use directory structure from this paper?

[NickleDave]

Hey @neuRowsATL and @bark-rach I promise not to get chatty on your repos but I just wanted to suggest maybe having a directory structure like in this paper? https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510 You'd have to give it a quick skim to get their reasoning, but basically they propose this, which I like because it doesn't overwhelm someone at first glance and makes it obvious what each pile of files is for:

Box 3. Project layout
.
|-- CITATION
|-- README
|-- LICENSE
|-- requirements.txt
|-- data
|  |-- birds_count_table.csv
|-- doc
|  |-- notebook.md
|  |-- manuscript.md
|  |-- changelog.txt
|-- results
|  |-- summarized_results.csv
|-- src
|  |-- sightings_analysis.py
|  |-- runall.py

[neuRowsATL]

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