perf(autoFIPC): read model column metadata without copying data

.Rbuildignore

@@ -5,8 +5,6 @@
 ^\.Rprofile$
 ^\.github$
 ^\.github/.*
-^\.cursor$
-^\.cursor/.*
 ^\.codegraph$
 ^\.codegraph/.*
 ^.*\.Rcheck$
@@ -24,3 +22,4 @@
 ^\.jules(/.*)?$
 ^\.trivyignore\.yaml$
 ^trivy\.yaml$
+^\.semgrepignore$

.github/workflows/r.yml

@@ -35,33 +35,12 @@ jobs:
           r-version: release
           use-public-rspm: true
 
-      # ponytail: source-build stringfish BEFORE dependency setup — packages built
-      # from source during install (e.g. SimDesign) load it at build time and die
-      # on the broken prebuilt binary (oneTBB ABI skew). Drop with the step below.
-      # repos= must be a real source repo: RSPM serves prebuilt Linux binaries via
-      # source-style URLs, so type="source" against RSPM does NOT recompile.
-      # repos= is explicit because R_PROFILE_USER=/dev/null blanks setup-r's repos.
-      - name: Source-build stringfish (RcppParallel oneTBB ABI skew)
-        run: >-
-          Rscript -e 'install.packages(c("RcppParallel", "stringfish"), type = "source",
-          repos = "https://cloud.r-project.org")'
-
       - name: Set up R package dependencies
         uses: r-lib/actions/setup-r-dependencies@d3c5be51b12e724e68f33216ca3c148b66d5f0b6
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      # ponytail: CRAN/RSPM binary skew — prebuilt binaries (stringfish, qs2, ...) lag
-      # RcppParallel's oneTBB update (undefined tbb::internal / tbb::task symbols).
-      # Rebuild everything LinkingTo RcppParallel from source so it links the installed
-      # copy. Drop once upstream binaries re-sync.
-      - name: Rebuild RcppParallel-linked packages from source (oneTBB ABI skew)
-        run: >-
-          Rscript -e 'r <- "https://cloud.r-project.org"; install.packages("RcppParallel", type = "source", repos = r);
-          bad <- tools::dependsOnPkgs("RcppParallel", dependencies = "LinkingTo");
-          if (length(bad)) install.packages(bad, type = "source", repos = r)'
-
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590
         with:

.jules/bolt.md

@@ -16,3 +16,6 @@
 ## 2025-02-12 - R 언어에서 반복적인 mirt 모델 생성 시 불필요한 데이터프레임 부분집합 추출 최적화
 **Learning:** R에서 데이터프레임의 특정 열을 추출하는 작업(`df[cols]`)은 O(N)의 메모리 복사를 수반합니다. `autoFIPC`에서 `mirt` 모델의 파라미터를 설정하거나 호출하는 과정 중에 `newformXDataK[colnames(newFormModel@Data$data)]` 코드가 반복해서 사용되었고, 심지어 `ncol()`을 위해 단순히 개수를 구할 때도 사용되어 불필요한 메모리 할당과 오버헤드를 초래했습니다.
 **Action:** 조건문이나 반복문 내부에서 불필요하게 데이터프레임 부분집합 연산이 반복되지 않도록 외부에서 한 번만 `linkedFormData <- newformXDataK[colnames(newFormModel@Data$data)]`로 캐싱(caching)한 뒤, `ncol(linkedFormData)`와 `data = linkedFormData` 형태로 재사용하여 메모리 복사와 O(N) 오버헤드를 방지해야 합니다.
+## 2024-07-23 - R 언어에서 열 이름 추출 시 데이터프레임 부분집합 추출을 피하여 O(N) 메모리 복사 방지
+**Learning:** R에서 열 이름을 확인하기 위해 `colnames(df[cols])` 형태로 데이터프레임을 서브셋팅하면, 단순히 이름만 추출하는 경우에도 데이터를 복사하는 과정에서 불필요한 O(N) 메모리 할당과 복사 오버헤드가 발생합니다.
+**Action:** 열 이름만 필요할 때는 모델의 이름 벡터를 직접 사용하여 행 수에 비례하는 데이터 프레임 복사를 피해야 합니다. 이름 비교 자체는 열 수에 비례하며, 필수 열을 선택할 때는 직접 서브셋팅하여 누락 열에서 실패하도록 보존해야 합니다.

AGENTS.md

@@ -19,9 +19,6 @@ parameter calibration and test linking.
 - Keep `.github/dependabot.yml` active for GitHub Actions updates.
 - Keep `ARCHITECTURE.md` up to date when structure changes.
 - Keep README accurate for local verification commands.
-- Keep `.cursor/install.sh` revision-agnostic: provision R + CRAN deps only.
-  Do not `R CMD INSTALL` the current tree in `install` (environment builds
-  freeze that copy). Use `testthat::test_local()` / `rcmdcheck` on the checkout.
 
