v2.0 add unit-tests for tbl_survfit for add_n, add_nevent, add_p

.Rbuildignore

@@ -18,6 +18,7 @@
 ^revdep$
 ^CRAN-RELEASE$
 ^\.covrignore$
+^\.DS_Store$
 ^lastMiKTeXException$
 ^bench$
 ^benchmark$
@@ -37,3 +38,4 @@
 ^CRAN-SUBMISSION$
 ^man-images$
 ^vignettes/articles$
+^_archive$

.github/pull_request_template.md → .github/PULL_REQUEST_TEMPLATE.md

@@ -8,20 +8,16 @@
 
 Reviewer Checklist (if item does not apply, mark is as complete)
 
-- [ ] Ensure all package dependencies are installed by running `renv::install()`
-- [ ] PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
-- [ ] If an update was made to `tbl_summary()`, was the same change implemented for `tbl_svysummary()`?
-- [ ] If a new function was added, function included in `_pkgdown.yml`
-- [ ] If a bug was fixed, a unit test was added for the bug check
+- [ ] Ensure all package dependencies are installed: `renv::install()`
+- [ ] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()`
+- [ ] If a bug was fixed, a unit test was added.
 - [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website.
-- [ ] Code coverage is suitable for any new functions/features. Review coverage with `withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report())`. Begin in a fresh R session without any packages loaded. 
-- [ ] R CMD Check runs without errors, warnings, and notes
+- [ ] Code coverage is suitable for any new functions/features: `devtools::test_coverage()`
 - [ ] `usethis::use_spell_check()` runs with no spelling errors in documentation
 
 When the branch is ready to be merged into master:
 - [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# gtsummary (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
 - [ ] Increment the version number using `usethis::use_version(which = "dev")` 
-- [ ] Run `codemetar::write_codemeta()`
 - [ ] Run `usethis::use_spell_check()` again
 - [ ] Approve Pull Request
 - [ ] Merge the PR. Please use "Squash and merge".

.github/workflows/R-CMD-check-as-cran.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    # branches: [main, master]
+
+name: R-CMD-check-as-cran
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
 # NOTE: This workflow is overkill for most R packages and
@@ -8,7 +8,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    # branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,12 +22,13 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
+          # use 4.1 to check with rtools40's older compiler
+          # - {os: windows-latest, r: '4.1'}
 
-          # Use older ubuntu to maximise backward compatibility
-          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           # - {os: ubuntu-latest,   r: 'oldrel-2'}
@@ -39,7 +40,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,24 +52,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update -y
-          sudo apt-get install -y texlive-fonts-extra
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      # this is hopefully a transitory issue and we can delete in the future (2024-05-02)
+      # https://github.com/lme4/lme4/issues/763
+      - name: Install Matrix and lme4 from CRAN
+        run: utils::install.packages(c("Matrix", "lme4"), repos = c(CRAN = "https://cloud.r-project.org"))
+        shell: Rscript {0}
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      # not using the default '--as-cran' arg, because it sets up private libs (see https://github.com/r-lib/devtools/issues/2044#issuecomment-526209877)
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          args: 'c("--no-manual")'

.github/workflows/pkgdown.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    # branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -19,8 +19,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -31,15 +33,15 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.
-          needs: website
+          needs: check
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages