<!-- README.md is generated from README.Rmd. Please edit that file -->
# biocthis
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*[biocthis](https://github.com/lcolladotor/biocthis)* is an R package
that expands *[usethis](https://CRAN.R-project.org/package=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.
*[biocthis](https://github.com/lcolladotor/biocthis)* has functions that
can also enhance your current R packages that either are already
distributed by Bioconductor or have Bioconductor dependencies.
*[biocthis](https://github.com/lcolladotor/biocthis)* also includes a
Bioconductor-friendly [GitHub
Actions](https://github.com/features/actions) workflow for your R
package(s).
Note that *[biocthis](https://github.com/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/](https://lcolladotor.github.io/pkgs/).
Hopefully *[biocthis](https://github.com/lcolladotor/biocthis)* will be
helpful for you too.
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `biocthis` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("biocthis")
```
And the development version from
[GitHub](https://github.com/lcolladotor/biocthis) with:
``` r
BiocManager::install("lcolladotor/biocthis")
```
## Example
Here is how you can use
*[biocthis](https://github.com/lcolladotor/biocthis)* to create a new
Bioconductor-friendly R package (illustrated using a temporary
directory):
``` r
## 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()
#> ✔ Creating '/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample/'
#> ✔ Setting active project to '/private/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample'
#> ✔ Creating 'R/'
#> ✔ Writing 'DESCRIPTION'
#> Package: biocthisexample
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#> * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#> license
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.2.1
#> ✔ Writing 'NAMESPACE'
#> ✔ Setting active project to '<no active project>'
#> ✔ Setting active project to '/private/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/Rtmp4fYodr/biocthisexample'
## Create the bioc templates
biocthis::use_bioc_pkg_templates()
#> ✔ Creating 'dev/'
#> ✔ Adding '^dev$' to '.Rbuildignore'
#> ✔ Writing 'dev/01_create_pkg.R'
#> ✔ Writing 'dev/02_git_github_setup.R'
#> ✔ Writing 'dev/03_core_files.R'
#> ✔ Writing 'dev/04_update.R'
```
The template `dev` scripts include comments and steps you can follow for
making your Bioconductor-friendly R package or updating a current
package. In particular, you might want to use a Bioconductor-friendly
GitHub Actions workflow. If this is your first time seeings this words,
we highly recommend that you watch [Jim Hester’s `rstudio::conf(2020)`
talk on this
subject](https://www.jimhester.com/talk/2020-rsc-github-actions/).
``` r
## Create a GitHub Actions workflow that is Bioconductor-friendly
biocthis::use_bioc_github_action()
#> ✔ Creating '.github/'
#> ✔ Adding '^\\.github$' to '.Rbuildignore'
#> ✔ Adding '*.html' to '.github/.gitignore'
#> ✔ Creating '.github/workflows/'
#> ✔ Writing '.github/workflows/check-bioc.yml'
```
``` r
## Alternatively, use the general GitHub Actions workflow maintained by
## r-lib/actions
usethis::use_github_action("check-standard")
#> ✔ Saving 'r-lib/actions/examples/check-standard.yaml@v2' to '.github/workflows/check-standard.yaml'
#> • Learn more at <https://github.com/r-lib/actions/blob/v2/examples/README.md>.
```
## 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**.
``` r
print(citation("biocthis"), bibtex = TRUE)
#>
#> To cite package 'biocthis' in publications use:
#>
#> Collado-Torres L (2022). _Automate package and project setup for
#> Bioconductor packages_. doi:10.18129/B9.bioc.biocthis
#> <https://doi.org/10.18129/B9.bioc.biocthis>,
#> https://github.com/lcolladotor/biocthisbiocthis - R package version
#> 1.9.1, <http://www.bioconductor.org/packages/biocthis>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {Automate package and project setup for Bioconductor packages},
#> author = {Leonardo Collado-Torres},
#> year = {2022},
#> url = {http://www.bioconductor.org/packages/biocthis},
#> note = {https://github.com/lcolladotor/biocthisbiocthis - R package version 1.9.1},
#> doi = {10.18129/B9.bioc.biocthis},
#> }
#>
#> Collado-Torres L (2022). "Automate package and project setup for
#> Bioconductor packages." _bioRxiv_. doi:10.1101/TODO
#> <https://doi.org/10.1101/TODO>,
#> <https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Automate package and project setup for Bioconductor packages},
#> author = {Leonardo Collado-Torres},
#> year = {2022},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
#> url = {https://www.biorxiv.org/content/10.1101/TODO},
#> }
```
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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)*
customized to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.15/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://lcolladotor.github.io/biocthis)
is automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.15/biocthis)*.
