Changelog

Source: NEWS.md

biocthis 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.

biocthis 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.

biocthis 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.

biocthis 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.

biocthis 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!

biocthis 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.

biocthis 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.

biocthis 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.

biocthis 1.1.10

NEW FEATURES

• Added the function use_bioc_coc() as requested by Luke Zappia et al.

biocthis 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.

biocthis 1.1.7

BUG FIXES

• Switch to match usethis 2.0.1 which changed a lot of the internal code in biocthis.

biocthis 1.1.4

NEW FEATURES

• Switched from knitcitations to RefManageR given the discussion at https://github.com/cboettig/knitcitations/issues/107.

biocthis 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.

biocthis 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.