Contributing#

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

Types of Contributions#

Report Bugs#

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs#

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features#

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation#

You can never have enough documentation! Please feel free to contribute to any part of the documentation, such as the official docs, docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback#

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!#

Ready to contribute? Here’s how to set up opengenome for local development.

Setup your environment

$ conda create -n opengenome python=3.12
$ conda activate opengenome
$ python -m pip install --upgrade pip
$ cd PATH/opengenome

Install Packages (run in anaconda prompt)

$ pip install --upgrade setuptools wheel twine
$ pip install -e .[dev]

Remember to use Mypy Type Checker extension for VS Code. Add configuration to settings.json

{
    ...
    "mypy-type-checker.args": [
        "--ignore-missing-imports",
        "--follow-imports=silent",
        "--show-column-numbers",
        "--strict"
        ],
    ...
}

For other IDE run mypy with the following flags:

$ mypy yourscript.py --ignore-missing-imports --follow-imports=silent --show-column-numbers --strict

Use git (or similar) to create a branch for local development and make your changes:
```
$ git checkout -b name-of-your-bugfix-or-feature
```
When you’re done making changes, check that your changes conform to any code formatting requirements and pass any tests.
```
$ pytest tests/ --cov=opengenome
```
To test locally build the sdits and wheel with:
```
$ python setup.py sdist bdist_wheel
```
Commit your changes and open a pull request.

Sphinx Generated HTML#

Look at your documentation HTML locally
```
$ cd docs
$ make clean
$ make html
```
generated files can be found in docs/_build/html

Pull Request Guidelines#

Before you submit a pull request, check that it meets these guidelines:

The pull request should include additional tests if appropriate.
If the pull request adds functionality, the docs should be updated.
The pull request should work for all currently supported operating systems and versions of Python.

Useful Tips#

For Windows + VS Code users, configure terminal to start on your environment
1. Open your project
2. CTRL + SHIFT + ‘P’ enter Python: Select Interpreter
3. Select opengenome env
4. CTRL + SHIFT + ‘P’ enter Terminal: Select Default Profile
5. Select Command Prompt cmd.exe

Code of Conduct#

Please note that the opengenome project is released with a Code of Conduct. By contributing to this project you agree to abide by its terms.