Contributing¶

There are various ways for contributing to this project. Be that answering questions on the nf-core Slack channel or in GitHub issues, writing documentation and providing examples, testing the software in various settings, or submitting code through pull requests. A different, but very important way of contributing is to support new taxonomic profilers.

Example Contributions¶

Some typical ways are described in more details below:

Report bugs
Fix Bugs
Implement Features
Write Documentation
Submit Feedback

Report Bugs¶

Report bugs at https://github.com/taxprofiler/taxpasta/issues.

If you are reporting a bug, please follow the template guidelines. The more detailed your report, the easier and thus faster we can help you.

Fix Bugs¶

Look through the GitHub issues for bugs. Anything labelled with bug and help wanted is open to whoever wants to implement it. When you decide to work on such an issue, please assign yourself to it and add a comment that you'll be working on that, too. If you see another issue without the help wanted label, just post a comment, the maintainers are usually happy for any support that they can get.

Implement Features¶

Look through the GitHub issues for features. Anything labelled with enhancement and help wanted is open to whoever wants to implement it. As for fixing bugs, please assign yourself to the issue and add a comment that you'll be working on that, too. If another enhancement catches your fancy, but it doesn't have the help wanted label, just post a comment, the maintainers are usually happy for any support that they can get.

Write Documentation¶

TAXPASTA could always use more documentation, whether as part of the official documentation, in docstrings, or even on the web in blog posts, articles, and such. Just open an issue to let us know what you will be working on so that we can provide you with guidance.

Submit Feedback¶

The best way to send feedback is to file an issue at https://github.com/taxprofiler/taxpasta/issues. If your feedback fits the format of one of the issue templates, please use that. Remember that this is a volunteer-driven project and everybody has limited time.

Get Started!¶

Ready to contribute? Here's how to set up TAXPASTA for local development.

Fork the https://github.com/taxprofiler/taxpasta repository on GitHub.

Clone your fork locally

git clone git@github.com:your_name_here/taxpasta.git

Install your local copy into a Python virtual environment. You can read this guide to learn more about them and how to create one. Alternatively, particularly if you are a Windows or Mac user, you can also use Anaconda. Once you have created a virtual environment and activated it, this is how you set up your fork for local development
```
cd taxpasta
pip install -e '.[dev]'
pre-commit install
```
The commands above install the package with all of its normal and development dependencies into your virtual environment. The package itself is installed in editable mode (-e) such that any modifications that you make are immediately reflected in the installed package. Furthermore, we use pre-commit hooks to ensure consistent code formatting. They are installed with the command above and will run when you try to git commit your changes.
Create a branch for local development using the dev branch as a starting point. Use fix or feat as a prefix for your branch name.
```
git checkout dev
git checkout -b fix-name-of-your-bugfix
```
Now you can make your changes locally.
When you're done making changes, apply the quality assurance tools and check that your changes pass our test suite. This is all included with tox
```
tox
```
You can also run tox in parallel to speed this up.
```
tox -p auto
```
To render docs locally, change into docs and serve the pages
```
mkdocs build --clean
mkdocs serve
```

Commit your changes and push your branch to GitHub. Please use semantic commit messages.

git add .
git commit -m "fix: summarise your changes"
git push origin fix-name-of-your-bugfix

Open the link displayed in the message when pushing your new branch in order to submit a pull request.

Pull Request Guidelines¶

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

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
Your pull request will automatically be checked by the full tox test suite. It needs to pass all of them before it can be considered for merging.