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Closes #45, #46: support inst/workflow and inst/workflows and avoid name clash#50

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Closes #45, #46: support inst/workflow and inst/workflows and avoid name clash#50
Zelos Zhu (zdz2101) wants to merge 12 commits into
fix-43from
fix-45

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@zdz2101 Zelos Zhu (zdz2101) commented May 15, 2026 •
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Overview

Updated pull_workflows() to support both workflow directory conventions used across GSM repos. It now checks inst/workflow first, then falls back to inst/workflows, and only logs a skip message when neither path exists.

Added collision detection for destination paths under workflows/ so cross-package filename collisions are no longer silent. Behavior is configurable via collision_action:

  • "warn" (default): emit a warning and continue (last write wins)
  • "error": stop on first collision

Also updated roxygen docs and generated Rd files for pull_workflows(), pull_workflow_dir(), and pull_workflow_file().

Test Notes/Sample Code

  • Ran devtools::test(filter = 'snapshot-gh-mocks') (passing)
  • Added/updated mocked unit coverage for:
    • singular/plural workflow directory resolution
    • collision warning behavior
    • collision error behavior
  • Ran full devtools::test(); existing unrelated baseline failures remain in: 
    • est-finalize-workflows.R (#34 expectation mismatch)

    • est-remove-site-explorer.R (#19 expectation mismatch)

Connected Issues

@zdz2101
Fix workflow dir lookup for singular and plural paths
1b7be5e 
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 21:11:21 UTC

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{qcthat} Reports

PR-Associated Issues

⚠️ A qcthat issue test matrix with 1 milestone, 2 issues, and 8 tests 
└─█─Milestone: v1.1.0 (2 issues, 8 tests)
  ├─📥─Issue 46: [workr] Workflow filename collisions silently overwrite
  │ ├─✅─pkgManifest forwards collision_action to pull_workflows #46
  │ ├─✅─pull_workflows does not register missing files as collisions #46
  │ ├─⚠️─pull_workflows warns on destination collisions by default #46
  │ ├─✅─pull_workflows can error on destination collisions #46
  │ ├─⚠️─pull_workflows warns on nested destination collisions in directories #46
  │ └─✅─pull_workflows warns and skips file-vs-directory structural collisions #46
  └─📥─Issue 45: [workr] Snapshot silently skips packages that use inst/workflows (plural)
    ├─✅─pull_workflows skips packages with no workflow directory #45
    └─✅─pull_workflows falls back to inst/workflows when singular path is missing #45
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
⚠️ 2 tests generated warnings

🟢 All issues have at least one test

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 21:11:22 UTC

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purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-05-15 [1] Github (Gilead-BioStats/qcthat@d0958dc)

R6 2.6.1 2025-02-15 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

Rcpp 1.1.1-1.1 2026-04-24 [1] RSPM

rex 1.2.2 2026-03-28 [1] RSPM

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

rpart 4.1.27 2026-03-27 [3] CRAN (R 4.6.0)

rprojroot 2.1.1 2025-08-26 [1] RSPM

rrapply 1.2.8 2025-11-25 [1] RSPM

rstudioapi 0.18.0 2026-01-16 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

sessioninfo 1.2.3 2025-02-05 [1] RSPM

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

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.

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

@zdz2101
Tag snapshot tests for issues 43 and 45
328f0bd 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 15, 2026
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Pull request overview

This PR updates workflow snapshot pulling so repositories using either inst/workflow or inst/workflows are discovered before being skipped.

Changes:

  • Adds ordered lookup across singular and plural workflow directories.
  • Updates skip messaging when neither directory exists.
  • Adds mocked tests for missing directories and plural fallback behavior.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File Description
R/utils-workflows.R Adds fallback lookup for inst/workflows in pull_workflows().
tests/testthat/test-snapshot-gh-mocks.R Updates/extends mocked coverage for workflow directory probing and plural-path dispatch.

