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_coc() as requested by Luke Zappia et al.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.