search

Bioconductor / BiocParallel

Bioconductor facilities for parallel evaluation
https://bioconductor.org/packages/BiocParallel
65 stars 29 forks source link

@Bioconductor/sweave2rmd: Conversion of Introduction_to_BiocParallel.Rnw to Rmd #226

Closed phyleria closed 1 year ago

phyleria commented 1 year ago

Hello, As part of the Sweave2rmd project, I have made commits that:

  1. Convert the Introduction_To_BiocParallel.Rnw to Rmd
  2. Remove the Rnw file

Please find both the PDF and HTML files below:

Kindly review the PR and I will appreciate your feedback. Thank you! Close #225

phyleria commented 1 year ago

Sorry for that, I'll make sure to correct it. Thank you!

On Wed, Oct 19, 2022, 8:39 PM Martin Morgan @.***> wrote:

@.**** commented on this pull request.

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999753896 :

@@ -0,0 +1,961 @@ +--- +title: "Introduction to BiocParallel" +author: "Phyllis Atieno"

I do not think it is correct for you to claim sole authorship of this vignette. The material was developed by others, and they deserve (primary) credit

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999754355 :

+vignette: >

  • %\VignetteIndexEntry{Vignette Title}
  • %\VignetteEngine{knitr::rmarkdown}
  • %\VignetteEncoding{UTF-8} +output:
  • BiocStyle::html_document

  • +---

  • +Introduction +============

  • +Numerous approaches are available for parallel computing in R. The CRAN Task View for +high performance and parallel computing provides useful high-level summaries and package +categorization. +Most Task View packages cite or identify one or more of snow , Rmpi, multicore or foreach as

In the original these packages were italicized and linked to their CRAN 'landing pages', snow

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999755821 :

  • %\VignetteEncoding{UTF-8} +output:
  • BiocStyle::html_document

  • +---

  • +Introduction +============

  • +Numerous approaches are available for parallel computing in R. The CRAN Task View for +high performance and parallel computing provides useful high-level summaries and package +categorization. +Most Task View packages cite or identify one or more of snow , Rmpi, multicore or foreach as +relevant parallelization infrastructure. Direct support in R for parallel computing started +with release 2.14.0 with inclusion of the parallel package which contains modified versions of +multicore and snow .

Packages should be treated consistently -- linked to CRAN, same font -- but here they are now italic whereas previously they were bold. I do not know what the appropriate style is, but I would imagine it is whatever the BiocStyle package implements for the LaTeX macro \CRANpkg{}.

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999757743 :

  • the parallel back end uses BiocParallelParam instances.

  • +Quick start +===========

  • +The BiocParallel package is available at bioconductor.org and can be downloaded via BiocManager:

  • +``` +if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager") +BiocManager::install("BiocParallel") +```

  • +Load BiocParallel

  • +library(BiocParallel)

This and all (?) code chunks must be evaluated. This is a central feature of vignettes -- the code in the vignette has to actually work.

library(BiocParallel)

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999762400 :

+ +Load BiocParallel + +library(BiocParallel) + + +The test function simply returns the square root of "x". + +FUN <- function(x) { round(sqrt(x), 4) } + + +Functions in BiocParallel use the registered back-ends for parallel evaluation. The +default is the top entry of the registry list. + +``` +registered()

The evaluated code will insert the output into the processed document; you only need to provide the code to be evaluated

registered()

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/BiocParallel/pull/226#pullrequestreview-1148014625, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIVVBJQJFE76X6CDBJGLN3WEAW6FANCNFSM6AAAAAARITNZ6Q . You are receiving this because you were assigned.Message ID: @.***>

phyleria commented 1 year ago

Thank you so much @mtmorgan for the feedback. I'm working on the changes requested 👍

On Wed, Oct 19, 2022, 8:39 PM Martin Morgan @.***> wrote:

@.**** commented on this pull request.

