CONTRIBUTING.md

# Contributing to pyFastANI

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 FastANI which is exposed as a ``git`` submodule:

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

## Compiling the extension

Compiling requires the `boost::math` module from [Boost](https://www.boost.org/).
Depending on your system, you may have to install them yourself.

To compile the extension, use the following command:

```console
$ python setup.py build_ext
```

## 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 3.6 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) or in variable assignments (supported from Python 3.6
onward).

### Interfacing with C

When interfacing with C, and in particular with pointers, use assertions
everywhere you assume the pointer to be non-NULL.

### Interfacing with C++

When wrapping objects, use stack allocation where possible.