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 clone --recursive https://github.com/althonos/pyhmmer
Tests are written as usual Python unit tests with the
unittest module of
the standard library. Running them requires the extension to be built
$ python setup.py build_ext --debug --inplace $ python -m unittest discover -vv
Benchmarks require the HMMER binaries to be available in the
as well as the
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:
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
Interfacing with C¶
When interfacing with C, and in particular with pointers, use assertions everywhere you assume the pointer to be non-NULL.