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Demo project FAIR-data

This is a dummy project to demonstrate the Deltares FAIR-data Cookbook. Note that it is a dummy project, so no realistic calculations are performed. More information about the FAIR cookbook is available at the Deltares wiki. This dummy project is meant to get a basic understanding and working knowledge of version control for scripts and data, workflow management and sensible folder structure. For this we use GIT, DVC, Snakemake and Cookiecutter. More information and instructions can be found in Deltares documentation and other online sources, but for the practical example the instructions below will suffice.

Version control and retrieving the repository

GIT is used as version control system for the scripts.

First, if you do not have git already installed:

Then: Open Windows Powershell

To get a clone of the repository use the following command in powershell:

git clone https://github.com/Deltares-research/FAIR-data-example-project.git

Note

Probably the first time you try a powershell command, it will throw you an error about execution policies or not being able to run a script. In this case use the command:

Set-ExecutionPolicy RemoteSigned -Scope CurrentUser

Scripting environment

To be able to run this dummy project Python is required, in this case we use pixi to install a Python environment and all the required dependencies.

Download & install pixi with the command in Windows Powershell:

iwr -useb https://pixi.sh/install.ps1 | iex

Change directory (cd in short) in windows powershell with:

cd FAIR-data-example-project

Install the python environment:

pixi install

Data version control

Dcv is used as a data version control system for the data that is required for this dummy project. This provides Git-like data version control to keep track of changes in data and to share data with colleagues.

Manage the worklow

Snakemake is used to manage the workflow. These are managed in a single snakefile Individual steps (e.g. script/shell command) are added as Snakemake "rules". Each rule defines which input and output is required and generated in each step. Based on this snakemake determines the order in which multiple rules need to be executed.

Folder structure of the project

Cookiecutter is used to create a standardized template for a folder structure for projects. Below is an example of such a template created using Cookiecutter:

├── AUTHORS.md
├── LICENSE
├── README.md
├── bin                 <- Your compiled model code can be stored here (not tracked by git)
├── config              <- Configuration files, e.g., for doxygen or for your model if needed
├── data                
│   ├── 1-external      <- Data external to the project.
│   ├── 2-interim       <- Intermediate data that has been altered.
│   ├── 3-input         <- The processed data sets, ready for modeling.
│   ├── 4-output        <- Data dump from the model.
│   └── 5-visualization <- Post-processed data, ready for visualisation.
├── docs                <- Documentation, e.g., doxygen or scientific papers (not tracked by git)
├── notebooks           <- Jupyter notebooks
├── reports             <- For a manuscript source, e.g., LaTeX, Markdown, etc., or any project reports
│   └── figures         <- Figures for the manuscript or reports
└── src                 <- Source code for this project
    ├── 0-setup         <- Install necessary software, dependencies, pull other git projects, etc.
    ├── 1-prepare       <- Scripts and programs to process data, from 1-external to 2-interim.
    ├── 2-build         <- Scripts to create model specific inputm from 2-interim to 3-input. 
    ├── 3-model         <- Scripts to run model and convert or compress model results, from 3-input to 4-output.
    ├── 4-analyze       <- Scripts to post-process model results, from 4-output to 5-visualization.
    └── 5-visualize     <- Scripts for visualisation of your results, from 5-visualization to ./report/figures.

Explanation of the project

In this dummy project some very basic calculations are done using the SWAN wave model. For a more detailed explanation, read TECHNICAL.md.

Pizza course exercises

This pizza course consists of two exercises. This repository contains the first exercise, where you will reproduce an existing example project. You can find the first excercise here.

The second exercise is contained in a different Github repository. This exercise will walk you through the steps to upgrade your project from a set of scripts to a fully reproducible workflow. You can find it here.