workr 1.0.0

Initial Release

{workr} provides a minimal framework for describing and executing step-by-step R data pipelines using YAML-defined workflows.

Core Features

RunStep() — execute a single workflow step
RunWorkflow() — execute a full workflow specification (YAML)
RunWorkflows() — run multiple workflows in sequence
RunProject() — orchestrate multi-phase workflow pipelines (experimental)
MakeWorkflowList() — read a folder of YAML workflows into a list
RunQuery() — execute database queries via DBI/duckdb
loadExample() — load bundled example workflows for learning and testing

Shiny Demo App

DemoApp_init() — launch an interactive Shiny app for exploring and running workflows
Hosted version available at jwildfire.shinyapps.io/workr-demoapp

Package Manifests

pkgManifest() — resolve GitHub packages to pinned versions with manifest.csv and rproject.toml
Snapshot branches (ss-*) for reproducible package environments
GitHub Actions for nightly manifest updates

GitHub Actions

manifest.yaml — reusable workflow for generating manifest artifacts
nightly-manifest.yaml — scheduled manifest updates
R-CMD-check.yaml — R CMD check CI
R-CMD-check-dev.yaml — development R CMD check CI
pkgdown-with-examples.yaml — pkgdown site deployment
pkgdown-cleanup.yaml — pkgdown cleanup

Documentation

pkgdown site at gilead-biostats.github.io/workr
Vignettes covering overview, Pharmaverse integration, ADaM/SDTM examples, and visualization

{qcthat} Reports

Milestone

✅ A qcthat issue test matrix with 1 milestone, 3 issues, and 71 tests

└─█─Milestone: v1.0.0 (3 issues, 71 tests)
  ├─☑️─Issue 26: Improve unit test coverage for v1.0 release
  │ ├─✅─MakeWorkflowList loads YAML and RunStep executes workflow correctly #26
  │ ├─✅─Complex workflow: multi-step loaded from YAML and executed end-to-end #26
  │ ├─✅─Workflow from YAML loads and executes with meta reference #26
  │ ├─✅─loadExample returns input data when initData.R is missing (#9, #26)
  │ ├─✅─loadExample loads initData.R and merges with lData (#9, #26)
  │ ├─✅─loadExample validates initData return type (#9, #26)
  │ ├─✅─loadExample does not create duplicate names on repeated calls (#9, #26)
  │ ├─✅─MakeWorkflowList output is a named list with expected structure #26
  │ ├─✅─MakeWorkflowList returns metadata as expected #26
  │ ├─✅─MakeWorkflowList errors on invalid strPath #26
  │ ├─✅─MakeWorkflowList errors on invalid strPackage #26
  │ ├─✅─MakeWorkflowList filters by strNames #26
  │ ├─✅─MakeWorkflowList bExact filters exactly #26
  │ ├─✅─MakeWorkflowList names list elements by meta$ID #26
  │ ├─✅─MakeWorkflowList sorts by Priority #26
  │ ├─✅─MakeWorkflowList sets default Priority to 0 #26
  │ ├─✅─MakeWorkflowList loads from package #26
  │ ├─✅─MakeWorkflowList bRecursive finds nested workflows #26
  │ ├─✅─RunProject runs all phases in sorted order #26
  │ ├─✅─RunProject passes data between phases #26
  │ ├─✅─RunProject respects strPhases subset and order #26
  │ ├─✅─RunProject errors on missing strPath #26
  │ ├─✅─RunProject errors on missing requested phases #26
  │ ├─✅─RunProject errors on empty project directory #26
  │ ├─✅─RunProject bReturnResult and bKeepInputData pass through #26
  │ ├─✅─RunQuery returns correct result (#26)
  │ ├─✅─RunQuery handles empty df #26
  │ ├─✅─RunQuery handles invalid input #26
  │ ├─✅─RunQuery checks if strQuery contains 'FROM df' #26
  │ ├─✅─RunQuery applies schema appropriately #26
  │ ├─✅─RunQuery applies incomplete schema appropriately #26
  │ ├─✅─RunQuery parses invalid date/times correctly #26
  │ ├─✅─RunQuery requires lColumnMapping when bUseSchema is TRUE #26
  │ ├─✅─RunStep handles lMeta and lData parameters correctly #26
  │ ├─✅─RunStep handles parameters referencing elements within lMeta and lData #26
  │ ├─✅─RunStep passes direct value parameters correctly #26
  │ ├─✅─RunStep passes direct value vector parameters correctly #26
  │ ├─✅─RunStep handles multiple parameters and function invocation correctly #26
  │ ├─✅─RunStep will run a function from a namespace #26
  │ ├─✅─RunStep will run a function without a namespace #26
  │ ├─✅─RunStep will run a function with no parameters #26
  │ ├─✅─RunStep recognizes rlang::expr() string parameters #26
  │ ├─✅─RunStep recognizes expr() shorthand parameters #26
  │ ├─✅─RunStep recognizes rlang::exprs() parameters #26
  │ ├─✅─RunStep recognizes exprs() shorthand parameters #26
  │ ├─✅─RunStep passes lSpec parameter correctly #26
  │ ├─✅─RunWorkflow returns final step result by default #26
  │ ├─✅─RunWorkflow returns full workflow object when bReturnResult = FALSE #26
  │ ├─✅─RunWorkflow bKeepInputData = FALSE removes input data from lData #26
  │ ├─✅─RunWorkflow bKeepInputData = TRUE preserves input data in lData #26
  │ ├─✅─RunWorkflow multi-step preserves intermediate results in lData #26
  │ ├─✅─RunWorkflow invokes lConfig$LoadData #26
  │ ├─✅─RunWorkflow invokes lConfig$SaveData on bReturnResult = TRUE #26
  │ ├─✅─RunWorkflow validates spec when present #26
  │ ├─✅─RunWorkflow runs without spec #26
  │ ├─✅─RunWorkflow runs with YAML files #26
  │ ├─✅─RunWorkflows returns named list #26
  │ ├─✅─RunWorkflows passes prior workflow results as data to later workflows #26
  │ ├─✅─RunWorkflows custom strResultNames #26
  │ ├─✅─RunWorkflows passes lConfig through to RunWorkflow #26
  │ └─✅─RunWorkflows handles empty workflow list #26
  ├─☑️─Issue 25: Differentiate package manifests from execution snapshots
  │ ├─✅─pkgManifest function exists #25
  │ ├─✅─pkgManifest has correct parameters #25
  │ ├─✅─pkgSnapshot function name is deprecated/removed #25
  │ └─✅─pkgListFromManifest references correct function #25
  └─☑️─Issue 19: Remove Legacy /site Explorer From workr
    ├─✅─site/ directory does not exist #19
    ├─✅─site-build.yaml workflow does not exist #19
    ├─✅─site-deploy.yaml workflow does not exist #19
    ├─✅─pkgdown-with-examples.yaml has no Node/explorer steps #19
    ├─✅─_pkgdown.yml has no explorer navbar entry #19
    └─✅─.gitignore has no site/node_modules/ entry #19
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped

