diff --git a/.Rbuildignore b/.Rbuildignore index 084efac..715a82a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,6 @@ ^vignettes$ ^dont-build-vignettes$ ^\.github$ +^_pkgdown\.yml$ +^pkgdown$ +^codecov\.yml$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..a3ac618 --- /dev/null +++ b/.github/workflows/R-CMD-check.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 + +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@v3 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..ed7650c --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,48 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v3 + + - 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/github-pages-deploy-action@v4.4.1 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..27d4528 --- /dev/null +++ b/.github/workflows/test-coverage.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] + +name: test-coverage + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v3 + + - 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 + needs: coverage + + - name: Test coverage + run: | + covr::codecov( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "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 diff --git a/.gitignore b/.gitignore index aa72113..8f42c41 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ .RData *.Rproj +docs diff --git a/DESCRIPTION b/DESCRIPTION index 6784567..06123ae 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,7 +6,7 @@ Authors@R: c( person("Eric", "Hare", email = "eric@oaiti.org", role = c("aut", "cre")), person("GGobi Foundation", role = "aut")) License: GPL-3 -URL: https://github.com/heike/gglogo +URL: https://github.com/heike/gglogo, http://heike.github.io/gglogo/ BugReports: https://github.com/heike/gglogo/issues Depends: R (>= 3.6) diff --git a/README.Rmd b/README.Rmd index 6ff8a6a..2d67efa 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,6 +18,7 @@ R package for creating sequence logo plots [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/heike/gglogo/commits/main) [![codecov test coverage](https://codecov.io/gh/heike/gglogo/graph/badge.svg?token=zfeqffIjxY)](https://codecov.io/gh/heike/gglogo) [![R-CMD-check](https://github.com/heike/gglogo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/heike/gglogo/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/heike/gglogo/branch/main/graph/badge.svg)](https://app.codecov.io/gh/heike/gglogo?branch=main) diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..35e7f0d --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: http://heike.github.io/gglogo/ +template: + bootstrap: 5 + diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..04c5585 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,14 @@ +comment: false + +coverage: + status: + project: + default: + target: auto + threshold: 1% + informational: true + patch: + default: + target: auto + threshold: 1% + informational: true