BUG FIXES
- Fixed internal code on
use_bioc_news_md()
,use_bioc_readme_rmd()
, anduse_bioc_vignette()
afterusethis
changed some of their un-exported functions thatbiocthis
relies on.
BUG FIXES
- Ignore
remotes::system_requirements("ubuntu", "20.04")
for now since that leads to a JSON error. See #41 but also https://github.com/LieberInstitute/spatialLIBD/commit/edc8b72505af097895dcbf35887df28da8122e3c.
BUG FIXES
- Resolved #40 reported by @lmweber with help from @bschilder and @LiNk-NY noted at neurogenomics/rworkflows#58. Basically, there's no longer a need to explicitly list the AnVIL repositories to benefit from those gains.
BUG FIXES
use_bioc_github_action()
now properly works again whendocker = TRUE
. Behind the scenes, this function now usesdocker/build-docker-action@v4
instead of the deprecateddocker/build-docker-action@v1
. These updates were tested at https://github.com/lcolladotor/ExampleBiocWorkshop2023.
NEW FEATURES
use_bioc_pkgdown_css()
: helps you style yourpkgdown
website with Bioconductor colors. See #34 for details.use_bioc_badges()
: helps you list all the Bioconductor badges (for software packages). See #35 for details.use_bioc_feature_request_template()
: creates a feature request template for your GitHub repository. See #33 for details.use_bioc_issue_template()
anduse_bioc_support()
were also updated to be more Bioconductor-centric.use_tinytest()
adds support fortinytest
. See #32 for details.
BUG FIXES
- Fixed
pkgdown
website creation. See #29 for details. This is also tangentially related to #31. - Fixed usage of
r-lib/actions
. We now usev2
. See #36, #37, and r-lib/actions#639 for more. - Thanks to everyone who contributed pull requests and GitHub issues!
SIGNIFICANT USER-VISIBLE CHANGES
use_bioc_github_action()
has been updated to match as much as possible the changes inr-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 preventingtcltk
errors thanks to this pull request by Ben Laufer #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
- Added the function
use_bioc_coc()
as requested by Luke Zappia et al.
NEW FEATURES
- Now
use_bioc_github_action()
has adocker
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
- Switch to match usethis 2.0.1 which changed a lot of the internal code in
biocthis
.
NEW FEATURES
- Switched from
knitcitations
toRefManageR
given the discussion at cboettig/knitcitations#107.
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.
NEW FEATURES
- Added a
NEWS.md
file to track changes to the package. - Added
bioc_style()
which provides a partial Bioconductor coding style compatible withstyler
. - Added
usethis
-style functionsuse_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()
anduse_bioc_vignette()
. These functions provide Bioconductor-friendly alternatives to several functions in theusethis
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.