Development

To add a new annotator to the package, follow these steps:

1. Make a fork of the repository.

   • Go to the project’s GitHub page (https://github.com/kusterlab/psite_annotation).

   • In the top-right corner of the page, click Fork.

   • Choose your personal GitHub account (or organization) as the destination.

2. Make a clone of your forked repository:

   git clone https://github.com/YOUR_USERNAME/psite_annotation.git
   

3. Create a new file in psite_annotation/annotators, the easiest is to make a copy of an existing annotator such as domain.py.

4. Implement the __init__(), load_annotations() and annotate() functions.

5. Create unit tests in tests/unit_tests/annotators, strive for 100% code coverage and covering edge cases.

6. Add a function that uses your annotator to psite_annotation/functional_annotation.py and add that function’s name to the __all__ list in the top of that file.

7. Create a system test for that function in tests/system_tests/test_functional_annotation.py.

8. Create a pull request:

   • Go to your fork on GitHub (e.g. https://github.com/YOUR_USERNAME/psite_annotation).

   • You should see a “Compare & pull request” button — click it. Alter=natively, go to the Pull Requests tab and click “New pull request”.