NEWS.md
NEW FEATURES
use_bioc_github_action() now creates a .github/workflows/bioc-check.yml file that has the option 'bioc_version' set to "bioc-release" by default. It can also take the values "bioc-devel" or a specific Bioconductor version number in the X.YY format such as "3.20". This updated GitHub Actions workflow aims to be as static as possible across Bioconductor release versions. Meaning that in the future you won’t need to use use_bioc_github_action() again to update the GHA workflow after every Bioconductor release. This was motivated by the “dynamic matrix generation” documentation available at https://runs-on.com/github-actions/the-matrix-strategy/#dynamic-matrix-generation. For a detailed explanation of the changes in this version, check the LIBD RStats club presentation “[2025-03-21] biocthis v1.17.4 updated GitHub Actions workflow”. The video is available at https://www.youtube.com/watch?v=bzzPBt3Mz0A and the notes at https://docs.google.com/document/d/1z8xkC_3kAsGlpF_UyM9YfV-08o1lTer7xoBz2lQ1IjY/edit?usp=sharing.SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_github_action() now uses simpler code for caching R packages across GitHub Action runs. This code won’t need to be updated across versions, meaning that it’ll be easier to update the .github/workflows/check-bioc.yml file across Bioconductor versions. Also, @gaborcsardi’s recent commit to r-lib/actions as noted at https://github.com/r-lib/actions/issues/912#issuecomment-2667950006 gave me a hint on how to simplify code across macOS/winOS and linux for the caching of R packages. Also, note that thanks to https://github.com/r-lib/remotes/commit/0e4e23051041d9f1b15a5ab796defec31af6190d we will soon be able to re-enable automatic installation of linux system dependencies thanks to remotes::system_requirements("ubuntu", "24.04") being supported in the near future. Finally, we no longer need to specify RSPM although there are detailed instructions at https://packagemanager.posit.co/client/#/repos/bioconductor/setup on how to do so.SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_description() now has report_bioc set to FALSE by default to match the Bioconductor guidelines listed at https://contributions.bioconductor.org/description.html#description-bugreport. This was brought up in a December 2024 package review at https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199.use_bioc_pkg_templates() now adds the dev/ directory to the main .gitignore file. This was also brought up in the same package review.use_bioc_vignette() no longer creates a vignettes/.gitignore file. The rendered .R and .html files are instead ignored on the package main .gitignore file. This complies with the request from that same package review while also keeping in line with the behavior from usethis::use_vignette() https://github.com/r-lib/usethis/blob/a653d6e05f9172772cea1055f8415cda2f26de69/R/vignette.R#L11-L12.use_bioc_vignette()’s template no longer tracks how much time was used to render the vignette, nor shows the code used for obtaining the .R file with knit(tangle = TRUE), nor the date the vignette was generated. This was also brought up in the same package review from December 2024, as well as in a second one from October 2024 at https://github.com/Bioconductor/Contributions/issues/3501#issuecomment-2408081535.SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_github_action() now uses the actions/cache@v4 instead of v3.BUG FIXES
use_bioc_news_md(), use_bioc_readme_rmd(), and use_bioc_vignette() after usethis changed some of their un-exported functions that biocthis relies on.BUG FIXES
remotes::system_requirements("ubuntu", "20.04") for now since that leads to a JSON error. See https://github.com/lcolladotor/biocthis/issues/41 but also https://github.com/LieberInstitute/spatialLIBD/commit/edc8b72505af097895dcbf35887df28da8122e3c.BUG FIXES
BUG FIXES
use_bioc_github_action() now properly works again when docker = TRUE. Behind the scenes, this function now uses docker/build-docker-action@v4 instead of the deprecated docker/build-docker-action@v1. These updates were tested at https://github.com/lcolladotor/ExampleBiocWorkshop2023.NEW FEATURES
use_bioc_pkgdown_css(): helps you style your pkgdown website with Bioconductor colors. See https://github.com/lcolladotor/biocthis/issues/34 for details.use_bioc_badges(): helps you list all the Bioconductor badges (for software packages). See https://github.com/lcolladotor/biocthis/pull/35 for details.use_bioc_feature_request_template(): creates a feature request template for your GitHub repository. See https://github.com/lcolladotor/biocthis/pull/33 for details. use_bioc_issue_template() and use_bioc_support() were also updated to be more Bioconductor-centric.use_tinytest() adds support for tinytest. See https://github.com/lcolladotor/biocthis/pull/32 for details.BUG FIXES
pkgdown website creation. See https://github.com/lcolladotor/biocthis/issues/29 for details. This is also tangentially related to https://github.com/lcolladotor/biocthis/issues/31.r-lib/actions. We now use v2. See https://github.com/lcolladotor/biocthis/issues/36, https://github.com/lcolladotor/biocthis/pull/37, and https://github.com/r-lib/actions/issues/639 for more.SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_github_action() has been updated to match as much as possible the changes in r-lib/actions up to the latest commit https://github.com/r-lib/actions/commit/630f4c9d8b813f45d0327a2fc20eb264fd518450.NEW FEATURES
use_bioc_github_action() is now more robust in preventing tcltk errors thanks to this pull request by Ben Laufer https://github.com/lcolladotor/biocthis/pull/19.NEW FEATURES
use_bioc_github_action() now uses the AnVIL-powered package binaries, which greatly speed up the dependency installation steps in the docker (Linux) GitHub Actions builds. Details are available in Nitesh Turaga’s BioC2021 slides https://github.com/nturaga/bioc2021-bioconductor-binaries.NEW FEATURES
use_bioc_github_action() has a docker argument which controls whether to build a docker image at the end of the GHA workflow (only on Linux) as requested by Kévin Rue-Albrecht.BUG FIXES
biocthis.NEW FEATURES
knitcitations to RefManageR given the discussion at https://github.com/cboettig/knitcitations/issues/107.BUG FIXES
NEW FEATURES
NEWS.md file to track changes to the package.bioc_style() which provides a partial Bioconductor coding style compatible with styler.usethis-style functions use_bioc_citation(), use_bioc_description(), use_bioc_github_action(), use_bioc_issue_template(), use_bioc_news_md(), use_bioc_pkg_templates(), use_bioc_readme_rmd(), use_bioc_support() and use_bioc_vignette(). These functions provide Bioconductor-friendly alternatives to several functions in the usethis package.use_bioc_github_action() allows you to use a Bioconductor-friendly GitHub Actions workflow for checking your Bioconductor package (or one that depends on Bioconductor packages). Check the vignettes for details on its features as well as the developer notes.