Contributing

Contributing¶

In order to contibute to this repository you will need developer access to this repo. To know more about the project go to the README first.

From the root of this repo, run conda env create -f environment_dev.yaml

Pre-commits hooks have been configured for this project using the pre-commit library:

To get them going on your side, make sure to have python installed, and run the following commands from the root directory of this repository:

pip install pre-commit
pre-commit install
pre-commit run --all-files

Please respect the following conventions to contribute to the code:

Use hard wrap at 88
Respect black, isort and flake8 conventions
Classes’ names are Caml case (example: MyClass)
Functions and variables are in lower case with _ as separator (example: my_function, my_var)
Names are explicit: avoid mathematical notations, functions’ names start with a verb
Use python typing library: each class and method should be typed (both for inputs and outputs)
Create custom types if needed
All classes and functions should have a docstring
Avoid repeating arguments and returns in docstring (should be explicit with the types) except when it is truly necessary
A function (or a class) does not take more than 5 arguments, if you need more create a data class
Avoid dictionaries to pass arguments when possible and prefer dataclasses instead
Repeat inputs names when calling a function: ex: compute_custom(arg1=arg1, arg2=my_arg2)
Use list comprehension when it is possible
Use f strings to add variables in strings: ex: print(f’my var value is {my_var}’)
Use PathLib to handle pathes
Prefer shutil to os to manage files/ folders creations and deletions

Bio-transformers method