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Generate API docs #2347

Merged
merged 10 commits into from
Oct 13, 2024
Merged

Generate API docs #2347

merged 10 commits into from
Oct 13, 2024

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penelopeysm
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@penelopeysm penelopeysm commented Sep 26, 2024

Description

This PR generates API docs for Turing.jl itself. This exposes documentation for important things like samplers which are otherwise undocumented.

Many of the exported identifiers are defined in other packages (DynamicPPL, etc.) and re-exported and/or extended by Turing. Rather than inserting the actual docs (which can actually be quite difficult sometimes as it requires locating the right method), I've generally opted to put them in a table with links to the corresponding package documentation.

This PR also adds docstrings to exported identifiers where necessary, and fixes some inaccuracies in the MH() docstrings.

Closes #2344.

Preview the docs

https://turinglang.org/Turing.jl/previews/PR2347/

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codecov bot commented Sep 26, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 0.00%. Comparing base (40a0d84) to head (446f278).
Report is 1 commits behind head on master.

❗ There is a different number of reports uploaded between BASE (40a0d84) and HEAD (446f278). Click for more details.

HEAD has 16 uploads less than BASE
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Additional details and impacted files
@@            Coverage Diff             @@
##           master   #2347       +/-   ##
==========================================
- Coverage   86.67%   0.00%   -86.68%     
==========================================
  Files          24      22        -2     
  Lines        1599    1533       -66     
==========================================
- Hits         1386       0     -1386     
- Misses        213    1533     +1320     

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@penelopeysm penelopeysm force-pushed the pysm/docs branch 2 times, most recently from dda13b9 to 2efffe2 Compare September 27, 2024 01:21
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coveralls commented Sep 27, 2024

Pull Request Test Coverage Report for Build 11252307560

Details

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • 1325 unchanged lines in 21 files lost coverage.
  • Overall coverage decreased (-87.0%) to 0.0%

Files with Coverage Reduction New Missed Lines %
src/variational/VariationalInference.jl 4 0.0%
src/Turing.jl 9 0.0%
src/mcmc/gibbs_conditional.jl 12 0.0%
src/mcmc/is.jl 16 0.0%
src/stdlib/RandomMeasures.jl 22 0.0%
src/essential/container.jl 27 0.0%
ext/TuringDynamicHMCExt.jl 29 0.0%
src/mcmc/emcee.jl 47 0.0%
ext/TuringOptimExt.jl 50 0.0%
src/mcmc/ess.jl 51 0.0%
Totals Coverage Status
Change from base Build 11180921169: -87.0%
Covered Lines: 0
Relevant Lines: 1533

💛 - Coveralls

@penelopeysm penelopeysm force-pushed the pysm/docs branch 2 times, most recently from 8c368c5 to 8d408b4 Compare October 2, 2024 19:48
@penelopeysm penelopeysm changed the title (WIP) Generate API docs Generate API docs Oct 8, 2024
@penelopeysm penelopeysm marked this pull request as ready for review October 8, 2024 15:22
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penelopeysm commented Oct 8, 2024

I think this is finally ready :) Most of the changes can be seen via the preview docs (https://turinglang.org/Turing.jl/previews/PR2347/) but also please do check over the docstrings I added.

(There are no source code changes in this PR)

@yebai yebai requested review from sunxd3 and removed request for yebai October 8, 2024 16:34
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yebai commented Oct 8, 2024

@sunxd3 can you help review @penelopeysm's PR?

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1.11 tests failing because of compintell/Mooncake.jl#180

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Great work @penelopeysm

.github/workflows/Docs.yml Outdated Show resolved Hide resolved
docs/src/api.md Show resolved Hide resolved
# API: `Turing.Inference`

```@autodocs
Modules = [Turing.Inference]
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ideally, this page is more structured. but I think we should merge this now and fix it later.

src/Turing.jl Show resolved Hide resolved
Co-authored-by: Xianda Sun <5433119+sunxd3@users.noreply.github.com>
@penelopeysm penelopeysm merged commit 24e6870 into master Oct 13, 2024
45 of 62 checks passed
@penelopeysm penelopeysm deleted the pysm/docs branch October 13, 2024 11:33
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Just saw this; really like this @penelopeysm :)

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Regenerate API docs
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