Merge pull request #94 from inbo/terminology

version 0.3.0
inbo · Mar 8, 2023 · c1e200b · c1e200b
2 parents b162fbd + 60f3b39
commit c1e200b
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diff --git a/.github/workflows/check_on_branch.yml b/.github/workflows/check_on_branch.yml
@@ -13,8 +13,8 @@ jobs:
     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]
diff --git a/.github/workflows/check_on_different_r_os.yml b/.github/workflows/check_on_different_r_os.yml
@@ -32,16 +32,15 @@ jobs:
       _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 }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -52,13 +51,18 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         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
+      - 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

diff --git a/.github/workflows/check_on_main.yml b/.github/workflows/check_on_main.yml
@@ -7,15 +7,15 @@ on:
     - cron: '6 0 15 * *'
 
 name: "check package on main"
+permissions:
+  contents: write
 
 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]
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,30 +1,24 @@
+name: Releases
+
 on:
   push:
     tags:
       - 'v*'
 
-name: Create Release
-
 jobs:
+
   build:
-    name: Create Release
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Get tag message
         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 }}
+      - uses: ncipollo/release-action@v1
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
+          name: Release ${{ github.ref }}
           body: ${{ steps.tag-body.outputs.TAG_BODY }}
-          draft: false
-          prerelease: false
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,45 +1,50 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.2.6",
-  "description": "An opinionated set of rules for R packages and R source code projects.",
-  "creators": [
-    {
-      "name": "Onkelinx, Thierry",
-      "orcid": "https://orcid.org/0000-0001-8804-4216"
-    }
-  ],
-  "upload_type": "software",
-  "access_right": "open",
+  "version": "0.3.0",
   "license": "GPL-3.0",
-  "communities": [
-    {
-      "identifier": "inbo"
-    }
+  "upload_type": "software",
+  "description": "<p>An opinionated set of rules for R packages and R source code\nprojects.<\/p>",
+  "keywords": [
+    "quality control",
+    "documentation",
+    "publication"
   ],
+  "language": "eng",
   "contributors": [
+    {
+      "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8804-4216",
+      "type": "ContactPerson"
+    },
     {
       "name": "Lommelen, Els",
-      "type": "ProjectMember",
-      "orcid": "https://orcid.org/0000-0002-3481-5684"
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0002-3481-5684",
+      "type": "ProjectMember"
     },
     {
       "name": "Van Calster, Hans",
-      "type": "ProjectMember",
-      "orcid": "https://orcid.org/0000-0001-8595-8426"
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8595-8426",
+      "type": "ProjectMember"
     },
     {
-      "name": "Research Institute for Nature and Forest",
+      "name": "Research Institute for Nature and Forest (INBO)",
       "type": "RightsHolder"
-    },
+    }
+  ],
+  "creators": [
     {
       "name": "Onkelinx, Thierry",
-      "type": "ContactPerson",
-      "orcid": "https://orcid.org/0000-0001-8804-4216"
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8804-4216"
     }
   ],
-  "language": "eng",
-  "keywords": [
-    "R package",
-    "quality control"
+  "access_right": "open",
+  "communities": [
+    {
+      "identifier": "inbo"
+    }
   ]
 }
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,25 +1,28 @@
 cff-version: 1.2.0
-message: If you use this software, please cite it as below.
+message: If you use this software, please cite it using these metadata.
+title: 'checklist: A Thorough and Strict Set of Checks for R Packages and Source Code'
 authors:
-- family-names: Onkelinx
-  given-names: Thierry
-  orcid: https://orcid.org/0000-0001-8804-4216
+- given-names: Thierry
+  family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+keywords:
+- quality control
+- documentation
+- publication
 contact:
-- email: [email protected]
+- given-names: Thierry
   family-names: Onkelinx
-  given-names: Thierry
-- email: [email protected]
-  name: Research Institute for Nature and Forest
-title: 'checklist: A Thorough and Strict Set of Checks for R Packages and Source Code'
-version: 0.2.6
-abstract: An opinionated set of rules for R packages and R source code projects.
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+doi: 10.5281/zenodo.4028303
 license: GPL-3.0
+repository-code: https://github.com/inbo/checklist/
 type: software
-doi: 10.5281/zenodo.4028303
-repository-code: https://github.com/inbo/checklist
+abstract: An opinionated set of rules for R packages and R source code projects.
 identifiers:
+- type: doi
+  value: 10.5281/zenodo.4028303
 - type: url
   value: https://inbo.github.io/checklist/
-keywords:
-- R package
-- quality control
+version: 0.3.0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.2.6
+Version: 0.3.0
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8804-4216")),
+           comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Els", "Lommelen", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0002-3481-5684")),
+           comment = c(ORCID = "0000-0002-3481-5684", affiliation = "Research Institute for Nature and Forest (INBO)")),
     person("Hans", "Van Calster", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0001-8595-8426")),
-    person("Research Institute for Nature and Forest", , , "[email protected]", role = c("cph", "fnd"))
+           comment = c(ORCID = "0000-0001-8595-8426", affiliation = "Research Institute for Nature and Forest (INBO)")),
+    person("Research Institute for Nature and Forest (INBO)", , , "[email protected]", role = c("cph", "fnd"))
   )
 Description: An opinionated set of rules for R packages and R source code
     projects.
@@ -18,7 +18,7 @@ URL: https://inbo.github.io/checklist/, https://github.com/inbo/checklist,
     https://doi.org/10.5281/zenodo.4028303
 BugReports: https://github.com/inbo/checklist/issues
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.1.0)
 Imports:
     assertthat,
     codemetar,
@@ -29,21 +29,20 @@ Imports:
     httr,
     hunspell,
     jsonlite,
+    knitr,
     lintr (>= 2.0.1.9000),
     pkgdown,
     R6,
     rcmdcheck,
     renv,
     rmarkdown,
-    rorcid,
     sessioninfo,
     utils,
     withr,
     yaml
 Suggests:
     covr,
     curl,
-    knitr,
     mockery,
     roxygen2,
     rstudioapi,
@@ -52,7 +51,10 @@ Suggests:
     testthat
 VignetteBuilder: 
     knitr
+Config/checklist/communities: inbo
+Config/checklist/keywords: quality control; documentation; publication
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
+SystemRequirements: Pandoc (>= 1.17.2)