run_telemetry allows users to disable workflow telemetry.GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }} to all code check steps.reticulate is installed (for noSuggests tests in CRAN).repository: ${{ github.repository }} --> repository: ${{ env.packageName }}testthat function skip_if_offline.rmarkdown::html_vignette
instead of BiocStyle::html_document.devtools::test_coverage() in the terminal) #112rworkflows package versioning with rworkflows action
Release versioning.use_vignette_docker/use_vignette_getstarted
package arg if not provided.construct_cont,
as not everyone will have rworkfows installed on the machine where
the vignette is being rendered.\itemize --> describe to avoid CRAN check errors.gha_python_versions() within construct_runnersminiforge_variantminiforge_versionactivate_environmentenvironment_filechannelsconstruct_conda_ymlconstruct_conda_yml and building conda envs
from the generated yamls.fill_yaml
is_defaultforce=TRUE to the remotes::install_local steps. #86runforesight/workflow-telemetry-action step.rspm explicitly by default.construct_cont:
default_registrycheck_registrydocker_registry arg to let users choose which registry to push to.
Defaults to "ghcr.io" instead of "docker.io" so that no additional credentials
are needed.
use_workflowget_github_url_desc
free_diskspace
use_workflowuse_workflow
template arg can now be "rworkflows_static:dev" to use the "dev" branch's
version of action.yml as a workflow template.use_vignette_docker
infer_docker_orgno visible global function definition for internal function check_miniconda_args
check_miniconda_args was clearly defined in its own file.
The only way to fix it was copying the function into the same one where it
was called fill_yaml.echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENVrunforesight/workflow-telemetry-action step and move to top.infer_deps
infer_deps the DESCRIPTION path directly
within the fill_description func.conda_*
setup-miniconda.use_codespace
run_vignettes.tinytex_installer, tinytex_version, pandoc_versiontinytex R package.construct_runners
bioc is of length one, the same value is automatically
applied across all 3 OS.use_workflow
name arg into two args: name + template,
so that you can create multiple separate workflow files
using the same template.tinytex_installer, tinytex_version, pandoc_versionsave_yamlcheck_bioc_versioncheck_r_versionconstruct_contBiocPkgTools + biocViews to Suggests
fill_yaml
omit_if_default to omit tinytex args from yaml.is_rstudio: new interal helper function.github_token parameter docs between
action.yml and use_workflow.BiocPkgTools/biocViews to Suggests to
compensate for issues with the CRAN server: #65fill_yaml:
template="rworkflows_static", prevent with2 from simplifying to vector.construct_runners
rspm wasn't getting added.get_github_url_db
docs size by rendering PNG instead of html in depgraph vignette.get_hex and get_description
get_description
use_repos arg.@returns in Roxygen notes.action.yml
repos before it was defined.bibentry for CITATION.To compensate for this had to modify test-bioc_r_versions.
use_workflow
branch to align with Bioc's recent changes to their standards.get_description unit tests.construct_authors unit tests.infer_biocviews tests.codecov_graphs: Fix link with redirect.timeout arg to R package installation steps too.AnVIL usage, as the URLs are now deprecated and BiocManager uses the pre-compiled binaries by default.get_description
description obj directly to any argument returns that obj.refs at onceget_hex
output style arg to vignette functions.use_vignette_docker
port_in and port_outport_out=8900 to align with the available
Imperial Private Cloud ports (8900-9000).fill_descriptioninfer_depsinfer_biocviewsis_ghaBiocCheck in rworkflow yamls.require() calls in action.yml quiet.use_badges
add_codecov_graphscodecov_graphsbioc_r_version:
depth and internal func parse_versionget_hex / use_badges
add_hex is a character string, interpret it as the hex path instead.use_badges
add_lifecycle: badger::badge_lifecycle()biocViews: WorkflowManagementget_hex: Remove extra breaksif statements when rworkflows_static gets saved.is_default as it is never used. Document in gist for later use:
https://gist.github.com/bschilder/f02a5b564977f52fd665728a22c0d005use_badges:
pkg arg for explicit package specification.get_descriptionuse_badges:
ref and pkg explicitly in relevant functions to avoid inference.r-lib/setup-r-dependenciesr-lib/setup-tinytexgrimbough/bioc-actions/setup-bioctimeoutr-lib/setup-r-dependencies
node_modules$package-lock\.json$package\.json$no-check-CRAN arg to BiocCheck step to allow using bioc checks for
packages already on CRAN.get_hex in cases where multiple links in DESCRIPTION URL.New functions:
use_issue_templateRemove unnecessary Suggests:
rvestUpSetRgithubinstallBiocManagerAutomatically synchronize R and Bioc versions:
bioc_r_versionsconstruct_runnersrcmdcheck \link with \hrefuse_badges: remove unnecessary ref arg.has_latex
use_workflowrworkflow action.add_badges
use_readmeuse_vignette_dockeruse_vignettte_getstarted|> was introduced.badger a Importvignette field in use_vignette_* functions.run_crancheck --> run_rcmdcheckDOCKER_ORG --> docker_orgDOCKER_USERNAME --> docker_useras_cran: separate from run_rcmdchecktag: specify action version.use_workflow(run_docker=FALSE)repositorybadgeNEWS.md file to track changes to the package.