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GlyLES Contribution Guide

Code

In order to fix bugs or request features, you have two options. Creating an issue in the issue-tracker of the GitHub repository or submitting a pull request with a fix for the bug of an implementation of the feature you'd like to have. Both options have advantages and disadvantages

Method Advantage Disadvantage
Issue easy fix not immediately available
Pull request fast solution includes coding

Open an Issue

When opening an issue in the Issue-Tracker, please indicate what is wrong and provide a small example to reproduce your problem. In non-obvious cases of wrong behaviour, please also provide/link an explanation of why tools behaviour is wrong.

You can also open an issue if you have a feature-request. In this case, please provide a short example of how the requested feature would look like for an exemplary glycan.

Create a Pull Request

The pull request should contain a comment on what feature has been added or which bug has been removed. For this, please include a pytest-based test-case that highlights the bug. That means, you provide a test that fails in the current implementation but passes after applying your changes. In non-obvious cases of wrong behaviour, please also provide/link an explanation of why the new behaviour is correct and why the old behaviour was wrong.

You can also open a pull request for a new feature implementation. Feature requests should always be opened to the dev branch of the repository. In case your bug fix or feature implementation requires a new dependency, please update the pyproject.toml accordingly or state that package and its used version in the comment of the pull request.

If you need help with opening pull requests: These two articles might provide help for you:

Circumvent poetry

If you want to contribute to this project but don't want to install another package manager, you can use poetry within a conda environment by executing the following command in the root directory of this project:

conda create --name glyles python=3.7
conda activate glyles
conda install poetry
poetry install

Now, you have a conda environment with all the dependencies you need for development of GlyLES.

Documentation

In order to update the documentation, please you need to install sphinx and sphinx_rtd_theme to build the documentation by executing

rm -rf build & sphinx-build ./ ./build -a

in the docs folder. This will first remove the old documentation build and create a completely new one. Removing is necessary as in some cases malfunctions accumulate and the number of warnings increase and the documentation even might not build successfully.