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999753896 :

@@ -0,0 +1,961 @@ +--- +title: "Introduction to BiocParallel" +author: "Phyllis Atieno"

I do not think it is correct for you to claim sole authorship of this vignette. The material was developed by others, and they deserve (primary) credit

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999754355 :

+vignette: >

  • %\VignetteIndexEntry{Vignette Title}
  • %\VignetteEngine{knitr::rmarkdown}
  • %\VignetteEncoding{UTF-8} +output:
  • BiocStyle::html_document

  • +---

  • +Introduction +============

  • +Numerous approaches are available for parallel computing in R. The CRAN Task View for +high performance and parallel computing provides useful high-level summaries and package +categorization. +Most Task View packages cite or identify one or more of snow , Rmpi, multicore or foreach as

In the original these packages were italicized and linked to their CRAN 'landing pages', snow

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999755821 :

  • %\VignetteEncoding{UTF-8} +output:
  • BiocStyle::html_document

  • +---

  • +Introduction +============

  • +Numerous approaches are available for parallel computing in R. The CRAN Task View for +high performance and parallel computing provides useful high-level summaries and package +categorization. +Most Task View packages cite or identify one or more of snow , Rmpi, multicore or foreach as +relevant parallelization infrastructure. Direct support in R for parallel computing started +with release 2.14.0 with inclusion of the parallel package which contains modified versions of +multicore and snow .

Packages should be treated consistently -- linked to CRAN, same font -- but here they are now italic whereas previously they were bold. I do not know what the appropriate style is, but I would imagine it is whatever the BiocStyle package implements for the LaTeX macro \CRANpkg{}.

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999757743 :

  • the parallel back end uses BiocParallelParam instances.

  • +Quick start +===========

  • +The BiocParallel package is available at bioconductor.org and can be downloaded via BiocManager:

  • +``` +if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager") +BiocManager::install("BiocParallel") +```

  • +Load BiocParallel

  • +library(BiocParallel)

This and all (?) code chunks must be evaluated. This is a central feature of vignettes -- the code in the vignette has to actually work.

library(BiocParallel)

In vignettes/Introduction_To_BiocParallel.Rmd https://github.com/Bioconductor/BiocParallel/pull/226#discussion_r999762400 :

+ +Load BiocParallel + +library(BiocParallel) + + +The test function simply returns the square root of "x". + +FUN <- function(x) { round(sqrt(x), 4) } + + +Functions in BiocParallel use the registered back-ends for parallel evaluation. The +default is the top entry of the registry list. + +``` +registered()

The evaluated code will insert the output into the processed document; you only need to provide the code to be evaluated

registered()

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/BiocParallel/pull/226#pullrequestreview-1148014625, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIVVBJQJFE76X6CDBJGLN3WEAW6FANCNFSM6AAAAAARITNZ6Q . You are receiving this because you were assigned.Message ID: @.***>

jwokaty commented 1 year ago

@mtmorgan Thanks for your feedback. I also wanted to mention that @phyleria is also making this contribution as part of their application to Bioconductor for Outreachy. If it's okay, I'll review the changes as well.

phyleria commented 1 year ago

Hello @mtmorgan @jwokaty Kindly review the changes I've made from the feedback and changes requested. Thank you!

phyleria commented 1 year ago

Thanks Phylis for the updates. There are a few things that still need to be done, in particular getting the use of {r} correct in code chunks.

This is very close to being complete!

Thank you, let me work on them!

phyleria commented 1 year ago

Hi @mtmorgan Please review the changes I've made. I'll appreciate it thank you!

mtmorgan commented 1 year ago

Thanks @phyleria; I merged these changes after a few small updates outlined in https://github.com/Bioconductor/BiocParallel/commit/534ac1a726728975f9d5f5cddefc1362603c3b72.

This was a pretty challenging vignette! Thanks for your hard work, it would never have been translated without your help.

phyleria commented 1 year ago

Thank you so much @mtmorgan for the guidance. I learnt so much while translating this particular vignette. I really appreciate your corrections and feedback.