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VUMC Software Carpentry Workshop

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This repository contains teaching materials for the VUMC Software Carpentry Workshop, held each summer by the Department of Biostatistics and the Department of Biomedical Informatics.

To obtain and use the materials for the workshop, you will need to have both Git and Python (version 3.5) installed on your system. Instructions for this are provided on the workshop website.

Having done this, follow the steps below for getting up and running with the course materials.

Getting this repository

git clone https://github.com/vubiostat/swc_workshop.git

If you are not familiar with Git and GitHub, you can simply download the zip file of the repository at the top of the main repository page.

Then, move to the directory created by the clone/zip file:

cd swc_workshop

and install everything using conda:

conda config --add channels conda-forge
conda env create -f environment.yml

This will create an environment called workshop that includes the packages required for the course.

To use the environment, you may type:

source activate workshop

on MacOS and Linux, or:

activate workshop

on Windows.

Enabling parallel IPython

To enable IPython parallel computing in the notebook environment, type:

ipcluster nbextension enable 

from the command line.

Running Jupyter notebooks

To use any of the Jupyter notebooks included in this repository, run the following command from the terminal:

jupyter notebook

This will open your default browser to Jupyter running on your system.

Jupyter

Click on the notebooks directory, then on one of the enclosed notebook files (.ipynb extension) within.

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