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.