How to develop on this project

CheckAtlas welcomes contributions from the community.

You need PYTHON3!

This project is in a very early development phase. All helpers are welcome. Please contact us or submit an issue.

Read the CONTRIBUTING.md file.

Checkatlas has two repositories: - The checkatlas module - The checkatlas nextflow workflow

It has a module on MultiQC - MultiQC checkatlas branch

The checkatlas package is available on PyPI - Checkatlas PyPI

The bioconda recipe has been submitted - Checkatlas bioconda recipe

These instructions are for linux base systems. (Linux, MacOS, BSD, etc.)

Setting up your own fork of this repo.

• On github interface click on Fork button.
• Clone your fork of this repo. git clone git@github.com:YOUR_GIT_USERNAME/checkatlas.git
• Enter the directory cd checkatlas
• Add upstream repo git remote add upstream https://github.com/becavin-lab/checkatlas

Setting up your own environment

Checkatlas relies on poetry packaging tool. Install poetry and run make virtualenv to create a virtual environment. Then activate it with source .venv/bin/activate.

Install the project in develop mode

Run make install --with dev to install the project in develop mode.

Run the tests to ensure everything is working

Run make test to run the tests.

Create a new branch to work on your contribution

Run git checkout -b my_contribution

Make your changes

Edit the files using your preferred editor. (we recommend VSCode)

Format the code

Run make fmt to format the code.

Run the linter

Run make lint to run the linter.

Test your changes

Run make test to run the tests.

Ensure code coverage report shows 100% coverage, add tests to your PR.

Build the docs locally

Run make docs to build the docs.

Ensure your new changes are documented.

Commit your changes

This project uses conventional git commit messages.

Example: fix(package): update setup.py arguments 🎉 (emojis are fine too)

Push your changes to your fork

Run git push origin my_contribution

Submit a pull request

On github interface, click on Pull Request button.

Wait CI to run and one of the developers will review your PR.

Makefile utilities

This project comes with a Makefile that contains a number of useful utility.

❯ make
Usage: make <target>

Targets:
help:             ## Show the help.
install:          ## Install the project in dev mode.
fmt:              ## Format code using black & isort.
lint:             ## Run pep8, black, mypy linters.
test: lint        ## Run tests and generate coverage report.
watch:            ## Run tests on every change.
clean:            ## Clean unused files.
virtualenv:       ## Create a virtual environment.
release:          ## Create a new tag for release.
docs:             ## Build the documentation.
switch-to-poetry: ## Switch to poetry package manager.
init:             ## Initialize the project based on an application template.