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Mini state blog #1

Open matthewlawrenceklein opened 2 years ago

matthewlawrenceklein commented 2 years ago

This PR serves to bring @meren and @mschecht into the fold for a state-centric blogpost. Matt's going to add a section related to his usage of mini states in the ecophylo workflow, and Meren will hopefully fact-check and review the post for tone and other intangibles ;)

Meren, let me know if this would make more sense as a fiesta issue until the post is in 'publishable condition' and I can migrate the discussion there!

meren commented 2 years ago

This is a great place to discuss this, @matthewlawrenceklein! Thank you for the PR. I look forward to reading both sections from you and Matt together :)

One quick note: lines like this don't render well:

(...) we can run anvi-export-state -p PROFILE.db -o my_perfect_figure.json -s my_perfect_figure to export (...)

It is better to have a code block that is dedicated to that command so it looks more like this everywhere:

(...) we can run,

anvi-export-state -p PROFILE.db \
                  -o my_perfect_figure.json \
                  -s my_perfect_figure

to export (...)

Another quick note is that minified states are best for programmers, and not users. For instance, here is a mini state used by anvi-display-functions, where the programmer replaces __FUNCTIONS_LAYER_NAME__ in this template with whatever is the function layer name is right before putting it into a new profile database to generate. I think it would be great to cover this aspect of mini states somehow :)

matthewlawrenceklein commented 2 years ago

It is better to have a code block

good call. done!

minified states are best for programmers, and not users.

Do you think it would make more sense to branch this post off into two discrete posts: one covering the basic concepts and programs related to working with state in anvio, the other going into mini states and their programmatic use cases?

meren commented 2 years ago

I'm sure programmers could benefit from learning more about the utility of state, and users from seeing additional ways to use it.

I would start from a general description of state, and then mention that there are two main sections in this post, for users, and for developers, and then divide the content into two :)

meren commented 2 years ago

divide the content into two

by which I mean distinct subsections in the same post :)

matthewlawrenceklein commented 2 years ago

mention that there are two main sections in this post, for users, and for developers,

perfect! A state-centric blog post for everyone!