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.
Some typical ways are described in more details below:
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.
Look through the GitHub issues for bugs. Anything labelled with
help wanted is open to whoever wants to implement it. When you decide to work on
such an issue, please assign yourself to
and add a comment that you'll be working on that, too. If you see another issue
help wanted label, just post a comment, the maintainers are
usually happy for any support that they can get.
Look through the GitHub issues for features. Anything labelled with
help wanted is open to whoever wants to implement it. As for
fixing bugs, please assign yourself to the
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.
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.
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.
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
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
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 commityour changes.
Create a branch for local development using the
devbranch as a starting point. Use
featas a prefix for your branch name.
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
You can also run tox in parallel to speed this up.
To render docs locally, change into docs and serve the pages
Commit your changes and push your branch to GitHub. Please use semantic commit messages.
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.