 ## Editing priorities
 

ARCHITECTURE.md

@@ -19,7 +19,6 @@ metadata and CI are wired, and which parts are safe to evolve.
 - `.github/ISSUE_TEMPLATE/` - structured issue intake templates
 - `.github/CODEOWNERS` - code ownership map for reviews
 - `.github/dependabot.yml` - Automated Actions dependency updates
-- `.cursor/` - Cloud Agent environment (`environment.json` + `install.sh`)
 - `docs/coderabbit/review-commands.md` - CodeRabbit command quick reference
 - `docs/operations/maintenance-runbook.md` - recurring maintainer operations checklist
 - `README.md` - User/developer entrypoint
@@ -92,10 +91,6 @@ package metadata, and CI workflow definitions in Git.
 - Primary check: `R CMD check` via GitHub Actions
 - Local check command:
   - `Rscript -e 'rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"))'`
-- Cloud Agent: `.cursor/environment.json` runs `.cursor/install.sh` to provision
-  CRAN-release R and r2u binaries (`mirt`, `testthat`, `roxygen2`, `rcmdcheck`).
-  `install` is snapshot-scoped and must not `R CMD INSTALL` the current tree;
-  use `testthat::test_local()` / `rcmdcheck` against the checkout.
 
 ## 9. Future Considerations / Roadmap
 
@@ -108,9 +103,9 @@ package metadata, and CI workflow definitions in Git.
 ## 10. Project Identification
 
 - Project Name: aFIPC
-- Repository URL: `https://github.com/ContextualWisdomLab/aFIPC`
+- Repository URL: `https://github.com/seonghobae/aFIPC`
 - Primary Contact: Seongho Bae
-- Date of Last Update: 2026-08-16
+- Date of Last Update: 2026-02-15
 
 ## 11. Glossary / Acronyms
 

CLAUDE.md

@@ -78,8 +78,6 @@ See `ARCHITECTURE.md` for the full map. Essentials:
 - `.github/workflows/` — `r.yml` (R CMD check), `code-quality.yml`
   (yamllint + markdownlint + actionlint), `security-audit.yml` (gitleaks +
   actionlint). All action refs are pinned to full commit SHAs.
-- `.cursor/` — Cloud Agent environment. `install.sh` provisions R + CRAN
-  deps only; do not `R CMD INSTALL` the current tree there.
 
 Runtime is single-process and fileless: in-memory old/new form data ->
 `autoFIPC()` -> `mirt` calibration -> optional item parameter drift (IPD)

R/aFIPC.R

@@ -620,8 +620,8 @@ autoFIPC <-
       IPDItemCount <- 0
 
       # IPD target item checking
-      newFormColNames <- colnames(newformXDataK[colnames(newFormModel@Data$data)])
-      oldFormColNames <- colnames(oldformYDataK[colnames(oldFormModel@Data$data)])
+      newFormColNames <- colnames(newFormModel@Data$data)
+      oldFormColNames <- colnames(oldFormModel@Data$data)
 
       # ⚡ Bolt: Vectorized match() to avoid dynamic array growth overhead inside a for loop
       idxNew <- match(newformCommonItemNames, newFormColNames)
@@ -749,8 +749,8 @@ autoFIPC <-
       }
     }
 
-    newFormColNames <- colnames(newformXDataK[colnames(newFormModel@Data$data)])
-    oldFormColNames <- colnames(oldformYDataK[colnames(oldFormModel@Data$data)])
+    newFormColNames <- colnames(newFormModel@Data$data)
+    oldFormColNames <- colnames(oldFormModel@Data$data)
 
     # ⚡ Bolt: Cache parameter indices to avoid O(N) linear search inside loop
     newScaleParmsItemIdxCache <- split(seq_len(nrow(NewScaleParms)), NewScaleParms$item)
@@ -848,7 +848,7 @@ autoFIPC <-
     message('\nestimating Linked Form Eq(X) parameters')
 
     # ⚡ Bolt: Cache subsetted dataframe to avoid repeated O(N) memory copies during mirt model setup
-    linkedFormData <- newformXDataK[colnames(newFormModel@Data$data)]
+    linkedFormData <- newformXDataK[, colnames(newFormModel@Data$data), drop = FALSE]
 
     if (forceNormalZeroOne) {
       freeMEAN <- F

tests/testthat/test-bolt-intersect.R

@@ -0,0 +1,31 @@
+test_that("intersect column name extraction works properly in autoFIPC", {
+  skip_if_not_installed("mirt")
+  set.seed(42)
+
+  a <- matrix(c(1, 1.2, 0.8, 1.5, 0.9, 1.1, 1.0, 1.3), ncol=1)
+  d <- matrix(c(1, -1, 0, 0.5, -0.5, 0, 0.2, -0.2), ncol=1)
+  oldformYData <- mirt::simdata(a, d, 250, itemtype = '2PL')
+  colnames(oldformYData) <- paste0("Item", 1:8)
+
+  a2 <- matrix(c(1, 1.2, 0.8, 1.0, 1.3), ncol=1)
+  d2 <- matrix(c(1, -1, 0, 0.2, -0.2), ncol=1)
+  newformXData <- mirt::simdata(a2, d2, 250, itemtype = '2PL')
+  colnames(newformXData) <- c("Item1", "Item2", "Item3", "NewItem1", "NewItem2")
+
+  result <- aFIPC::autoFIPC(
+    newformXData = newformXData,
+    oldformYData = oldformYData,
+    newformCommonItemNames = c('Item1', 'Item2', 'Item3'),
+    oldformCommonItemNames = c('Item1', 'Item2', 'Item3'),
+    confirmCommonItems = TRUE,
+    tryEM = TRUE,
+    checkIPD = FALSE,
+    freeMEAN = FALSE,
+    forceNormalZeroOne = FALSE,
+    tryFitwholeOldItems = FALSE,
+    tryFitwholeNewItems = FALSE
+  )
+
+  expect_true(!is.null(result$LinkedModel))
+  expect_true(methods::is(result$LinkedModel, "SingleGroupClass"))
+})