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BayesMixR - an R interface to BayesMix #124

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merged 110 commits into from
Oct 10, 2023
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TeoGiane
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@TeoGiane TeoGiane commented Apr 11, 2022

This PR introduces bayesmixr, the R command line interface to bayesmix. The idea is the development of an R package which is almost identical to bayesmixpy, its Python counterpart.

As a demonstration, I reproduced the gaussian_mix_uni.Rmd notebook copy-pasting the .ipynb version.

Documentation is already available. There is still something to do, in the meantime, any suggestion is appreciated!

What to do:

  • Type checks for function inputs
  • Tests and CI

@TeoGiane TeoGiane linked an issue Apr 12, 2022 that may be closed by this pull request
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OK, I guess the package is ready for review. Let me know what you think!

@TeoGiane TeoGiane marked this pull request as ready for review April 12, 2022 12:46
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@mberaha mberaha left a comment

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I think this is a great addition! Thanks a lot @TeoGiane :)

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@brunoguindani brunoguindani left a comment

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Apart from a few minor documentation chores missing, this is great! Thank you!

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@TeoGiane TeoGiane marked this pull request as draft April 13, 2022 10:13
@TeoGiane TeoGiane marked this pull request as ready for review April 13, 2022 12:01
@TeoGiane TeoGiane marked this pull request as draft April 13, 2022 17:17
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TeoGiane commented Oct 3, 2023

I guess we are finally read to merge. Since last major review:

  • We rely on testthat to provide unit tests. Once bayesmixr is installed, we can run tests via testthat::test_package("bayesmixr") in R
  • CI is also available for bayesmixr. GitHub actions have been fixed and updated. Once merged, we only need to uncomment lines in resources/docker/test/Dockerfile (where we install the package) and in .github/workflows/test.yaml (where we run unit tests).
  • Just like the python counterpart, run_mcmc can also return the whole MCMC chain. We interact with protobuf in R via the RProtoBuf package, an R wrapper for the C++ protobuf interface.
  • Many small fixes in the code.

Enjoy!

@TeoGiane TeoGiane marked this pull request as ready for review October 3, 2023 14:02
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mberaha commented Oct 3, 2023

Definitely good to go!

Sync to bayesmix-dev/bayesmix:master
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Awesome! Thank you! Just one very small observation below...

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@TeoGiane TeoGiane merged commit e74eaba into bayesmix-dev:master Oct 10, 2023
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@TeoGiane TeoGiane deleted the bayesmixr branch October 10, 2023 22:14
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Python and R (command line) interface
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