Improve documentation

.github/dependabot.yml

@@ -9,3 +9,4 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+

.github/workflows/cff-validator.yml

@@ -17,4 +17,5 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Validate CITATION.cff
-        uses: dieghernan/cff-validator@main
+        uses: dieghernan/cff-validator@main
+

.github/workflows/check-full.yaml

@@ -1,58 +1,59 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/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
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
-on:
-  push:
-    branches: [main, master]
-  pull_request:
-    branches: [main, master]
-  schedule:
-    - cron:  '0 17 * * 1,4'
-
-name: R-CMD-check
-
-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: 'devel'}
-          - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel'}
-          #- {os: macOS-latest, r: 'devel'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'oldrel'}
-          - {os: ubuntu-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'devel'}
-          - {os: ubuntu-latest, r: 'oldrel'}
-          - {os: ubuntu-latest, r: '3.6'}
-
-    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
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    - cron:  '0 17 * * 1,4'
+
+name: R-CMD-check
+
+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: 'devel'}
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'oldrel'}
+          #- {os: macOS-latest, r: 'devel'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: macOS-latest, r: 'oldrel'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel'}
+          - {os: ubuntu-latest, r: 'oldrel'}
+          - {os: ubuntu-latest, r: '3.6'}
+
+    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
+

.github/workflows/cran-status.yaml

@@ -8,16 +8,17 @@ on:
 jobs:
   check:
     runs-on: ubuntu-latest
-    permissions: write-all 
+    permissions: write-all
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-        
+
       - name: Check
         uses: dieghernan/cran-status-check@v1
         with:
           fail-on-error: "true"
-          create-issue: "false" 
+          create-issue: "false"
+

.github/workflows/lint.yaml

@@ -1,31 +1,71 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# lintr provides static code analysis for R.
+# It checks for adherence to a given style,
+# identifying syntax errors and possible semantic issues,
+# then reports them to you so you can take action.
+# More details at https://lintr.r-lib.org/
+
+name: lintr
+
 on:
   push:
-    branches: [main, master]
+    branches:
+      - main
+      - master
+  workflow_dispatch:
   pull_request:
-    branches: [main, master]
+    # The branches below must be a subset of the branches above
+    branches:
+      - main
+      - master
+  schedule:
+    - cron: '56 11 * * 5'
 
-name: lint
+permissions:
+  contents: read
 
 jobs:
-  lint:
+  lintr:
+    name: Run lintr scanning
     runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read # for checkout to fetch code
+      security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
+      actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout code
+        uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Setup lintr
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::lintr
-          needs: lint
+          extra-packages: |
+            local::.
+            any::lintr
 
-      - name: Lint
-        run: lintr::lint_package()
+      - name: Run lintr
+        run: |
+          # Lintr package
+          out <- lintr::lint_package()
+          # Create SARIF report
+          lintr::sarif_output(out, "lintr-results.sarif")
+          # Display
+          out
         shell: Rscript {0}
-
+        continue-on-error: true
+
+      - name: Upload analysis results to GitHub
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: lintr-results.sarif
+          wait-for-processing: true
+

.github/workflows/pkgcheck.yaml

@@ -0,0 +1,21 @@
+name: pkgcheck
+
+# This will cancel running jobs once a new run is triggered
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  # Manually trigger the Action under Actions/pkgcheck
+  workflow_dispatch:
+
+jobs:
+  pkgcheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: ropensci-review-tools/pkgcheck-action@main
+        with:
+          summary-only: false
+          post-to-issue: true
+          append-to-issue: true
+

.github/workflows/pkgdown-gh-pages-clean.yaml

@@ -31,4 +31,5 @@ jobs:
         run: |
           git config --local user.name "github-actions[bot]"
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE)'
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE)'
+

.github/workflows/rostemplate-gh-pages.yaml

@@ -7,7 +7,7 @@ on:
     tags: ['*']
   schedule:
     - cron:  '0 22 15 * *'
-    
+
 name: rostemplate-gh-pages
 
 jobs:
@@ -38,4 +38,5 @@ jobs:
         run: |
           git config --local user.name "github-actions[bot]"
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = FALSE)'
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = FALSE)'
+

.github/workflows/test-coverage.yaml

@@ -27,5 +27,25 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+

.github/workflows/update-citation-cff.yaml

@@ -54,5 +54,3 @@ jobs:
           git commit -m 'Update CITATION.cff' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
-
-

.github/workflows/update-docs.yaml

@@ -30,7 +30,7 @@ jobs:
 
       - name: Update docs
         run: |
-          
+
           pkgdev::update_docs()
 
         shell: Rscript {0}
@@ -44,7 +44,7 @@ jobs:
           git push origin || echo "No changes to commit"
 
       - uses: r-lib/actions/check-r-package@v2
-      
+
       - name: Deploy package
         run: |
           git config --local user.name "github-actions[bot]"

.github/workflows/wipe-cache.yaml

@@ -8,3 +8,4 @@ jobs:
 
     steps:
       - uses: easimon/wipe-cache@main
+

CONTRIBUTING.md

@@ -0,0 +1,46 @@
+# CONTRIBUTING
+
+## Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitHub web interface, so long as the changes are made in the *source* file.
+
+-   YES ✔️: you edit a roxygen comment in a `.R` file below `R/`.
+-   NO ❌: you edit an `.Rd` file below `man/`.
+
+## Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and
+make sure someone from the team agrees that it's a problem. If you've found a
+bug, create an associated issue and illustrate the bug with a minimal
+[reprex](https://www.tidyverse.org/help/#reprex).
+
+## Pull request process
+
+-   We recommend that you create a Git branch for each pull request (PR).
+-   Look at the `R-CMD-check` build status before. After making changes, run
+    `devtools::check()` and ensure no new Notes, Warnings or Errors are
+    appearing.
+-   We recommend the tidyverse [style guide](http://style.tidyverse.org). We
+    also use the [styler](https://CRAN.R-project.org/package=styler) package to
+    apply these styles, but please **don't restyle code that has nothing to do
+    with your PR**.
+-   We use [roxygen2](https://cran.r-project.org/package=roxygen2).
+-   We use [testthat](https://cran.r-project.org/package=testthat).
+    Contributions with test cases included are easier to accept.
+-   For user-facing changes, add a bullet to the top of `NEWS.md` below the
+    current development version header describing the changes made followed by
+    your GitHub username, and links to relevant issue(s)/PR(s).
+
+## Prefer to Email?
+
+Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
+
+Though note that private discussions over email don't help others - of course
+email is totally warranted if it's a sensitive problem of any kind.
+
+## Thanks for contributing!
+
+This contributing guide is adapted from the tidyverse contributing guide
+available at
+<https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md>