# Contributing to PytrimAl

For bug fixes or new features, please file an issue before submitting a
pull request. If the change isn't trivial, it may be best to wait for
feedback.

## Setting up a local repository

Make sure you clone the repository in recursive mode, so you also get the
wrapped code of trimAl which is exposed as a ``git`` submodule:

```console
$ git clone --recursive https://github.com/althonos/pytrimal
```

## Running tests

Tests are written as usual Python unit tests with the `unittest` module of
the standard library. Running them requires the extension to be built
locally:

```console
$ python setup.py build_ext --debug --inplace
$ python -m unittest discover -vv
```

## Coding guidelines

This project targets Python 3.5 or later.

Python objects should be typed; since it is not supported by Cython,
you must manually declare types in type stubs (`.pyi` files). In Python
files, you can add type annotations to function signatures (supported in
Python 3.5) but not in variable assignments (supported only from Python
3.6 onward). However, Cython allows you to use
[f-strings](https://www.python.org/dev/peps/pep-0498/)
even when compiling the code for Python 3.5.

### Interfacing with C/C++

When interfacing with C or C++, and in particular with pointers, use
assertions everywhere you assume the pointer to be non-NULL. Also consider
using assertions when accessing raw C arrays, if applicable.