NEWS.md

In rworkflows: Test, Document, Containerise, and Deploy R Packages

rworkflows 1.0.2

New features

• Update to R 4.4.1 and ensure everything stil 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• Remove .Rprofile (didn't seem to help CRAN and was getting outdated)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.

rworkflows documentation built on Sept. 23, 2024, 1:08 a.m.