The code (and datasets) written for and used in the microbiome ML benchmark paper we're writing. The goal is to have this in the form of an actionable python package as soon as we're done.

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Installation for development

Clone this repository to a location on your computer

git clone https://git.io-warnemuende.de/sperlea/microbiome_ML_benchmark.git

git@git.io-warnemuende.de:sperlea/microbiome_ML_benchmark.git

Install poetry

Full instructions can be found on https://python-poetry.org/docs/.

Short version (Unix/Win-WSL):

curl -sSL https://install.python-poetry.org | python3 -

Short version (Win-Powershell):

(Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | py -

Check for success: poetry --version.

Install project

Run poetry install in the folder with the pyproject.toml. This will read the pyproject.toml file from the current project, resolves the dependencies, and installs them to the (possibly newly created) virtual environment .venv in your project folder.

In your IDE use project_dir/.venv/bin/python.

To activate/deactivate the virtual environment from command line use poetry shell and deactivate.

Install dependencies

Instead of pip install ... or conda install ... use poetry add ....
Use poetry add ... -G dev for adding a development dependency.
This will check if there are any conflicts with other dependencies and (on success) add the dependency to the pyproject.toml as well as installing it.

See here for further details, e.g. adding repositories or local sources.