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project-template

@eeshanbot's project template for organized exploratory computational research

welcome

Welcome to my project template! I see automation and transparency as key components for following FAIR data principles:

  • Findability
  • Accessibility
  • Interoperability
  • Reusability

As this is a GitHub "template", the best way to use it is to download to your own computer or click "use this template".

structure

data

This folder holds local data. This is a read-only folder. I will put project specific data here and more general or multiple-project data products somewhere else.

src

This folder holds functions. I like to use the following syntax. I put anything into a function that I might use more than once.

function calls

Helper functions tend to start with eb_ for autocompletion (eager beaver). They are then followed by one of:

  • view_ = makes a figure (does not save it automatically)
  • get_ = runs a small computation
  • compute_ = runs a large computation
  • read_ = reads some kind of input file, generally customized by data stream
  • write_ = writes some kind of output file
  • h_ = helper for miscellaneous, useful tasks
variable style guide
  • constants = A_CONSTANT_VARIABLE
  • number of = nVal, nSamples, num_samples
  • important / dynamic = importantVariablesHere
  • scratch = k, m, n, x, y, z, a, b, c, d (never i or j)
  • iterator = iVal, iSamples or kk,mm,nn...

pipeline

This folder holds scripts. These scripts access data from data and functions from src. Each script or collection of scripts lives in an aptly named sub-folder based on the desired task. Scripts are named with the following prefixes:

  • io = a simple input/output script
  • v = viewer
  • p = process

results

This folder holds figures, tables, etc, that you may want to decouple from the processing pipeline. You can always automate this with a symbolic link.

doc

This folder holds LaTeX code, makefiles, bib files, etc for eventual journal submission. Sometimes I like to add a journal folder and write entries in Markdown; this is a nice Markdown cheat sheet.