Contributing to Phables project

We love to have your contributions to the Phables project, whether it's:

• Reporting a bug
• Submitting a fix
• Proposing new features

Clone and install Phables onto your machine

First, make sure you have git installed on your machine.

On GitHub, fork the Phables repository and clone it to your machine.

# clone repository to your local machine
git clone https://github.com/Vini2/phables.git

Move to the Phables directory

cd phables

Create and activate the conda environment. Make sure to have conda installed.

# Create the phables environment
conda env create -f build/environment.yml

# Activate the phables environment
conda activate phables

Now install Phables via pip.

pip install -e .

Test Phables installation

Print the help message using the following command.

phables -h

Use the following command to launch the phables test run and all the tests should pass.

phables test

Coding Style

We adhere to the PEP 8 style guide.

Before committing, make sure to run black and isort.

black phables/workflow/scripts
isort --atomic phables/workflow/scripts 

Report bugs using GitHub's issues

We use GitHub issues to track public bugs. Report a bug by opening a new issue in GitHub issues. You will get to select between templates for bug report and feature request. If none of these templates match what you want to report, you can use the custom issue template.

Committing code

Once you have finished coding and all the tests pass, commit your code and make a pull request.

# Add changed/added files
git add <file name>

# Commit changes
git commit -m "<commit message>"

# Push changes
git push

Make sure to follow the commit style of c3dev. Relevant prefixes are replicated below for convenience.

Commit Prefix	For
DEV:	development tool or utility
DOC:	documentation
TST:	addition or modification of tests
REL:	related to a release
MAINT:	maintenance commit (refactoring, typos, etc.)
BUG:	bug fix
GIT:	git related
REV:	revert an earlier commit

Your contribution will be reviewed before accepting it.

License

By contributing, you agree that your contributions will be licensed under the MIT License.

References

This document was adapted from the open-source contribution guidelines for Transcriptase and c3dev.