The future of summaries

[cleme]

Is your feature request related to a problem? Please describe.
Summaries take a significant amount of effort to generate, and the code is getting increasingly complex to keep functional and to maintain. We already had a release (0.7.0.1) to address these issues, but unsuccessfully as we later found out. Currently summaries do not work in production, and the final PDF has to be manually generated.

Describe the solution you'd like

• Continue using current approach: not ideal, as it means we cannot fully automate analysis. Code will be hard to maintain and modify in the future if we want to include additional analyses in results (which we want)
• Redo the notebooks to simplify dependencies: convert all code to R so we only depend on libraries that can be directly managed under R.
• Basic HTML solution: generate an index.html file that links to individual plots with some text describing result.
• Full visualization through web interface: similar to current Q2 solution.

[adamcantor22]

Since we did succeed in getting summaries to work in production, do we want to close this issue? Or do we still want to consider this down the line?

[cleme]

Let's keep open. The PDF is nice, but I think at some point in the future we'll want to re-evaluate what is the best way to summarize results for users.

[adamcantor22]

Consider embedding Qiime2 viewer into a new MMEDS tab so results can be accessed without a summary.

[cleme]

Consider how adding tools to MMEDS impacts summary generation. The current implementation is not automated and likely not generalizable (see #457 also)