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Add a getting started tutorial #109

Merged
merged 28 commits into from
Mar 6, 2024
Merged

Add a getting started tutorial #109

merged 28 commits into from
Mar 6, 2024

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SamuelBrand1
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This is WIP aimed at addressing #100 (and contributing to #97) using a Pluto notebook approach to documentation examples.

The approach is to create the getting started tutorial as a notebook, which is easy to develop and also works as a .jl script. HTML render for documentation can be supplied by PlutoStaticHTML.

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Additions:

  • The getting started example Pluto notebook is here.
  • The build step very closely follows TuringGLM docs approach here.

Not implemented

This PR only addresses a single notebook. We will add some method to automate adding all the examples to the linked pages in the docs in a future PR.

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seabbs commented Mar 5, 2024

This is all looking great to me. I guess we need the build uncomment and the toy model example in tests removed and this is good to go?

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SamuelBrand1 commented Mar 5, 2024

This is all looking great to me. I guess we need the build uncomment and the toy model example in tests removed and this is good to go?

Yep. Also, CI check. It builds the docs locally, but still waiting for CI.

EDIT: ofc, I'd forgotten I'd left build commented...

@SamuelBrand1 SamuelBrand1 marked this pull request as ready for review March 5, 2024 13:52
@SamuelBrand1 SamuelBrand1 requested a review from seabbs March 5, 2024 13:52
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seabbs commented Mar 5, 2024

The docs are broken on main (so I'm not sure how they build for you locally) due to #108

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The docs are broken on main (so I'm not sure how they build for you locally) due to #108

Hmmmm....

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codecov-commenter commented Mar 5, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.74%. Comparing base (93eb67c) to head (e805792).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #109   +/-   ##
=======================================
  Coverage   97.74%   97.74%           
=======================================
  Files           6        6           
  Lines         133      133           
=======================================
  Hits          130      130           
  Misses          3        3           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@seabbs seabbs force-pushed the add-doc-examples branch from ca2707e to d97c92a Compare March 5, 2024 17:32
@seabbs seabbs enabled auto-merge March 5, 2024 17:33
@seabbs seabbs disabled auto-merge March 5, 2024 17:33
@seabbs seabbs enabled auto-merge (squash) March 5, 2024 17:33
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This is looking really good. Two minor points

EpiAware/docs/Project.toml Show resolved Hide resolved
EpiAware/docs/src/examples/getting_started.jl Outdated Show resolved Hide resolved
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seabbs commented Mar 6, 2024

Note I think that #115 should be addressed here as its linked to this PR and @SamuelBrand1 likely has all the context here from freshly porting over the example

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Note I think that #115 should be addressed here as its linked to this PR and @SamuelBrand1 likely has all the context here from freshly porting over the example

OK, and I hadn't updated the notebook to reflect the new latent_model kwarg. Annoying.

@seabbs seabbs disabled auto-merge March 6, 2024 11:44
@seabbs seabbs enabled auto-merge (squash) March 6, 2024 11:44
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SamuelBrand1 commented Mar 6, 2024

I think the only dep we didn't want in Test env was CSV. The DataFramesMeta dep gets used in testing spread_draws

This PR closes #115

@SamuelBrand1 SamuelBrand1 requested a review from seabbs March 6, 2024 12:30
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Nice. LGTM

@seabbs seabbs merged commit fc349d7 into main Mar 6, 2024
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@seabbs seabbs deleted the add-doc-examples branch March 6, 2024 13:33
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Add content to or replace the getting-started example
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