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Introduction

This is a command-line interface (CLI) for the PhenoPLIER project. PhenoPLIER is a flexible computational framework that combines gene-trait and gene-drug associations with gene modules expressed in specific contexts. This CLI program aims to provide a more user-friendly interface for users to interact with the PhenoPLIER project and integrate it into their own computational pipelines.

Installation & Usage

Please refer to our Wiki page for the insturctions: Tutorial

Development Environment Setup

To set up the development environment for this program, we provided a bootstrap script. Simply run this command at the root directory of the project:

. ./scripts/setup_env.sh

This script will use Conda to create a new virtual environment named "phenoplier-cli", with Poetry inside for Python package management.

If no errors occur, you can activate the environment by running the following command:

conda activate phenoplier-cli-dev

Then check if the environment is set up correctly by running the following command:

poetry run python -m phenoplier -v

You should see the version of the program printed out.

Package Publishing

This project is managed by Poetry. To publish the package to PyPI. Poetry supports the use of PyPI and private repositories for package discovery and publishing. During this development phase, we will TestPyPI to publish the package.

First we need to save the credentials for the TestPyPI repository. Run the following command:

# Add the TestPyPI repository
poetry config repositories.test-pypi https://test.pypi.org/legacy/
# Add the TestPyPI token
poetry config pypi-token.test-pypi <Your_Test_PyPI_Token>

Then we can build and publish the package to TestPyPI by running the following command:

poetry build
poetry publish -r test-pypi

After the package is published, you can install using the pip command. Note that, for testing purposes, you may want to create a new virtual environment to install the package. Thus, instead of installing the package globally by running the above command, you can create a new virtual environment and install the package there:

python3 -m venv /tmp/phenoplier-env
source /tmp/phenoplier-env/bin/activate
python3 -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple phenoplier

(The --extra-index-url option is used to specify the default PyPI repository for dependencies, as packages such as and pandas are not available on TestPyPI.)

Check if the package is installed correctly by running the following command:

phenoplier -v

Testing

In the root directory of the project, run the following command:

PYTHONPATH=. pytest -rs --color=yes test/

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