NEWS.md

rworkflows 1.0.6

Bug fixes

• Update to actions/upload-artifact@v4 as v3 is now deprecated. Contributed in PR #139

rworkflows 1.0.5

New features

• New arg force_install allows users to bypass cache while installing dependencies.

rworkflows 1.0.4

Bug fixes

• Remove deprecated package (pandoc-citeproc) from Dockerfile.

rworkflows 1.0.3

New features

• New arg run_telemetry allows users to disable workflow telemetry.

Bug fixes

• Add GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }} to all code check steps.

rworkflows 1.0.2

New features

• Update to R 4.4.1 and ensure everything still works.
• Update rworkflows.yml to use new Bioc release, 3.19

Bug fixes

• Get back up on CRAN after deprecation occurred while I was away.
• Remove .Rprofile (didn't seem to help CRAN and was getting outdated)
• test-construct_conda_yml.R: Add conditional to only run certain steps if reticulate is installed (for noSuggests tests in CRAN).

rworkflows 1.0.1

New features

• Change command "\nodocker" to "[nodocker]" for consistency with other commands.

Bug fixes

• action.yml
  • repository: ${{ github.repository }} --> repository: ${{ env.packageName }}
• CRAN:
  • Add convenient testthat function skip_if_offline.
• Reduce package size by making vignettes rmarkdown::html_vignette instead of BiocStyle::html_document.
• URL: https://github.com/runforesight/workflow-telemetry-action (moved to https://github.com/catchpoint/workflow-telemetry-action)
• Skip tests that are sensitive to working directory location (which can cause issues when running devtools::test_coverage() in the terminal) #112

rworkflows 1.0.0

New features

• Synchronise rworkflows package versioning with rworkflows action Release versioning.
• use_vignette_docker/use_vignette_getstarted
  • Autofill package arg if not provided.

Bug fixes

• inst/template/docker.Rmd
  • Remove the need to include construct_cont, as not everyone will have rworkfows installed on the machine where the vignette is being rendered.
• use_vignette_docker
  • Add -autolink_bare_uris bit to avoid CRAN check errors.
• Change \itemize --> describe to avoid CRAN check errors.

rworkflows 0.99.14

New features

• Add step to enable conda envs: #78
  • Add subfunction: gha_python_versions() within construct_runners
  • Add new action.yml args:
    • miniforge_variant
    • miniforge_version
    • activate_environment
    • environment_file
    • channels
  • New function to construct conda env yaml files:
    • construct_conda_yml
  • New unit tests to test construct_conda_yml and building conda envs from the generated yamls.
• fill_yaml
  • Add subfunction is_default
• actions.yml:
  • Add force=TRUE to the remotes::install_local steps. #86
  • Add runforesight/workflow-telemetry-action step.
  • Avoid setting rspm explicitly by default.
• construct_cont:
  • Make registry explicit.
  • New arg: default_registry
  • New subfunction: check_registry
• Add docker_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.
  • actions.yml
  • use_workflow
• get_github_url_desc
  • Improve logic to catch more GH URLs.
• vignettes/depgraph.Rmd
  • Update plots with new data and resave PNG.
• New arg free_diskspace
  • actions.yml
  • use_workflow
• use_workflow
  • template arg can now be "rworkflows_static:dev" to use the "dev" branch's version of action.yml as a workflow template.
• Add .devcontainer/devcontainer.json
• use_vignette_docker
  • New helper func: infer_docker_org

Bug fixes

• no visible global function definition for internal function check_miniconda_args
  • This weird error only came up during Rstudio R CMD checks. The function 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.
  • Thought it might be a permissions issues with check_miniconda_args.R but the permissions are identical with all the others.
• action.yml
  • Remove unnecessary export:echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENV
  • Fix runforesight/workflow-telemetry-action step and move to top.
• infer_deps
  • Pass infer_deps the DESCRIPTION path directly within the fill_description func.
  • Fix unit tests.
• conda_*
  • Try to get reticularte to find the path to conda installed by setup-miniconda.
• New func: use_codespace
  • Create dev container config file.
• .Rprofile
  • Added to avoid CRAN issues with bioc packages.

