Contributing to Pyrodigal¶
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.
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
even when compiling the code for Python 3.5.
Interfacing with C¶
When interfacing with 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.
Setting up a local repository¶
Make sure you clone the repository in recursive mode, so you also get the
wrapped code of Prodigal which is exposed as a
$ git clone --recursive https://github.com/althonos/pyrodigal
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
benches folder contains benchmarks for evaluating the performance of
the node connection scoring step, essentially to make sure that the SIMD
code makes it faster.
Start by building
$ python setup.py build_ext --debug --inplace
Then make sure you have the required packages and data:
$ pip install --user -r benches/connection_scoring/requirements.txt $ python benches/connection_scoring/data/download.py
Finally, run the benchmarks and plot the results:
$ python benches/connection_scoring/bench.py -d benches/connection_scoring/data/ -o times.json $ python benches/connection_scoring/plot.py -i times.json --show
Setting up the Prodigal comparison¶
Julian Hahnfeld has developed a pipeline for comparing Pyrodigal and Prodigal to make sure they produce exactly the same results on a set of genomes: https://github.com/jhahnfeld/prodigal-pyrodigal-comparison
To use it, first install the local version of Pyrodigal that you want to compare against Prodigal:
$ pip install --user . --force-reinstall
Then compile the patched Prodigal binary from the code that is ditributed with Pyrodigal:
$ make -C vendor/Prodigal/
Finally, clone the comparison repository, download example genomes, and run the comparison:
$ git clone https://github.com/jhahnfeld/prodigal-pyrodigal-comparison $ cd prodigal-pyrodigal-comparison $ wget -i test_genomes.txt -P genomes $ python compare.py --prodigal ../vendor/Prodigal/prodigal --genome genomes/*