✅ All tests passed

🟢 All issues have at least one test

🙈 5 issues with label "qcthat-nocov" were ignored

Completed Issues

🚫 A qcthat issue test matrix with 1 milestone, 5 issues, and 78 tests

├─█─Milestone: v1.0.0 (3 issues, 71 tests)
│ ├─☑️─Issue 26: Improve unit test coverage for v1.0 release
│ │ ├─✅─MakeWorkflowList loads YAML and RunStep executes workflow correctly #26
│ │ ├─✅─Complex workflow: multi-step loaded from YAML and executed end-to-end #26
│ │ ├─✅─Workflow from YAML loads and executes with meta reference #26
│ │ ├─✅─loadExample returns input data when initData.R is missing (#9, #26)
│ │ ├─✅─loadExample loads initData.R and merges with lData (#9, #26)
│ │ ├─✅─loadExample validates initData return type (#9, #26)
│ │ ├─✅─loadExample does not create duplicate names on repeated calls (#9, #26)
│ │ ├─✅─MakeWorkflowList output is a named list with expected structure #26
│ │ ├─✅─MakeWorkflowList returns metadata as expected #26
│ │ ├─✅─MakeWorkflowList errors on invalid strPath #26
│ │ ├─✅─MakeWorkflowList errors on invalid strPackage #26
│ │ ├─✅─MakeWorkflowList filters by strNames #26
│ │ ├─✅─MakeWorkflowList bExact filters exactly #26
│ │ ├─✅─MakeWorkflowList names list elements by meta$ID #26
│ │ ├─✅─MakeWorkflowList sorts by Priority #26
│ │ ├─✅─MakeWorkflowList sets default Priority to 0 #26
│ │ ├─✅─MakeWorkflowList loads from package #26
│ │ ├─✅─MakeWorkflowList bRecursive finds nested workflows #26
│ │ ├─✅─RunProject runs all phases in sorted order #26
│ │ ├─✅─RunProject passes data between phases #26
│ │ ├─✅─RunProject respects strPhases subset and order #26
│ │ ├─✅─RunProject errors on missing strPath #26
│ │ ├─✅─RunProject errors on missing requested phases #26
│ │ ├─✅─RunProject errors on empty project directory #26
│ │ ├─✅─RunProject bReturnResult and bKeepInputData pass through #26
│ │ ├─✅─RunQuery returns correct result (#26)
│ │ ├─✅─RunQuery handles empty df #26
│ │ ├─✅─RunQuery handles invalid input #26
│ │ ├─✅─RunQuery checks if strQuery contains 'FROM df' #26
│ │ ├─✅─RunQuery applies schema appropriately #26
│ │ ├─✅─RunQuery applies incomplete schema appropriately #26
│ │ ├─✅─RunQuery parses invalid date/times correctly #26
│ │ ├─✅─RunQuery requires lColumnMapping when bUseSchema is TRUE #26
│ │ ├─✅─RunStep handles lMeta and lData parameters correctly #26
│ │ ├─✅─RunStep handles parameters referencing elements within lMeta and lData #26
│ │ ├─✅─RunStep passes direct value parameters correctly #26
│ │ ├─✅─RunStep passes direct value vector parameters correctly #26
│ │ ├─✅─RunStep handles multiple parameters and function invocation correctly #26
│ │ ├─✅─RunStep will run a function from a namespace #26
│ │ ├─✅─RunStep will run a function without a namespace #26
│ │ ├─✅─RunStep will run a function with no parameters #26
│ │ ├─✅─RunStep recognizes rlang::expr() string parameters #26
│ │ ├─✅─RunStep recognizes expr() shorthand parameters #26
│ │ ├─✅─RunStep recognizes rlang::exprs() parameters #26
│ │ ├─✅─RunStep recognizes exprs() shorthand parameters #26
│ │ ├─✅─RunStep passes lSpec parameter correctly #26
│ │ ├─✅─RunWorkflow returns final step result by default #26
│ │ ├─✅─RunWorkflow returns full workflow object when bReturnResult = FALSE #26
│ │ ├─✅─RunWorkflow bKeepInputData = FALSE removes input data from lData #26
│ │ ├─✅─RunWorkflow bKeepInputData = TRUE preserves input data in lData #26
