export: Automatically minify JSON

[victorlin]

proposed by @tsibley on Slack

Context

Currently, JSON minification is opt-in with the --minify-json option. However, it is not uncommon for large-scale analyses to have thousands of tips resulting in a dataset file that takes significantly more time to load compared to a minified version.

Related issues

• Cannot open 750Mb Auspice JSON in Chrome auspice#1622
• Other discussions and emails from users that have been affected by large Auspice JSONs

Proposed solution

Make JSON minification the default behavior for anything >1000 tips (threshold used by @trvrb's example on Slack). This allows smaller JSONs (which don't gain much performance benefit with minification) to be in the indented, human-readable format.

[corneliusroemer]

I support minification by default. Should we offer an option for pretty printing or is that unnecessary as one can simply use jq '.' or similar to do so?

[tsibley]

@corneliusroemer Yeah, that would be the (new) --no-minify-json option to disable minification (i.e. the current default behaviour). Discussed in the linked Slack thread, but not noted here.

[victorlin]

Implemented in Augur version 24.0.0:

export v2: Automatically minify large outputs. Use --no-minify-json to disable this default behavior.