Final CRAN prep

.Rbuildignore

@@ -11,4 +11,16 @@
 ^CODE_OF_CONDUCT.md
 ^.github
 ^\.github$
-^.lintr
+^.lintr
+^doc$
+^Meta$
+^.quarto
+^_freeze
+^\.claude$
+.*\.log$
+^renv$
+^renv\.lock$
+^test_vignettes\.R$
+^test_vignettes_with_timeout\.sh$
+^vignette_.*\.txt$
+^vignette_.*\.log$

.Rprofile

@@ -0,0 +1,18 @@
+# Activate renv for reproducible package management
+source("renv/activate.R")
+
+# Use binary packages (no compiler needed)
+# Posit Package Manager provides binaries for faster installation
+options(
+  pkgType = "binary",
+  repos = c(CRAN = "https://cloud.r-project.org")
+)
+
+# Warn if R version is below the package floor
+if (getRversion() < "4.0") {
+  warning(
+    "chmsflow requires R >= 4.0.0. ",
+    "You are using R ", getRversion(), ". ",
+    "Some features may not work correctly."
+  )
+}

.github/workflows/test-coverage.yaml

@@ -15,32 +15,33 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
-      - name: Install Codecov CLI
-        run: pip install codecov-cli
-
-      - name: Run tests and generate coverage report
+      - name: Test coverage
         run: |
-          cov <- covr::package_coverage()
-          covr::to_cobertura(cov, "coverage.xml")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov, filename = "coverage.xml")
         shell: Rscript {0}
 
-      - name: Upload coverage report to Codecov
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-        run: |
-          codecov-cli upload-process -f "coverage.xml" -t "$CODECOV_TOKEN"
-        shell: bash
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Show testthat output
         if: always()

.gitignore

@@ -64,9 +64,12 @@ src/*.o
 src/*.so
 src/*.dll
 
-# If you use renv for package dependency management, ignore these files
-renv.lock
-renv/
+# renv for package dependency management
+# Keep renv.lock and renv/activate.R in git for reproducibility
+# Ignore the local library and cache
+renv/library/
+renv/local/
+renv/staging/
 
 # If you use packrat for package dependency management, ignore these files
 packrat/
@@ -79,7 +82,13 @@ packrat.lock
 # If you use lintr for code linting, ignore these files
 .R/lintr_cache/
 
+/doc/
+/Meta/
+
 # Quarto files
 /.quarto/
 /_freeze/
 *_files/
+
+# Claude use
+.claude/

.lintr

@@ -1,2 +1,2 @@
-linters: linters_with_defaults(line_length_linter = NULL, object_name_linter = NULL, object_length_linter = NULL, cyclocomp_linter = cyclocomp_linter(complexity_limit = 100), return_linter = NULL)
+linters: linters_with_defaults(line_length_linter = NULL, object_name_linter = NULL, object_length_linter = NULL, object_usage_linter = NULL, cyclocomp_linter = cyclocomp_linter(complexity_limit = 100), return_linter = NULL, pipe_consistency_linter = NULL)
 

DESCRIPTION

@@ -2,27 +2,26 @@ Package: chmsflow
 Type: Package
 Title: Transforming and Harmonizing CHMS Variables
 Version: 0.1.0
-Author: Rafidul Islam [aut, cre], Douglas Manuel [aut], Therese Chan [aut]
-Maintainer: Rafidul Islam <raislam@ohri.ca>
 Authors@R: c(
     person("Rafidul", "Islam", email = "raislam@ohri.ca", role = c("aut", "cre")),
-    person("Douglas", "Manuel", email = "dmanuel@ohri.ca", role = c("aut"), comment = c(ORCID = "0000-0003-0912-0845")),    
+    person("Douglas", "Manuel", email = "dmanuel@ohri.ca", role = c("aut"), comment = c(ORCID = "0000-0003-0912-0845")),
     person("Therese", "Chan", email = "TChan@bruyere.org", role = c("aut")))
 Description: Supporting the use of the Canadian Health Measures Survey (CHMS)
     by transforming variables from each cycle into harmonized, consistent 
     versions that span survey cycles 1-6. This package uses rec_with_table(), 
     which was developed from 'sjmisc' rec(). Ludecke D (2018). "sjmisc: Data 
     and Variable Transformation Functions". Journal of Open Source Software, 
     3(26), 754. <doi:10.21105/joss.00754>.
-Depends: 
-    R (>= 3.5)
-Imports: haven, logger
+Depends:
+    R (>= 4.0)
+Imports: dplyr, haven, logger
 License: MIT + file LICENSE
 URL: https://github.com/Big-Life-Lab/chmsflow, https://big-life-lab.github.io/chmsflow/
 BugReports: https://github.com/Big-Life-Lab/chmsflow/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Suggests: dplyr, DT, kableExtra, knitr, quarto, readr, recodeflow, testthat (>= 3.0.0)
+RoxygenNote: 7.3.3
+Suggests: DT, kableExtra, knitr, quarto, readr, recodeflow, testthat (>= 3.0.0)
 VignetteBuilder: quarto
+Config/build/clean-inst-doc: FALSE
 LazyData: true

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
-COPYRIGHT HOLDER: Rafidul Islam, Douglas Manuel and The Ottawa Hospital Research Institute
+YEAR: 2026
+COPYRIGHT HOLDER: Rafidul Islam