Update CI

.Rbuildignore

@@ -13,3 +13,4 @@ LICENSE
 ^CRAN-RELEASE$
 ^\.github$
 ^CRAN-SUBMISSION$
+^pkgdown$

.github/workflows/R-CMD-check.yaml

@@ -1,15 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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:
- - develop
- - master
- - ci
+ branches: [main, develop, ci]
  pull_request:
- branches:
- - develop
- - master
+ branches: [main, develop]
 
 name: R-CMD-check
 
@@ -23,69 +18,32 @@ jobs:
  fail-fast: false
  matrix:
  config:
+ - {os: macos-latest, r: 'release'}
  - {os: windows-latest, r: 'release'}
- - {os: macOS-latest, r: 'release'}
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'oldrel-1'}
 
  env:
- R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
- RSPM: ${{ matrix.config.rspm }}
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - 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-pandoc@v1
-
- - name: Install pak and query dependencies
- run: |
- install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
- saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
- shell: Rscript {0}
-
- - name: Cache R packages
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
- restore-keys: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
- - name: Install system dependencies
- if: runner.os == 'Linux'
- run: Rscript -e 'pak::local_system_requirements(execute = TRUE)'
-
- - name: Install dependencies
- run: |
- pak::local_install_dev_deps(upgrade = TRUE)
- pak::pkg_install("rcmdcheck")
- shell: Rscript {0}
-
- - name: Session info
- run: |
- options(width = 100)
- pkgs <- installed.packages()[, "Package"]
- sessioninfo::session_info(pkgs, include_base = TRUE)
- shell: Rscript {0}
-
- - name: Check
- env:
- _R_CHECK_CRAN_INCOMING_: false
- run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
- shell: Rscript {0}
-
- - name: Show testthat output
- if: always()
- run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
- shell: bash
+ extra-packages: any::rcmdcheck
+ needs: check
 
- - name: Upload check results
- if: failure()
- uses: actions/upload-artifact@main
+ - uses: r-lib/actions/check-r-package@v2
  with:
- name: ${{ runner.os }}-r${{ matrix.config.r }}-results
- path: check
+ upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,53 +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:
- - develop
- - ci
+ branches: [main]
+ pull_request:
+ branches: [main]
+ release:
+ types: [published]
+ workflow_dispatch:
 
 name: pkgdown
 
 jobs:
  pkgdown:
- runs-on: macOS-latest
+ 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@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: r-lib/actions/setup-pandoc@v2
 
- - uses: r-lib/actions/setup-pandoc@v1
-
- - name: Install pak and query dependencies
- run: |
- install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
- saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
- shell: Rscript {0}
-
- - name: Cache R packages
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-r@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
- - name: Install dependencies
- run: |
- pak::local_install_dev_deps(upgrade = TRUE)
- pak::pkg_install("rcmdcheck")
- shell: Rscript {0}
+ use-public-rspm: true
 
- - name: Install package
- run: R CMD INSTALL .
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::.
+ needs: website
 
  - name: Build site
- if: github.ref != 'refs/heads/develop'
- run: |
- Rscript -e 'pkgdown::build_site()'
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
 
- - name: Deploy package
- if: github.ref == 'refs/heads/develop'
- run: |
- git config --local user.email "[email protected]"
- git config --local user.name "GitHub Actions"
- Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/[email protected]
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs

.github/workflows/test-coverage.yaml

@@ -1,47 +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:
- - develop
- - master
- - ci
+ branches: [main, develop, ci]
  pull_request:
- branches:
- - develop
- - master
+ branches: [main, develop]
 
 name: test-coverage
 
 jobs:
  test-coverage:
- runs-on: macOS-latest
+ runs-on: ubuntu-latest
  env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
 
- - uses: r-lib/actions/setup-pandoc@v1
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::covr
+ needs: coverage
 
- - name: Install pak and query dependencies
+ - name: Test coverage
  run: |
- install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
- saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
+ covr::codecov(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+ )
  shell: Rscript {0}
 
- - name: Cache R packages
- uses: actions/cache@v2
- with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
- - name: Install dependencies
+ - name: Show testthat output
+ if: always()
  run: |
- pak::local_install_dev_deps(upgrade = TRUE)
- pak::pkg_install("rcmdcheck")
- shell: Rscript {0}
+ ## --------------------------------------------------------------------
+ find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
 
- - name: Test coverage
- run: covr::codecov()
- shell: Rscript {0}
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package

.gitignore

@@ -6,3 +6,4 @@ doc
 .Ruserdata
 inst/doc
 docs/*
+docs

DESCRIPTION

@@ -24,7 +24,7 @@ Description: Deciding what resolution to use can be a difficult question when
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-URL: https://github.com/lazappi/clustree
+URL: https://github.com/lazappi/clustree, https://lazappi.github.io/clustree/
 BugReports: https://github.com/lazappi/clustree/issues
 VignetteBuilder: knitr
 Depends: R (>= 3.5),

_pkgdown.yml

@@ -1,6 +1,6 @@
-title: clustree
-url: http://lazappi.github.io/clustree
+url: https://lazappi.github.io/clustree/
 template:
+ bootstrap: 5
  params:
  bootswatch: cosmo
  ganalytics: UA-52309538-5