From 9e2a7bb7324b4fef3b7a061a91724a564cf5f451 Mon Sep 17 00:00:00 2001 From: Jay Hesselberth Date: Thu, 29 Aug 2024 11:31:02 -0600 Subject: [PATCH] upkeep v0.8.1 (#416) * use pkgdown block tags * update gh actions * update readme --- .github/workflows/check-standard.yaml | 5 ++++- .github/workflows/pkgdown.yaml | 6 ++++-- .github/workflows/pr-commands.yaml | 6 ++++-- .github/workflows/test-coverage.yaml | 23 +++++++++++++++++------ README.Rmd | 20 +++++++++++--------- README.md | 16 +++++++++++----- 6 files changed, 51 insertions(+), 25 deletions(-) diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml index a3ac6182..0f2fe080 100644 --- 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 index ed7650c7..c9f0165d 100644 --- 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 index 71f335b3..d1f76509 100644 --- 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 index 2c5bb502..fefc52e2 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -8,6 +8,8 @@ on: name: test-coverage +permissions: read-all + jobs: test-coverage: runs-on: ubuntu-latest @@ -15,7 +17,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +25,37 @@ jobs: - 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 index d39812f1..ae349352 100644 --- 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 index d0e22537..d0747177 100644 --- a/README.md +++ b/README.md @@ -14,19 +14,25 @@ suite. ## Installation -The latest stable version can be installed from CRAN: +
``` r -install.packages('valr') +# 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') +# 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