rworkflows 0.99.13

New features

• Merge PR #66 by @js2264 to eliminate the PAT_GITHUB secret setup step.
• Merge PR #71 by @js2264 to skip vignettes when building if run_vignettes.
• Add fun emojis to action.
• Add vignette for checking Sweave (.Rnw) files can be rendered.
• action.yml
  • Add new args to control latex: tinytex_installer, tinytex_version, pandoc_version
  • Install extra latex deps using one step for all OS via tinytex R package.
• construct_runners
  • Simplify arguments so that user doesn't have to pass OS names.
  • When an arg like bioc is of length one, the same value is automatically applied across all 3 OS.
• bioconductor.Rmd
  • Add vignette specifically for Bioconductor packages.
• use_workflow
  • Split name arg into two args: name + template, so that you can create multiple separate workflow files using the same template.
  • Add new args to control latex: tinytex_installer, tinytex_version, pandoc_version
  • New internal subfunctions:
    • save_yaml
    • check_bioc_version
    • check_r_version
  • New exported subfunction: construct_cont
• Transition BiocPkgTools + biocViews to Suggests
  • Based on recc from CRAN maintainers, as they do not consistently install/update Bioc packages on the CRAN server.
• fill_yaml
  • Simplify code.
  • Add subfunction omit_if_default to omit tinytex args from yaml.
• is_rstudio: new interal helper function.
• Update rworkflows_static.yml
• Sync Docker vignettes with registry #99

Bug fixes

• Add "devel" as trigger branch in all 3 workflows.
• Harmonise github_token parameter docs between action.yml and use_workflow.
• CRAN checks:
  • Downgrade BiocPkgTools/biocViews to Suggests to compensate for issues with the CRAN server: #65
• fill_yaml:
  • When template="rworkflows_static", prevent with2 from simplifying to vector.
• construct_runners
  • rspm wasn't getting added.
• get_github_url_db
  • Properly coalesce hits from multiple columns searched for GitHub URLs.

rworkflows 0.99.12

New features

• Reduce clutter by removing subaction folders (will eventually come back to this idea).

Bug fixes

• CRAN's VMs are having issues.
• Reduce docs size by rendering PNG instead of html in depgraph vignette.
• Get code coverage back up to 91%+
• Revamp get_hex and get_description
  • Use lists more consistently
  • More robust in general
• get_description
  • Actually use use_repos arg.
• Fix "Documented arguments not in \usage in documentation object 'get_description_repo': 'pkgs'""
• Ensure all documented functions have @returns in Roxygen notes.
• action.yml
  • "Install dependencies pass 1" step was calling repos before it was defined.

rworkflows 0.99.11

New features

• Switch to using bibentry for CITATION.

To compensate for this had to modify test-bioc_r_versions.

rworkflows 0.99.10

New features

• use_workflow
  • Add "devel" as a new default trigger branch to align with Bioc's recent changes to their standards.
• Increase code coverage:
  • Expand get_description unit tests.
  • Add construct_authors unit tests.
  • Fix (sort of) infer_biocviews tests.

Bug fixes

• Fixed parsing error when writing "rworkflows_static". #60
• Get args from 'env.' (for workflows) instead of 'inputs.' (for actions)
• Update links with redirects
• codecov_graphs: Fix link with redirect.

rworkflows 0.99.9

New features

• Pass timeout arg to R package installation steps too.

Bug fix

• Remove explicit AnVIL usage, as the URLs are now deprecated and BiocManager uses the pre-compiled binaries by default.

rworkflows 0.99.8

New features

• get_description
  • Supplying a description obj directly to any argument returns that obj.
  • Reorder strategies so that local ones go first.
  • Add Liam Neeson reference.
  • Now caches DESCRIPTION files.
  • Add validation step at the end.
  • Upgrade to handle multiple refs at once
  • Add another subroutine for getting DESCRIPTION files from CRAN/Bioc
• get_hex
  • Now iterable
• Add output style arg to vignette functions.
• use_vignette_docker
  • Let users select port_in and port_out
  • Make default port_out=8900 to align with the available Imperial Private Cloud ports (8900-9000).