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Comment thread R/utils-workflows.R
Zelos Zhu (zdz2101) and others added 2 commits May 15, 2026 09:40
@zdz2101
Update pull_workflows roxygen for plural path
5b8f0e7 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
@zdz2101
Update pull_workflows roxygen and generate Rd
dd700c4 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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Pull request overview

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

Files not reviewed (1)
  • man/pull_workflows.Rd: Language not supported

Comment thread DESCRIPTION Outdated
@zdz2101
Handle workflow path collisions with warn/error policy
c42d3d8 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
@zdz2101 Zelos Zhu (zdz2101) changed the title Closes #45: support inst/workflow and inst/workflows Closes #45. #46: support inst/workflow and inst/workflows and avoid name clash May 15, 2026
This was linked to issues May 15, 2026
[workr] Snapshot silently skips packages that use inst/workflows (plural) #45
Open
[workr] Workflow filename collisions silently overwrite #46
Open
@zdz2101
Potential fix for pull request finding
8407d77 
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
@zdz2101 Zelos Zhu (zdz2101) changed the title Closes #45. #46: support inst/workflow and inst/workflows and avoid name clash Closes #45, #46: support inst/workflow and inst/workflows and avoid name clash May 15, 2026
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Pull request overview

Copilot reviewed 3 out of 6 changed files in this pull request and generated 3 comments.

Files not reviewed (3)
  • man/pull_workflow_dir.Rd: Language not supported
  • man/pull_workflow_file.Rd: Language not supported
  • man/pull_workflows.Rd: Language not supported
Comments suppressed due to low confidence (1)

R/utils-workflows.R:144

  • This records a destination as occupied before gh_api() and writeLines() confirm a file was actually written. Since pull_workflow_file() still treats Not Found as a skipped write, a later package with the same destination can incorrectly warn or fail even though no previous file exists.
    assign(collision_key, source_repo, envir = collision_registry)

Comment thread R/utils-workflows.R
Comment thread R/utils-workflows.R
Comment thread R/utils-workflows.R
@zdz2101
Expose and harden workflow collision handling
2ea5791 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 15, 2026
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Pull request overview

Copilot reviewed 4 out of 8 changed files in this pull request and generated 2 comments.

Files not reviewed (4)
  • man/pkgManifest.Rd: Language not supported
  • man/pull_workflow_dir.Rd: Language not supported
  • man/pull_workflow_file.Rd: Language not supported
  • man/pull_workflows.Rd: Language not supported

Comment thread R/utils-workflows.R
Comment thread R/utils-workflows.R
@zdz2101
catch up to preexisting chances in dev
9224919 
Merge branch 'fix-43' into fix-45
# 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 •
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📊 Test coverage: 48.55%

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 86.4%
R/utils-examples.R 95%
R/utils-github.R 63.1%
R/utils-manifest.R 0%
R/utils-toml.R 100%
R/utils-workflows.R 88%

Generated by this GitHub Action. Updated: 2026-05-15T21:11:19Z

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github-actions Bot commented May 15, 2026 •
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🌐 PR pkgdown deployed: https://Gilead-BioStats.github.io/workr/pr/50/dev

Generated by this GitHub Action. Updated: 2026-05-15T21:12:04Z

@zdz2101
Fix deferred collision registration
013c234 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Copilot AI reviewed May 15, 2026
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Pull request overview

Copilot reviewed 4 out of 8 changed files in this pull request and generated 1 comment.

Files not reviewed (4)
  • man/pkgManifest.Rd: Language not supported
  • man/pull_workflow_dir.Rd: Language not supported
  • man/pull_workflow_file.Rd: Language not supported
  • man/pull_workflows.Rd: Language not supported

Comment thread R/utils-workflows.R
Copilot AI reviewed May 15, 2026
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Pull request overview

Copilot reviewed 4 out of 8 changed files in this pull request and generated 1 comment.

Files not reviewed (4)
  • man/pkgManifest.Rd: Language not supported
  • man/pull_workflow_dir.Rd: Language not supported
  • man/pull_workflow_file.Rd: Language not supported
  • man/pull_workflows.Rd: Language not supported

Comment thread R/utils-workflows.R
Zelos Zhu (zdz2101) and others added 2 commits May 15, 2026 13:58
@zdz2101
will copilot ever be happy
1d57ac1
@zdz2101
Revert fallback warning suppression
20e6d9a 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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[workr] Workflow filename collisions silently overwrite [workr] Snapshot silently skips packages that use inst/workflows (plural)

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