diff --git a/README.md b/README.md index 4cccfde2a83c64da399c42fc00fd24bdcfbbf9d9..7f4f9691025901276b40b8a917b12000da94af7b 100644 --- a/README.md +++ b/README.md @@ -12,4 +12,66 @@ - demo interact - demo widget +## Materials requirements + +We will use jupyter notebook and some python libraries. +The are 2 ways to create a suitable environment for this course: + +- from a python environment +- from a conda/mamba environment + +But whatever your choice you need to have git installed to get the course materials + + +### from virtual environment + +To create a python environment (to do only once) + + python3 -m venv Scientific_Python + cd Scientific_Python + source bin/activate + git clone https://gitlab.pasteur.fr/hub-courses/scientific_python.git Scientific_Python_Course + cd Scientific_Python_Course + python -m pip install -r requirements.txt + +To exit from the environment + + deactivate + +To reactivate the environment + + cd Scientific_Python + source bin/activate + + # to run jupyter notenook server + jupyter-lab + +### from conda/mamba (recommended for windows guys) + + +To create a Conda/mamba environement you have to install Conda(anaconda or miniconda) or mamba +Then create your environement (to do only once) + + mamba env create -n Scientific_Python -c conda-forge bioconda + conda activate Scientic_Python + + # get the course materials + git clone https://gitlab.pasteur.fr/hub-courses/scientific_python.git Scientific_Python_Course + cd Scientific_Python_Course + + # install prerequisites + mamba install --file requirements.txt + +To exit from the conda environment/mamba + + conda deactivate + +To reactivate the environment + + conda activate Scientific_Python + + # to run jupyter notebook server + jupyter-lab + +