Changes in version 1.17.4 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. Changes in version 1.17.3 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. Changes in version 1.17.2 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. - Similarly, 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. Changes in version 1.17.1 SIGNIFICANT USER-VISIBLE CHANGES - use_bioc_github_action() now uses the actions/cache@v4 instead of v3. Changes in version 1.11.3 BUG FIXES - Fixed internal code on 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. Changes in version 1.11.2 BUG FIXES - Ignore 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. Changes in version 1.11.1 BUG FIXES - Resolved https://github.com/lcolladotor/biocthis/issues/40 reported by @lmweber with help from @bschilder and @LiNk-NY noted at https://github.com/neurogenomics/rworkflows/issues/58. Basically, there's no longer a need to explicitly list the AnVIL repositories to benefit from those gains. Changes in version 1.9.2 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. Changes in version 1.7.0 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 - Fixed 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. - Fixed usage of 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. - Thanks to everyone who contributed pull requests and GitHub issues! Changes in version 1.3.8 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. Changes in version 1.3.4 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. Changes in version 1.3.2 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. Changes in version 1.1.10 NEW FEATURES - Added the function use_bioc_coc() as requested by Luke Zappia et al. Changes in version 1.1.9 NEW FEATURES - Now 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. Changes in version 1.1.7 BUG FIXES - Switch to match usethis 2.0.1 which changed a lot of the internal code in biocthis. Changes in version 1.1.4 NEW FEATURES - Switched from knitcitations to RefManageR given the discussion at https://github.com/cboettig/knitcitations/issues/107. Changes in version 1.1.3 BUG FIXES - Updated to use usethis version 2.0.0 or newer. Check the following for more information on usethis changes: https://twitter.com/JennyBryan/status/1337858543404285952?s=20. Changes in version 0.99.0 NEW FEATURES - Added a NEWS.md file to track changes to the package. - Added bioc_style() which provides a partial Bioconductor coding style compatible with styler. - Added 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.