Merge in changes for CIDAtools v0.2.0

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^ReadMe.md
@@ -11,3 +13,6 @@ hex_sticker.R
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^vignettes/sas-macros.Rmd
+^altdoc$
+^_quarto$

.github/workflows/R-Build-Test_cleanupBranch.yml

@@ -10,7 +10,7 @@ name: R
 
 on:
   push:
-    branches: [] #branches: [ "cleanup_edits_SM" ]
+    branches: [ "cleanup_edits_SM" ]
 
 permissions:
   contents: read
@@ -22,8 +22,12 @@ jobs:
       fail-fast: true
       matrix:
         r-version: ['release']
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest] #[ubuntu-latest]
 
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v4
 
@@ -33,15 +37,43 @@ jobs:
           r-version: ${{ matrix.r-version }}
           use-public-rspm: true
 
+      - name: Cache R
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('DESCRIPTION') }}-${{ hashFiles('**/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('**/renv.lock') }}
+            ${{ runner.os }}-r-${{ matrix.r-version }}
+
+
+
       - name: Install dependencies
+        if: steps.cache-r.outputs.cache-hit != 'true'
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck,altdoc,quarto,roxygen2,remotes
           needs: check
 
       - name: Check Package
         uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
 

.github/workflows/altdoc_quarto.yaml

@@ -0,0 +1,65 @@
+# Workflow derived from https://github.com/CIDA-CSPH/CIDAtools/pkgdown.yaml
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: altdoc_quarto_site
+
+jobs:
+  build_doc:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        r-version: ['release']
+    # Only restrict concurrency for non-PR jobs
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set up R ${{ matrix.r-version }}
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r-version }}
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: local::.,any::rcmdcheck,any::altdoc,any::quarto,any::roxygen2
+          needs: check
+
+      - name: Cache R
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+
+      - name: Run Roxygen2
+        run: Rscript -e 'roxygen2::roxygenise()'
+
+      - name: Build Altdoc Site
+        run: Rscript -e 'altdoc::render_docs(path = ".", verbose = FALSE, parallel = FALSE, freeze = FALSE)'
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -7,3 +7,10 @@
 inst/doc
 *.DS_Store
 docs
+/tests/testthat/*.rds
+
+
+/.quarto/
+altdoc/freeze.rds
+_quarto/*
+!_quarto/_freeze/

DESCRIPTION

@@ -1,26 +1,28 @@
 Package: CIDAtools
 Title: This package contains tools for CIDA projects
-Version: 0.1.2
+Version: 0.2.0
 Authors@R: 
-  c(person("CIDA Research Tools Committee", role = c("aut", "cre"), email = "ryan.a.peterson@cuanschutz.edu"))
+  c(person("CIDA Research Tools Committee", role = c("aut", "cre"), email = "CIDA-RT@olucdenver.onmicrosoft.com"))
 Description: This package contains the numerous templates and tools to make life at CIDA (part of the Colorado School of Public Health) happier and more efficient!
-Depends: R (>= 3.5.0)
+Depends: R (>= 4.0)
 Imports: 
     dplyr,
     generics,
     flextable,
     table1, 
-    shiny
+    shiny,
+    fs
 Suggests: 
-    git2r, 
-    survey, 
-    xlsx, 
+    git2r,
+    survey,
+    quarto,
+    xlsx,
     knitr,
-    pander, 
+    pander,
     arsenal,
     rmarkdown,
     DT,
-    covr, 
+    covr,
     shinythemes,
     stats,
     Hmisc,
@@ -30,9 +32,11 @@ Suggests:
     tableone,
     cardx,
     stats,
-    broom.helpers
+    broom.helpers,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
 License: CC0
 Encoding: UTF-8
-RoxygenNote: 7.3.2
-VignetteBuilder: knitr
+RoxygenNote: 7.3.3
+VignetteBuilder: quarto, knitr
 URL: https://cida-csph.github.io/CIDAtools/

NAMESPACE

@@ -18,14 +18,40 @@ export(convertIntervalNotation)
 export(create_project)
 export(find_nearest)
 export(getProjectData)
+export(get_default_value)
+export(get_defaults)
+export(get_full_project_path)
+export(get_global_default_analyst)
+export(get_global_default_path)
+export(get_project_analyst)
+export(get_project_drive_path)
+export(get_project_github)
+export(get_project_location)
+export(get_project_meta_data)
+export(get_project_name)
+export(get_project_pi)
 export(list_kables)
 export(nLevelsP)
 export(nrowP)
+export(open_project)
 export(pvalr)
 export(randblinder_shiny_tool)
 export(read_xlsx_color)
 export(removeAnalyst)
+export(remove_global_default_analyst)
+export(remove_global_default_path)
 export(setAnalyst)
+export(setPermanentAnalyst)
+export(set_default_value)
+export(set_full_project_path)
+export(set_global_default_analyst)
+export(set_global_default_path)
+export(set_project_analyst)
+export(set_project_github)
+export(set_project_location)
+export(set_project_meta_data)
+export(set_project_name)
+export(set_project_pi)
 export(sum_ignore_NA)
 export(vec_power)
 import(flextable)
@@ -41,3 +67,4 @@ importFrom(stats,wilcox.test)
 importFrom(table1,stats.apply.rounding)
 importFrom(table1,stats.default)
 importFrom(table1,table1)
+importFrom(utils,head)

NEWS.md → NEWS.qmd

@@ -1,3 +1,11 @@
+---
+title: "CIDATools - News"
+format: html
+---
+# 0.2.0
+- Refactored most functions to use consistent camelCase naming conventions
+- Deprecated some unused/unsupported functions (if you encounter a deprecated function which you are actively using, please email CIDA-RT@olucdenver.onmicrosoft.com)
+
 # 0.1.1
 
 - Data only argument implemented