rworkflows 0.99.7

New features

• New functions: fill_description
• New function: infer_deps
• New function: infer_biocviews
• New function: is_gha
• Add yaml file to test workflow rworkflows_dev
• Run BiocCheck in rworkflow yamls.
• Make all require() calls in action.yml quiet.
• Further increase code coverage.
• use_badges
  • Add new arg for add_codecov_graphs
  • Subfunction codecov_graphs
  • Rearrange badges in a logical order
  • Add more breaks
• bioc_r_version:
  • Add new arg depth and internal func parse_version
• get_hex / use_badges
  • When add_hex is a character string, interpret it as the hex path instead.
• use_badges
  • Add add_lifecycle: badger::badge_lifecycle()

Bug fixes

• Add biocViews: WorkflowManagement
• Try to fix NEWS.md formatting for all platforms.
• Lengthen Description field.
• get_hex: Remove extra breaks
• Fix bad quotes in if statements when rworkflows_static gets saved.

rworkflows 0.99.6

New features

• Improve code coverage.
  • Remove is_default as it is never used. Document in gist for later use: https://gist.github.com/bschilder/f02a5b564977f52fd665728a22c0d005
• use_badges:
  • Pass up pkg arg for explicit package specification.
  • Make default hex height 300.
  • Make CRAN badge color yellow.
• New function:
  • get_description

Bug fixes

• use_badges:
  • Enable alternative ways of getting DESCRIPTION.
  • Use ref and pkg explicitly in relevant functions to avoid inference.
• Remove embedded HTML from depgraph.Rmd vignette, as it induces a NOTE in CRAN checks that the package is too large.

rworkflows 0.99.5

New features

• Use actions:
  • r-lib/setup-r-dependencies
  • r-lib/setup-tinytex
  • grimbough/bioc-actions/setup-bioc
• New workflow args:
  • timeout
• Update rworkflows_static.yml
• Remove unnecessary lines from .Rbuildignore, as this is now taken care of internally by r-lib/setup-r-dependencies
  • node_modules$
  • package-lock\.json$
  • package\.json$

Bug fixes

• Add no-check-CRAN arg to BiocCheck step to allow using bioc checks for packages already on CRAN.
• Remove redundant "Install package" step (now handled within Dockerfile).
• Fix get_hex in cases where multiple links in DESCRIPTION URL.
• Fix CodeCov checking and upload step.

rworkflows 0.99.4

New features

• New functions:

  • use_issue_template

• Remove unnecessary Suggests:

  • rvest
  • UpSetR
  • githubinstall
  • BiocManager

• Automatically synchronize R and Bioc versions:

  • bioc_r_versions
  • construct_runners

Bug fixes

• Fix workflows not getting filled with custom parameters.
  • Add unit tests to ensure this can't happen.
• Replace rcmdcheck \link with \href
• use_badges: remove unnecessary ref arg.

rworkflows 0.99.3

New features

• Add new arg has_latex
  • Added to action
  • Add to use_workflow
• New vignettes:
  • depgraph: Plot which R packages use the rworkflow action.
  • repos: Evaluate how R packages are distributed, and get data on most downloaded packages.

rworkflows 0.99.2

New features

• add_badges
  • Check whether hex URL actually exists first.
• New functions:
  • use_readme
  • use_vignette_docker
  • use_vignettte_getstarted
• Only require R >4.1 (instead of 4.2) bc that's when the native pipe |> was introduced.

Bug fixes

• Make badger a Import
• Use Dockerfile stored in inst/templates instead of getting from GitHub.
• Fix vignette field in use_vignette_* functions.
• Fix pdflatex-related errors on all 3 OS.

rworkflows 0.99.1

New features

• Renamed workflow args:
  • run_crancheck --> run_rcmdcheck
  • DOCKER_ORG --> docker_org
  • DOCKER_USERNAME --> docker_user
• Added new args:
  • as_cran: separate from run_rcmdcheck
  • tag: specify action version.
• Set default: use_workflow(run_docker=FALSE)
• Removed unused args: repository
• Add 'RELEASE_**' as one of the default trigger branches (for Bioconductor).
• New function: badge

Bug fixes

• Make sure all docker args actually get modified in template.
• Set default docker_org/docker_user to

rworkflows 0.99.0

New features

• Added a NEWS.md file to track changes to the package.