Merge pull request #104 from inbo/0.3.1

Add Zenodo support for bookdown

.github/workflows/check_on_branch.yml

@@ -1,7 +1,6 @@
 on:
   push:
     branches-ignore:
-      - master
       - main
       - ghpages
 
@@ -14,7 +13,8 @@ jobs:
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
     permissions:
       contents: read
     steps:
-      - uses: inbo/actions/[email protected].0
+      - uses: inbo/actions/[email protected].2

.github/workflows/check_on_different_r_os.yml

@@ -22,86 +22,52 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest,   r: 'release', skip_test: 'false'}
+          - {os: windows-latest, r: 'release', skip_test: 'true'}
+          - {os: ubuntu-22.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest", skip_test: 'false'}
+          - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest", skip_test: 'false'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       _R_CHECK_SYSTEM_CLOCK_: false
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
 
     steps:
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          extra-repositories: https://inbo.r-universe.dev
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
+      - name: linux dependencies
+        if: runner.os == 'linux'
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
+          sudo apt update
+          sudo apt install -y --no-install-recommends libcurl4-openssl-dev \
+            libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev \
+            libjpeg-dev libmagick++-dev libpng-dev libpoppler-cpp-dev \
+            libsecret-1-dev libtiff5-dev
+          sudo apt install -y --no-install-recommends r-cran-assertthat \
+            r-cran-bookdown r-cran-covr r-cran-curl r-cran-desc \
+            r-cran-devtools r-cran-fs r-cran-gert r-cran-httr r-cran-hunspell \
+            r-cran-jsonlite r-cran-knitr r-cran-mockery r-cran-pdftools \
+            r-cran-r6 r-cran-rcmdcheck r-cran-remotes r-cran-rmarkdown \
+            r-cran-roxygen2 r-cran-rstudioapi r-cran-sessioninfo \
+            r-cran-testthat r-cran-withr r-cran-yaml
+          Rscript --no-save --no-restore -e 'install.packages("remotes")'
+          Rscript --no-save --no-restore -e 'remotes::install_cran(c("assertthat", "bookdown", "codemetar", "covr", "curl", "desc", "devtools", "fs", "gert", "hexSticker", "httr", "hunspell", "jsonlite", "knitr", "lintr", "mockery", "pdftools", "pkgdown", "R6", "rcmdcheck", "renv", "rmarkdown", "roxygen2", "rstudioapi", "sessioninfo", "showtext", "sysfonts", "testthat", "withr", "yaml"))'
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        if: runner.os != 'linux'
+
+      - uses: r-lib/actions/check-r-package@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 macOS system dependencies
-        if: runner.os == 'macOS'
-        run: |
-          brew install fribidi
-
-      - name: Install linux system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-          sudo apt-get install -y libcurl4-openssl-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE,
-          type = ifelse(.Platform$OS.type=="unix", "source", "binary"))
-          remotes::install_cran("rcmdcheck")
-          install.packages("stringi")
-        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
+          error-on: '"error"'
         env:
-          _R_CHECK_CRAN_INCOMING_: true
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-          retention-days: 5
+          ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
+          SKIP_TEST: ${{ matrix.config.skip_test }}

.github/workflows/check_on_main.yml

@@ -17,5 +17,6 @@ jobs:
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
     steps:
-      - uses: inbo/actions/[email protected].0
+      - uses: inbo/actions/[email protected].2

.github/workflows/release.yml

@@ -3,7 +3,11 @@ name: Releases
 on:
   push:
     tags:
-      - 'v*'
+      - v*
+  workflow_run:
+    workflows: ["check package on main"]
+    types:
+      - completed
 
 jobs:
 

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.3.1",
+  "version": "0.3.2",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>An opinionated set of rules for R packages and R source code\nprojects.<\/p>",
@@ -9,6 +9,7 @@
     "documentation",
     "publication"
   ],
+  "access_right": "open",
   "language": "eng",
   "contributors": [
     {
@@ -41,7 +42,6 @@
       "orcid": "0000-0001-8804-4216"
     }
   ],
-  "access_right": "open",
   "communities": [
     {
       "identifier": "inbo"

CITATION.cff

@@ -25,4 +25,4 @@ identifiers:
   value: 10.5281/zenodo.4028303
 - type: url
   value: https://inbo.github.io/checklist/
-version: 0.3.1
+version: 0.3.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -30,8 +30,8 @@ Imports:
     hunspell,
     jsonlite,
     knitr,
-    lintr (>= 2.0.1.9000),
-    pkgdown,
+    lintr (>= 3.0.2.9000),
+    pkgdown (>= 2.0.7),
     R6,
     rcmdcheck,
     renv,
@@ -41,16 +41,19 @@ Imports:
     withr,
     yaml
 Suggests:
+    bookdown,
     covr,
     curl,
     mockery,
     roxygen2,
     rstudioapi,
     showtext,
     sysfonts,
-    testthat
+    testthat,
+    zen4R (>= 0.9)
 VignetteBuilder: 
     knitr
+Additional_repositories: https://inbo.r-universe.dev
 Config/checklist/communities: inbo
 Config/checklist/keywords: quality control; documentation; publication
 Encoding: UTF-8