In lcolladotor/biocthis: Automate package and project setup for Bioconductor packages

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

biocthis

r BiocStyle::Githubpkg("lcolladotor/biocthis") is an R package that expands r BiocStyle::CRANpkg("usethis") with Bioconductor-friendly templates. These templates will help you quickly create an R package that either has Bioconductor dependencies or that you are thinking of submitting to Bioconductor one day. r BiocStyle::Githubpkg("lcolladotor/biocthis") has functions that can also enhance your current R packages that either are already distributed by Bioconductor or have Bioconductor dependencies. r BiocStyle::Githubpkg("lcolladotor/biocthis") also includes a Bioconductor-friendly GitHub Actions workflow for your R package(s).

Note that r BiocStyle::Githubpkg("lcolladotor/biocthis") is not a Bioconductor-core package and as such it is not a Bioconductor official package. It was made by and for Leonardo Collado-Torres so he could more easily maintain and create Bioconductor packages as listed at lcolladotor.github.io/pkgs/. Hopefully r BiocStyle::Githubpkg("lcolladotor/biocthis") will be helpful for you too.

Installation instructions

Get the latest stable R release from CRAN. Then install biocthis from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("biocthis")

And the development version from GitHub with:

BiocManager::install("lcolladotor/biocthis")

Example

Here is how you can use r BiocStyle::Githubpkg("lcolladotor/biocthis") to create a new Bioconductor-friendly R package (illustrated using a temporary directory):

## Load biocthis
library("biocthis")

## Create an example package for illustrative purposes.
## Note: you do not need to run this for your own package!
pkgdir <- biocthis_example_pkg()

## Create the bioc templates
biocthis::use_bioc_pkg_templates()

The template dev scripts include comments and steps you can follow for making your Bioconductor-friendly R package or updating a current package. In particular, you might want to use a Bioconductor-friendly GitHub Actions workflow. If this is your first time seeings this words, we highly recommend that you watch Jim Hester's rstudio::conf(2020) talk on this subject.

## Create a GitHub Actions workflow that is Bioconductor-friendly
biocthis::use_bioc_github_action()

## Alternatively, use the general GitHub Actions workflow maintained by
## r-lib/actions
usethis::use_github_action("check-standard")

Citation

Below is the citation output from using citation('biocthis') in R. Please run this yourself to check for any updates on how to cite biocthis.

print(citation("biocthis"), bibtex = TRUE)

Please note that the biocthis was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the biocthis project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
• Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
• The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
• The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
• The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').

For more details, check the dev directory.

This package was developed using r BiocStyle::Biocpkg('biocthis').

lcolladotor/biocthis documentation built on Jan. 17, 2024, 8:07 p.m.