actions added: check, coverage and website

.Rbuildignore

@@ -6,3 +6,6 @@
 ^vignettes$
 ^dont-build-vignettes$
 ^\.github$
+^_pkgdown\.yml$
+^pkgdown$
+^codecov\.yml$

.github/.gitignore

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

.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

.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

.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

.gitignore

@@ -3,3 +3,4 @@
 .RData
 
 *.Rproj
+docs

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)

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)
 <!-- badges: end -->
 
 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://heike.github.io/gglogo/
+template:
+ bootstrap: 5
+

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