, remove the test_function and add a more meaningful function to show the functionality of the project and PIXI in general.

Semantic Versioning

This project uses Python Semantic Release for automatic versioning and changelog generation.

It is implemented via GitHub Actions and the configuration can be found in the pyproject.toml file.

For a detailed explanation of the release process, please refer to the GitFlow Process and Release Cycle.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

All contributions are welcome! To do so, fork the repository, create a new branch and submit a pull request

jjjermiah / snakemake-kubernetes-api Goto Github PK