From b61605bb40b2ca6c818d8854f3f2cbc47e5e84f4 Mon Sep 17 00:00:00 2001 From: Eva Hamrud <50098063+evaham1@users.noreply.github.com> Date: Fri, 22 Nov 2024 11:34:30 +1100 Subject: [PATCH] update github repo readme with updates from oct and nov --- README.md | 62 +++++++++++++++++++++++++++++++++------- inst/README-WhatsNew.Rmd | 19 ++++++++++++ inst/README.Rmd | 1 - 3 files changed, 71 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 1ade36ea..1ed889e5 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ -[![](https://img.shields.io/badge/release%20version-6.28.0-green.svg)](https://www.bioconductor.org/packages/mixOmics) [![download](http://www.bioconductor.org/shields/downloads/release/mixOmics.svg)](https://bioconductor.org/packages/stats/bioc/mixOmics) [![R build status](https://github.com/mixOmicsteam/mixOmics/workflows/R-CMD-check.yml/badge.svg)](https://github.com/mixOmicsteam/mixOmics/actions) @@ -43,14 +42,6 @@ BiocManager::install('mixOmics') library(mixOmics) ``` -You can also install the [development -version](https://github.com/mixOmicsTeam/mixOmics/tree/development) for -new features yet to be widely tested: - -``` r -BiocManager::install("mixOmicsTeam/mixOmics@development") -``` - ### From Github Bioconductor versions are updated twice a year, between these updates @@ -58,7 +49,15 @@ you can downlod the latest stable version of `mixOmics` from `Github` using: ``` r -devtools::install_github("mixOmicsTeam/mixOmics") +BiocManager::install('mixOmicsTeam/mixOmics') +``` + +You can also install the [development +version](https://github.com/mixOmicsTeam/mixOmics/tree/development) for +new features yet to be widely tested: + +``` r +BiocManager::install("mixOmicsTeam/mixOmics@development") ``` ### From `Docker` container @@ -268,6 +267,49 @@ Thank you for using `mixOmics`! ## What’s New +#### November 2024 + +- enhancement request + [\#216](https://github.com/mixOmicsTeam/mixOmics/issues/216) + implemented parallel processing using `BPPARAM` across all `tune()` + functions + +- feature request + [\#335](https://github.com/mixOmicsTeam/mixOmics/issues/335) added + `seed` argument to `perf()` functions for better reproducibility + +- feature request + [\#334](https://github.com/mixOmicsTeam/mixOmics/issues/334) added + `seed` argument to `tune()` functions for better reproducibility + +- bug fix implemented for + [\#307](https://github.com/mixOmicsTeam/mixOmics/issues/307) + `plotIndiv()` ellipses colours not matching points, now sample group + order is respected and colours can be customised for points and + ellipses + +- updated documentation to fix issue + [\#297](https://github.com/mixOmicsTeam/mixOmics/issues/297) broken + link in bookdown vignette + +- updated documentation to fix issue + [\#296](https://github.com/mixOmicsTeam/mixOmics/issues/296) typo in + vignette + +#### October 2024 + +\*\* Version 6.30.0 \*\* + +[Bioconductor release version +6.30.0](https://bioconductor.org/packages/release/bioc/html/mixOmics.html) +released end of October 2024 Minor bug fixes and updated deprecated code +and unit tests, no major code changes and no changes to user experience +of mixOmics. + +- bug fix implemented for + [\#293](https://github.com/mixOmicsTeam/mixOmics/issues/293) + `splsda()` example code error + #### March 2022 - bug fix implemented for [Issue diff --git a/inst/README-WhatsNew.Rmd b/inst/README-WhatsNew.Rmd index 53b6cae5..c46c49ae 100644 --- a/inst/README-WhatsNew.Rmd +++ b/inst/README-WhatsNew.Rmd @@ -17,6 +17,25 @@ opts_chunk$set( echo = TRUE, eval = FALSE, warning = FALSE, message = FALSE) ## What's New +#### November 2024 + +* enhancement request [#216](https://github.com/mixOmicsTeam/mixOmics/issues/216) implemented parallel processing using `BPPARAM` across all `tune()` functions +* feature request [#335](https://github.com/mixOmicsTeam/mixOmics/issues/335) added `seed` argument to `perf()` functions for better reproducibility +* feature request [#334](https://github.com/mixOmicsTeam/mixOmics/issues/334) added `seed` argument to `tune()` functions for better reproducibility + +* bug fix implemented for [#307](https://github.com/mixOmicsTeam/mixOmics/issues/307) `plotIndiv()` ellipses colours not matching points, now sample group order is respected and colours can be customised for points and ellipses + +* updated documentation to fix issue [#297](https://github.com/mixOmicsTeam/mixOmics/issues/297) broken link in bookdown vignette +* updated documentation to fix issue [#296](https://github.com/mixOmicsTeam/mixOmics/issues/296) typo in vignette + +#### October 2024 +** Version 6.30.0 ** + +[Bioconductor release version 6.30.0](https://bioconductor.org/packages/release/bioc/html/mixOmics.html) released end of October 2024 +Minor bug fixes and updated deprecated code and unit tests, no major code changes and no changes to user experience of mixOmics. + +* bug fix implemented for [#293](https://github.com/mixOmicsTeam/mixOmics/issues/293) `splsda()` example code error + #### March 2022 * bug fix implemented for [Issue #196](https://github.com/mixOmicsTeam/mixOmics/issues/196). `perf()` can now handle features with a `(s)pls` which have near zero variance. diff --git a/inst/README.Rmd b/inst/README.Rmd index ff9aa4aa..a73330fe 100644 --- a/inst/README.Rmd +++ b/inst/README.Rmd @@ -33,7 +33,6 @@ pkg_license <- read.dcf("../DESCRIPTION")[, "License"] pkg_license_badge <- sprintf("https://img.shields.io/badge/license-%s-lightgrey.svg", pkg_license) ``` -`r badge_bioc_release("mixOmics", "green")` `r badge_bioc_download_rank('mixOmics')` `r badge_github_actions(re = "mixOmicsteam/mixOmics", action = "R-CMD-check.yml")` `r badge_last_commit("mixOmicsTeam/mixOmics", branch='master')`