CONTRIBUTING.md

How to Contribute

Introduction

Thank you for your interest in contributing! All types of contributions are encouraged and valued. Please make sure to read the relevant section before making your contribution. We at the Durrant Lab look forward to your contributions.

Reporting a bug

If you're unable to find an open issue addressing the bug, feel free to open a new one. Be sure to include a title and clear description, as much relevant information as possible (e.g., the program, platform, or operating-system version numbers), and a code sample or test case demonstrating the expected behavior that is not occurring.

If you or the maintainers don't respond to an issue for 30 days, the issue may be closed. If you want to come back to it, reply (once, please), and we'll reopen the existing issue. Please avoid filing new issues as extensions of one you already made.

Project setup to make source-code changes on your computer

This project uses git to manage contributions, so start by reading up on how to fork a git repository if you've never done it before.

Forking will place a copy of the code on your own computer, where you can modify it to correct bugs or add features.

Integrating your changes back into the main codebase

Follow these steps to "push" your changes to the main online repository so others can benefit from them:

• Create a new merge request with your changes.
• Ensure the description clearly describes the problem and solution. Include the relevant issue number if applicable.
• Before submitting, please read this CONTRIBUTING.md file to know more about coding conventions and benchmarks.

Coding conventions

Be sure to adequately document your code with comments so others can understand your changes. All classes and functions should have associated doc strings, formatted as appropriate given the programming language. Here are some examples:

"""
This file does important calculations. It is a Python file with nice doc strings.
"""

class ImportantCalcs(object):
    """
    An important class where important things happen.
    """

    def __init__(self, vars=None, receptor_file=None,
                 file_conversion_class_object=None, test_boot=True):
        """
        Required to initialize any conversion.

        Inputs:
        :param dict vars: Dictionary of user variables
        :param str receptor_file: the path for the receptor file
        :param obj file_conversion_class_object: object that is used to convert
            files from pdb to pdbqt
        :param bool test_boot: used to initialize class without objects for
            testing purpose
        """

        pass

/**
 * Sets the curStarePt variable externally. A useful, well-documented
 * TypeScript function.
 * @param {number[]} pt  The x, y coordinates of the point as a list of
 *                       numbers.
 * @returns void
 */
export function setCurStarePt(pt: any): void {
    curStarePt.copyFrom(pt);
}

If writing Python code, be sure to use the Black formatter before submitting a merge request. If writing code in JavaScript or TypeScript, please use the Prettier formatter.

Fixing whitespace, formatting code, or making a purely cosmetic patch

Changes that are cosmetic in nature and do not add anything substantial to the stability, functionality, or testability of the program are unlikely to be accepted.

Asking questions about the program

Ask any question about how to use the program on the appropriate Durrant Lab forum.

Acknowledgements

This document was inspired by:

• Ruby on Rails CONTRIBUTING.md file (MIT License).
• weallcontribute (Public Domain License).