Contributing to PyHMMER

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 Easel and HMMER, which are exposed as git submodules:

$ git clone --recursive https://github.com/althonos/pyhmmer

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:

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

Running benchmarks

Benchmarks require the HMMER binaries to be available in the $PATH, as well as the hyperfine binary. Then make sure to have the extensions compiled in release mode:

$ python setup.py build_ext --inplace --force

Then run the benchmarks using the UNIX shell script:

$ ./benches/run.sh

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.