│ │ ├─✅─RunWorkflow multi-step preserves intermediate results in lData #26
│ │ ├─✅─RunWorkflow invokes lConfig$LoadData #26
│ │ ├─✅─RunWorkflow invokes lConfig$SaveData on bReturnResult = TRUE #26
│ │ ├─✅─RunWorkflow validates spec when present #26
│ │ ├─✅─RunWorkflow runs without spec #26
│ │ ├─✅─RunWorkflow runs with YAML files #26
│ │ ├─✅─RunWorkflows returns named list #26
│ │ ├─✅─RunWorkflows passes prior workflow results as data to later workflows #26
│ │ ├─✅─RunWorkflows custom strResultNames #26
│ │ ├─✅─RunWorkflows passes lConfig through to RunWorkflow #26
│ │ └─✅─RunWorkflows handles empty workflow list #26
│ ├─☑️─Issue 25: Differentiate package manifests from execution snapshots
│ │ ├─✅─pkgManifest function exists #25
│ │ ├─✅─pkgManifest has correct parameters #25
│ │ ├─✅─pkgSnapshot function name is deprecated/removed #25
│ │ └─✅─pkgListFromManifest references correct function #25
│ └─☑️─Issue 19: Remove Legacy /site Explorer From workr
│   ├─✅─site/ directory does not exist #19
│   ├─✅─site-build.yaml workflow does not exist #19
│   ├─✅─site-deploy.yaml workflow does not exist #19
│   ├─✅─pkgdown-with-examples.yaml has no Node/explorer steps #19
│   ├─✅─_pkgdown.yml has no explorer navbar entry #19
│   └─✅─.gitignore has no site/node_modules/ entry #19
└─█─Milestone: <none> (2 issues, 11 tests)
  ├─☑️─Issue 34: Finalize inst/workflows and demo Shiny app for shinyapps.io deployment
  │ ├─✅─03_AEKRI directory does not exist #34
  │ ├─✅─03_KRI initData.R does not reference gsm.core::lSource #34
  │ ├─✅─03_KRI initData.R does not reference PD domain #34
  │ ├─✅─03_KRI initData.R uses clindata package #34
  │ ├─✅─03_KRI initData.R returns Raw_SUBJ and Raw_AE #34
  │ ├─🚫─03_KRI RunWorkflows completes without error using initData #34
  │ └─✅─README contains link to hosted shinyapps.io demo #34
  └─☑️─Feature 9: Create Test data to initialize workflows
    ├─✅─loadExample returns input data when initData.R is missing (#9, #26)
    ├─✅─loadExample loads initData.R and merges with lData (#9, #26)
    ├─✅─loadExample validates initData return type (#9, #26)
    └─✅─loadExample does not create duplicate names on repeated calls (#9, #26)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped

🚫 1 test was skipped

🟢 All issues have at least one test

🙈 7 issues with label "qcthat-nocov" were ignored

This report was generated by this GitHub Actions run.

Last updated: 2026-04-09 19:14:02 UTC

Session Info

─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.5.3 (2026-03-11)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate C.UTF-8

ctype C.UTF-8

tz UTC

date 2026-04-09

pandoc 3.1.3 @ /usr/bin/pandoc

quarto 1.9.37 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────

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highr 0.12 2026-03-06 [1] RSPM

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withr 3.0.2 2024-10-28 [1] RSPM

workr 0.99.0 2026-04-08 [1] local

xfun 0.57 2026-03-20 [1] RSPM

xml2 1.5.2 2026-01-17 [1] RSPM

xtable 1.8-8 2026-02-22 [1] RSPM

yaml 2.3.12 2025-12-10 [1] RSPM

zip 2.3.3 2025-05-13 [1] RSPM

[1] /home/runner/work/_temp/Library

[2] /opt/R/4.5.3/lib/R/site-library

[3] /opt/R/4.5.3/lib/R/library

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workr 1.0.0

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