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
  • never install with pip in the base environment!
  • FAQ with...
    • What do I do if my conda is already broken because I wasn't following best practices?
    • Can I use the install commands from anaconda.org directly? (No, you must specify -c conda-forge unless it's in your channels list.)
• Git/Github
• Jupyter notebooks
• Docker #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