NEWS.md

In lcolladotor/biocthis: Automate package and project setup for Bioconductor packages

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.

lcolladotor/biocthis documentation built on Jan. 17, 2024, 8:07 p.m.