Merge pull request #74 from ropensci/rust

Update checklist and pkgdown infrastructure

Author: ThierryO

.Rbuildignore

@@ -1,22 +1,23 @@
 # checklist
-^_pkgdown.yml$
 ^.*\.Rproj$
 ^.zenodo\.json$
+^CITATION\.cff$
+^LICENSE.md$
+^Meta$
+^README\.Rmd$
+^\.Rproj\.user$
 ^\.github$
 ^\.httr-oauth$
-^\.Rproj\.user$
 ^\.zenodo\.json$
+^_pkgdown.yml$
 ^checklist.yml$
-^CITATION\.cff$
 ^codecov.yml$
 ^codecov\.yml$
 ^codemeta\.json$
 ^cran-comments\.md$
 ^data-raw$
 ^doc$
 ^docs$
-^LICENSE.md$
 ^man-roxygen$
-^Meta$
+^organisation.yml$
 ^pkgdown$
-^README\.Rmd$

.github/CODE_OF_CONDUCT.md

@@ -8,7 +8,7 @@ We are committed to making participation in this project a harassment-free exper
 everyone, regardless of level of experience, gender, gender identity and expression,
 sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
 
-Examples of unacceptable behavior by participants include the use of sexual language or
+Examples of unacceptable behaviour by participants include the use of sexual language or
 imagery, derogatory comments or personal attacks, trolling, public or private harassment,
 insults, or other unprofessional conduct.
 
@@ -17,7 +17,7 @@ commits, code, wiki edits, issues, and other contributions that are not aligned
 Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
 from the project team.
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by 
 opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant 

.github/CONTRIBUTING.md

@@ -2,55 +2,38 @@
 
 ### Fixing typos
 
-Small typos or grammatical errors in documentation may be edited directly using
-the GitHub web interface, so long as the changes are made in the _source_ file.
-
-*  YES: you edit a roxygen comment in a `.R` file below `R/`.
-*  NO: you edit an `.Rd` file below `man/`.
+Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
+E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
 
 ### Prerequisites
 
-Before you make a substantial pull request, you should always file an issue and
-make sure someone from the team agrees that it’s a problem. If you’ve found a
-bug, create an associated issue and illustrate the bug with a minimal 
-[reprex](https://www.tidyverse.org/help/#reprex).
+Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. 
+If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
 
 ### Pull request process
 
 *  We recommend that you create a Git branch for each pull request (PR).  
-*  Look at the Travis and AppVeyor build status before and after making changes.
-The `README` should contain badges for any continuous integration services used
-by the package.  
-*  We recommend the tidyverse [style guide](http://style.tidyverse.org).
-You can use the [styler](https://CRAN.R-project.org/package=styler) package to
-apply these styles, but please don't restyle code that has nothing to do with 
-your PR.  
-*  We use [roxygen2](https://cran.r-project.org/package=roxygen2).  
-*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
-with test cases included are easier to accept.  
-*  For user-facing changes, add a bullet to the top of `NEWS.md` below the
-current development version header describing the changes made followed by your
-GitHub username, and links to relevant issue(s)/PR(s).
+*  Look at the GitHub Actions build status before and after making changes.
+The `README` should contain badges for any continuous integration services used by the package.  
+*  We require the `tidyverse` [style guide](http://style.tidyverse.org).
+You can use the [`styler`](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+*  We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).  
+*  We use [`testthat`](https://cran.r-project.org/package=testthat). 
+Contributions with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
 
 ### Code of Conduct
 
-Please note that the git2rdata project is released with a
-[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
-project you agree to abide by its terms.
-
-### See rOpenSci [contributing guide](https://ropensci.github.io/dev_guide/contributingguide.html)
-for further details.
-
-### Discussion forum
-
-Check out our [discussion forum](https://discuss.ropensci.org) if you think your issue requires a longer form discussion.
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
+By contributing to this project you agree to abide by its terms.
 
 ### Prefer to Email? 
 
 Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
 
-Though note that private discussions over email don't help others - of course email is totally warranted if it's a sensitive problem of any kind.
+Though note that private discussions over email don't help others - of course
+email is totally warranted if it's a sensitive problem of any kind.
 
 ### Thanks for contributing!
 
-This contributing guide is adapted from the tidyverse contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 
+This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 

.github/pull_request_template.md

@@ -13,7 +13,7 @@ or similar - or if just relates to an issue make sure to mention
 it like "#4" -->
 
 ## Example
-<!--- if introducing a new feature or changing behavior of existing
+<!--- if introducing a new feature or changing behaviour of existing
 methods/functions, include an example if possible to do in brief form -->
 
 <!--- Did you remember to include tests? Unless you're just changing

.github/workflows/check_on_branch.yml

@@ -5,16 +5,16 @@ on:
       - master
       - ghpages
 
-name: "check package"
+name: "check package with checklist"
 
 jobs:
   check-package:
     runs-on: ubuntu-latest
     name: "check package"
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
     steps:
-      - uses: inbo/actions/check_pkg@master
-        with:
-          token: ${{ secrets.PAT }}
+      - uses: inbo/actions/[email protected]

.github/workflows/check_on_different_r_os.yml

@@ -22,78 +22,30 @@ jobs:
         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: ubuntu-22.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       _R_CHECK_SYSTEM_CLOCK_: false
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - 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@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        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@v1
+      - uses: r-lib/actions/setup-r-dependencies@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 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)
-          remotes::install_cran("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 = "error", 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@master
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-          retention-days: 5
+          error-on: '"error"'

.github/workflows/check_on_main.yml

@@ -3,19 +3,17 @@ on:
     branches:
       - main
       - master
-  schedule:
-    - cron: '6 0 15 * *'
+permissions:
+  contents: write
 
-name: "check package on main"
+name: "check package on main with checklist"
 
 jobs:
   check-package:
     runs-on: ubuntu-latest
     name: "check package"
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: inbo/actions/check_pkg@master
-        with:
-          token: ${{ secrets.PAT }}
+      - uses: inbo/actions/[email protected]

.github/workflows/release.yml

@@ -1,30 +1,30 @@
+name: Releases
+
 on:
   push:
     tags:
-      - 'v*'
-
-name: Create Release
+      - v*
+  workflow_run:
+    workflows: ["check package on main with checklist"]
+    types:
+      - completed
 
 jobs:
-  build:
-    name: Create Release
+  publish:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - name: Get tag message
+      - uses: actions/checkout@v3
+      - name: Get tag
         run: |
-          TAG_BODY=$(git tag --contains ${{ github.sha }} -n100 | awk '(NR>1)')
-          echo "::set-output name=TAG_BODY::$TAG_BODY"
-        id: tag-body
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          git fetch --tags --force
+          TAG=$(git tag --contains $(git rev-parse HEAD))
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "$TAG_BODY" > body.md
+      - uses: ncipollo/release-action@v1
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
-          body: ${{ steps.tag-body.outputs.TAG_BODY }}
-          draft: false
-          prerelease: false
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md