Merge pull request #22 from NIFU-NO/dev

Dev

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,52 @@
+# 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.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - 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]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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

_pkgdown.yml

@@ -1,45 +1,45 @@
 url: https://nifu-no.github.io/saros.utils/
 template:
   bootstrap: 5
-  light-switch: true
-
-
+  light-switch: yes
 reference:
-- title: "Website management tools"
-  desc: "Share reports to various recipients with password access and automatic sending of emails"
+- title: Website management tools
+  desc: Share reports to various recipients with password access and automatic sending
+    of emails
   contents:
   - setup_access_restrictions
   - create_email_credentials
-- title: "Project startup tools - main wrapper functions"
-  desc: "For project templates (might be dropped in favour of 3rd party packages focusing on this)"
+- title: Project startup tools - main wrapper functions
+  desc: For project templates (might be dropped in favour of 3rd party packages focusing
+    on this)
   contents:
   - initialize_saros_project
   - download_zip_to_folder
-- title: "Project startup tools - underlying functions"
-  desc: "For project templates (might be dropped in favour of 3rd party packages focusing on this)"
+- title: Project startup tools - underlying functions
+  desc: For project templates (might be dropped in favour of 3rd party packages focusing
+    on this)
   contents:
   - generate_yaml_from_directory
   - copy_folder_contents_to_dir
   - create_directory_structure
   - create_r_files
-- title: "MS Word <--> Quarto"
-  desc: "Resolving some current limitations of Quarto"
+- title: MS Word <--> Quarto
+  desc: Resolving some current limitations of Quarto
   contents:
   - post_render_docx_img_replacer
   - replace_docx_imgs_with_mscharts
-- title: "Column recoding tools"
-  desc: "Note: will be moved to 3rd party package in the future"
+- title: Column recoding tools
+  desc: 'Note: will be moved to 3rd party package in the future'
   contents:
   - col_to_binaries
   - combn_upto
   - recode_checkbox_sets
   - omitted_recoder_df
-- title: "Convenience tools for working with datasets"
-  desc: "Perhaps better suited in 3rd party packages, so might be moved later"
-  contents:
-  - handpick
-- title: "Label tools"
-  desc: "Note: will be moved to 3rd party package in the future"
+- title: Convenience tools for working with datasets
+  desc: Perhaps better suited in 3rd party packages, so might be moved later
+  contents: handpick
+- title: Label tools
+  desc: 'Note: will be moved to 3rd party package in the future'
   contents:
   - attach_qualtrics_labels
   - remove_special_chars_in_labels