science

Data science project for training

---

Setup

The environment

To run the notebooks you need to create an environment with the dependencies. There are two options:

Docker

If you have docker in your system, you run a jupyter lab server with:

docker compose up --build

And if you want to get into the container, use a terminal in jupyter lab, vscode remote development or run this command:

docker exec -it scivizz_notebooks /bin/bash

Conda environment

Create the environment with:

mamba env create -n science -f environment.yml

This will create an environment called science with a common set of dependencies.

git (if needed) and pre-commit hooks

If this project is a new and standalone (not a module in a bigger project), you need to initialize git:

git init

If the project is already in a git repository, you can skip this step.

To install the pre-commit hooks, with the environment activated and in the project root directory, run:

pre-commit install

Update the environment

If you need to update the environment installing a new package, you simply do it with:

mamba install [package]  # or `pip install [package]` if you want to install it via pip

then update the environment.yml file so others can clone your environment with:

mamba env export --no-builds -f environment.yml