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@lauramaxwell lauramaxwell released this 15 Apr 19:16
v1.1.3
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This minor update includes new/updated domain mapping specs, improved mapping documentation, and expanded qualification/unit testing and CI workflows.

Changes:

  • Added complete_death() to gsm.mapping and updated the Death workflow spec to use it (including Randomization input for death_dy).
  • Refreshed mapping-spec vignette to auto-discover YAML domains and render a richer, filterable mapping table.
  • Added qualification/unit tests (including snapshots) and modernized GitHub Actions workflows (qcthat + new pkgdown workflow), alongside version bump/remotes update.

What's Changed

New Contributors

Full Changelog: v1.1.2...v1.1.3

{qcthat} Reports

Milestone

✅ A qcthat issue test matrix with 1 milestone, 4 issues, and 3 tests 
└─█─Milestone: v1.1.3 (4 issues, 3 tests)
  ├─☑️─Technical Task 114: Add a new `death_days` column to `DEATH` domain
  │ ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
  │ └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
  ├─📥─Bug 112: Remove `setdiff` call for `db_lock_dt`
  │ └─(no tests)
  ├─☑️─Bug 101: Fix data types in AE, PK and SUBJ
  │ └─(no tests)
  └─☑️─Technical Task 97: Migrate appropriate qualification tests to gsm.mapping
    ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
    ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
    └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 3 mappings are completed as expected (#97)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

⭕ 2 issues lack tests

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

Completed Issues

✅ A qcthat issue test matrix with 3 milestones, 28 issues, and 11 tests 
├─█─Milestone: v1.1.0 (4 issues, 0 tests)
│ ├─☑️─Requirement 62: Business Requirement:  Add AE domains to data model
│ │ └─(no tests)
│ ├─☑️─Issue 61: Request New Domain or Variable: Dates
│ │ └─(no tests)
│ ├─☑️─Issue 35: Feature: Additional AE fields
│ │ └─(no tests)
│ └─☑️─Issue 34: Feature: Add "category" to PD.yaml
│   └─(no tests)
├─█─Milestone: v1.1.2 (2 issues, 0 tests)
│ ├─☑️─Feature 104: Make modifications to `EXCLUSION.yaml` to tweak text of ineligibility related components for legibility
│ │ └─(no tests)
│ └─☑️─Technical Task 91: Add `db_lock_dt` to `STUDY` domain
│   └─(no tests)
├─█─Milestone: v1.1.3 (3 issues, 3 tests)
│ ├─☑️─Technical Task 114: Add a new `death_days` column to `DEATH` domain
│ │ ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│ │ └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│ ├─☑️─Bug 101: Fix data types in AE, PK and SUBJ
│ │ └─(no tests)
│ └─☑️─Technical Task 97: Migrate appropriate qualification tests to gsm.mapping
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│   └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 3 mappings are completed as expected (#97)
└─█─Milestone: <none> (19 issues, 8 tests)
  ├─☑️─Issue 72: Feature: Include study ID in all data specifications.
  │ └─(no tests)
  ├─☑️─Issue 29: Feature: Create Issue templates for adding and editing new domain
  │ └─(no tests)
  ├─☑️─Issue 28: Feature: Add  `{gsm.endpoints}` mapping workflows
  │ └─(no tests)
  ├─☑️─Issue 25: Updates to Mapping Specification VIgnette
  │ └─(no tests)
  ├─☑️─Issue 24: Remove `util-` from file names
  │ └─(no tests)
  ├─☑️─Issue 21: refactor yamls to remove `_all` param/field
  │ └─(no tests)
  ├─☑️─Issue 20: Move additional data wrangling functions from gsm
  │ └─(no tests)
  ├─☑️─Issue 6: Feature: Expand AE.yaml
  │ └─(no tests)
  ├─☑️─Issue 5: Feature: Expand SUBJ.yaml
  │ └─(no tests)
  ├─☑️─Issue 2: Add ingestion-related functions
  │ ├─✅─Combining multiple specs with overlapping dfs, deduplicating cols (#2)
  │ ├─✅─Combining specs with non-overlapping dfs (#2)
  │ ├─✅─Combining specs with some empty dfs (#2)
  │ ├─✅─Combining empty list of specs returns an empty list (#2)
  │ ├─✅─Combining a single spec returns the same spec (#2)
  │ ├─✅─Combining specs with NULL entries is handled correctly (#2)
  │ ├─✅─warning if type doesn't match first instance (#2)
  │ └─✅─Ingest works with optional columns (#2)
  ├─☑️─Issue 1: Add mapping yamls from `{gsm}` 
  │ └─(no tests)
  ├─☑️─Bug 70: Data specification of `_all` coerces all columns to character.
  │ └─(no tests)
  ├─☑️─Technical Task 58: Request New Domain or Variable:  IE domain
  │ └─(no tests)
  ├─☑️─Issue 55: Keep Specified Columns
  │ └─(no tests)
  ├─☑️─Issue 53: Feature: Merge visit schedule onto PK domain.
  │ └─(no tests)
  ├─☑️─Issue 50: Bugfix: Fix source column names for endpoints mappings
  │ └─(no tests)
  ├─☑️─Issue 38: Add PK yaml
  │ └─(no tests)
  ├─☑️─Issue 37: Feature: Swap clindata with gsm.datasim
  │ └─(no tests)
  └─☑️─Issue 30: QC: Namespace all functions in workflow yamls
    └─(no tests)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

⭕ 25 issues lack tests

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

This report was generated by this GitHub Actions run.

Last updated: 2026-04-15 19:21:30 UTC

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  • ── Packages attached to the search path.

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

Contributors

jwildfire, samussiah, and 4 other contributors
Assets 3
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