Package installation for developpers

0 - Clone the repository

Start by cloning this repository

git clone git@github.com:owkin/fedpydeseq2.git

1 - Create a conda environment with python 3.10+

conda create -n fedpydeseq2 python=3.11 # or a version compatible
conda activate fedpydeseq2

2 - Install poetry

Run

conda install pip
pip install poetry==1.8.2

and test the installation with poetry --version.

3 - Install the package and its dependencies using poetry

cd to the root of the repository and run

poetry install --with linting,testing

4 - Download the data to run the tests on

To download the data, cd to the root of the repository run this command.

fedpydeseq2-download-data --raw_data_output_path data/raw

This way, you create a data/raw subdirectory in the directory containing all the necessary data. If you want to modify the location of this raw data, you can in the following way. Run this command instead:

fedpydeseq2-download-data --raw_data_output_path MY_RAW_PATH

And create a file in the tests directory named paths.json containing - A raw_data field with the path to the raw data MY_RAW_PATH - An optional assets_tcga field with the path to the directory containing the opener.py file and its description (by default present in the fedpydeseq2_datasets module, so no need to specify this unless you need to modify the opener). - An optional processed_data field with the path to the directory where you want to save processed data. This is used if you want to run tests locally without reprocessing the data during each test session. Otherwise, the processed data will be saved in a temporary file during each test session. - An optional default_logging_config field with the path to the logging configuration used by default in tests. For more details on how logging works, please refer to this dedicated section - An optional workflow_logging_config field with the path to the logging configuration used in the logging tests.