Reproducibility guide

[mikecuoco]

Started on a new branch here: 2a3fb93

Rough outline:

1. Background and Motivation:

• [ ] Reproducibility vs Replicability
• [ ] What if I'm developing a method?
• [ ] The reproducibility crisis
• [ ] Proposed reprodubility standards

2. Solutions and Strategies (maybe create new page for each)

• [ ] Conda
• [ ] Git/Github
• [ ] Jupyter notebooks
• [ ] #14
• [ ] Snakemake/Nextflow

Other TODOS:

• [ ] add citations with bibtex file and https://jupyterbook.org/en/stable/content/citations.html
• [ ] add images

[aryarm]

sounds great! let's do it

[aryarm]

I made some progress on the conda page while I was out of town

It's not done yet, though. I have a few more sections to fill out and a bunch of TODOs too

[aryarm]

for the conda page, it would also be great to have a page that discusses the "workflow" for maintaining a yml file

for example, we could mention:

• [ ] how to search for a package on anaconda.org
• [ ] how to figure out which version of the package that conda installed and then adding that version to the yml file
• [ ] the trick of deleting versions in the yml file and then adding them back to try to resolve conflicts