upkeep v0.8.1 (#416)

* use pkgdown block tags * update gh actions * update readme
rnabioco · Aug 29, 2024 · 9e2a7bb · 9e2a7bb
1 parent 9e03f64
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -8,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       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: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
@@ -23,18 +23,20 @@ valr provides tools to read and manipulate genome intervals and signals, similar
 
 ## Installation
 
-The latest stable version can be installed from CRAN:
-
-``` r
-install.packages('valr')
+::: .pkgdown-release
+```{r, eval = FALSE}
+# Install released version from CRAN
+install.packages("valr")
 ```
+:::
 
-The latest development version can be installed from github:
-
-``` r
-# install.packages("devtools")
-devtools::install_github('rnabioco/valr')
+::: .pkgdown-devel
+```{r, eval = FALSE}
+# Install development version from GitHub
+# install.packages("pak")
+pak::pak("rnabioco/valr")
 ```
+:::
 
 ## valr Example
 Functions in valr have similar names to their BEDtools counterparts, and so will be familiar to users coming from the BEDtools suite. Unlike other tools that wrap BEDtools and write temporary files to disk, valr tools run natively in memory. Similar to [pybedtools](https://daler.github.io/pybedtools/#why-pybedtools), valr has a terse syntax:

diff --git a/README.md b/README.md
@@ -14,19 +14,25 @@ suite.
 
 ## Installation
 
-The latest stable version can be installed from CRAN:
+<div class=".pkgdown-release">
 
 ``` r
-install.packages('valr')
+# Install released version from CRAN
+install.packages("valr")
 ```
 
-The latest development version can be installed from github:
+</div>
+
+<div class=".pkgdown-devel">
 
 ``` r
-# install.packages("devtools")
-devtools::install_github('rnabioco/valr')
+# Install development version from GitHub
+# install.packages("pak")
+pak::pak("rnabioco/valr")
 ```
 
+</div>
+
 ## valr Example
 
 Functions in valr have similar names to their BEDtools counterparts, and