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.