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Closes #42 fix: install workr in manifest workflow#47

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Zelos Zhu (zdz2101) wants to merge 4 commits into
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fix-42
Open

Closes #42 fix: install workr in manifest workflow#47
Zelos Zhu (zdz2101) wants to merge 4 commits into
devfrom
fix-42

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@zdz2101 Zelos Zhu (zdz2101) commented May 14, 2026

Overview

  • updates .github/workflows/manifest.yaml to install workr as a package instead of sourcing R/*.R
  • checks out workr at ${{ github.workflow_sha }} so the installed package matches the reusable workflow revision being executed
  • replaces the manifest step's ad hoc source loading with library(workr) before calling workr::pkgManifest()

Test Notes/Sample Code

  • Local validation:
    • pak::local_install('.', dependencies = FALSE, upgrade = FALSE, ask = FALSE)
    • library(workr)
    • confirmed packageVersion('workr') resolves after install

Connected Issues

@zdz2101
fix: install workr in manifest workflow
c9e1212 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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{qcthat} Report: User Acceptance

No issues are awaiting UAT.

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 17:59:03 UTC

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

[2] /opt/R/4.6.0/lib/R/site-library

[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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{qcthat} Reports

PR-Associated Issues

█ A qcthat issue test matrix with 1 milestone, 1 issue, and 0 tests 
└─█─Milestone: v1.1.0 (1 issue, 0 tests)
  └─📥─Issue 42: [workr] Switch manifest.yaml from source()-ing files to installing the package
    └─(no tests)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
⭕ 1 issue lacks tests

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-all.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: 2026-05-15 17:59:04 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

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spatial 7.3-18 2025-01-01 [3] CRAN (R 4.6.0)

splines 4.6.0 2026-04-24 [3] local

stats * 4.6.0 2026-04-24 [3] local

stats4 4.6.0 2026-04-24 [3] local

stringi 1.8.7 2025-03-27 [1] RSPM

stringr 1.6.0 2025-11-04 [1] RSPM

survival 3.8-6 2026-01-16 [3] CRAN (R 4.6.0)

sys 3.4.3 2024-10-04 [1] RSPM

tcltk 4.6.0 2026-04-24 [3] local

testthat 3.3.2 2026-01-11 [1] RSPM

tibble 3.3.1 2026-01-11 [1] RSPM

tidyr 1.3.2 2025-12-19 [1] RSPM

tidyselect 1.2.1 2024-03-11 [1] RSPM

tinytex 0.59 2026-03-28 [1] RSPM

tools 4.6.0 2026-04-24 [3] local

usethis 3.2.1 2025-09-06 [1] RSPM

utf8 1.2.6 2025-06-08 [1] RSPM

utils * 4.6.0 2026-04-24 [3] local

vctrs 0.7.3 2026-04-11 [1] RSPM

waldo 0.6.2 2025-07-11 [1] RSPM

whisker 0.4.1 2022-12-05 [1] RSPM

withr 3.0.2 2024-10-28 [1] RSPM

xfun 0.57 2026-03-20 [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/4.6.0/lib/R/site-library

[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

Copilot AI reviewed May 14, 2026
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Pull request overview

This PR updates the reusable manifest workflow so it installs and loads the workr package from the workflow revision instead of sourcing raw R files, aligning execution with the package NAMESPACE.

Changes:

  • Checks out the workr package source at ${{ github.workflow_sha }}.
  • Installs workr before manifest generation.
  • Replaces ad hoc source() loading with library(workr).

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Comment thread .github/workflows/manifest.yaml Outdated
Zelos Zhu (zdz2101) and others added 2 commits May 14, 2026 11:24
@zdz2101
fix: install only hard dependencies for manifest workflow
299c523 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
@zdz2101
fix: use pak local_install hard-dependency mode
afedb57 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 14, 2026
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Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated no new comments.

@zdz2101 Zelos Zhu (zdz2101) changed the title fix: install workr in manifest workflow Closes #42 fix: install workr in manifest workflow May 14, 2026
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Zelos Zhu (zdz2101) commented May 14, 2026

This Action demonstrates new manifest yaml still works

@zdz2101
catch up to dev
86696a2 
Merge branch 'dev' into fix-42
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
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github-actions Bot commented May 15, 2026

✅ All workflows are up to date

Generated by this GitHub Action. Updated: 2026-05-15T17:57:24Z

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github-actions Bot commented May 15, 2026

📊 Test coverage: 33.07%

Per-file coverage
File Coverage
R/DemoApp.R 0%
R/internal.R 75.6%
R/MakeWorkflowList.R 86.1%
R/RunProject.R 90.3%
R/RunQuery.R 90.7%
R/RunStep.R 97.6%
R/RunWorkflow.R 87.5%
R/RunWorkflows.R 100%
R/snapshot.R 0%
R/utils-examples.R 95%
R/utils-github.R 0%
R/utils-manifest.R 0%
R/utils-toml.R 0%
R/utils-workflows.R 0%

Generated by this GitHub Action. Updated: 2026-05-15T17:59:01Z

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github-actions Bot commented May 15, 2026

🌐 PR pkgdown deployed: https://Gilead-BioStats.github.io/workr/pr/47/dev

Generated by this GitHub Action. Updated: 2026-05-15T17:59:12Z

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Copilot code review Copilot Copilot left review comments

@jwildfire Jeremy Wildfire (jwildfire) Awaiting requested review from jwildfire

@lauramaxwell Laura Maxwell (lauramaxwell) Awaiting requested review from lauramaxwell

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[workr] Switch manifest.yaml from source()-ing files to installing the package

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