Revise and complete Reproducibility Principles & Practices

[nick-ulle]

Things to do for the new iteration:

• Set up pixi to manage the software environment
• Add narrative for blank sections
  • Version Control for Data (moving to Chapter 4)
  • Chapter 4
• Address remaining items in Review Suggestions #1
• Link to Intro to Databases reader in database section (currently 3.2.2.1)
  • The databases section is under artifact preservation (and emphasizes version control), but they're also important for data organization, which should be addressed somehow.
• Mention pixi in section about environment managers (currently 3.5.1)
• Mention strategies for organizing and naming notebooks (section TBD)
• Link to the slide deck
• Link to the cheat sheet

[nick-ulle]

More things to change:

• Chapter 1: edit phrasing for clarity
• Chapter 2: edit phrasing for clarity
• Section 2.1.1: the tip in this section overemphasizes data analysis (possibly belongs elsewhere)
• Section 2.1.2: the tip in this section needs more context
• Chapter 3: edit phrasing for clarity
• Rename "Core Practices" -> "Primary Practices" and "Case-by-case Core Practices" -> "Secondary Practices"