Check for new lints and following kebab-case for naming R files (#260)

* Check for new lints * avoid nesting inside function calls * more cleanup * more cleanup * to trigger CI again * fix regression and remaining lints * Update styler.yaml * bump parameters version * update README for linux installation * bump insight * to trigger CI * use consistent indentation for function args * starwars data has changed in latest dplyr * Update pkgdown.yaml * consistently follow kebab-case for filenames * Update .Rbuildignore * fix vignette paths to examples as well * run checks on windows instead * try macos instead * Apply automatic changes * Apply automatic changes * back to ubuntu * bump BayesFactor * Update .lintr * Update .lintr * use r-release for now * Update pre-commit.yaml * minor formatting changes * bump Pandoc * Update data.R * update snapshots * fix build failure * Revert "fix build failure" This reverts commit 4b15dbf. * Update switch-functions.R * bump Pandoc * Update codemeta.json * minor * minor * use pak to upgrade to latest pkg versions * Revert "use pak to upgrade to latest pkg versions" This reverts commit e482755. * bump pandoc * Apply automatic changes * Update meta_analysis.Rd * bump roxygen2 version * band-aid --------- Co-authored-by: IndrajeetPatil <[email protected]>
IndrajeetPatil · Jan 13, 2024 · 49efb5d · 49efb5d
1 parent 325c48d
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
+.ls-lint.yml
 ^.*\.Rproj$
 ^.gitlab-ci\.yaml$
 ^API$

diff --git a/.github/workflows/R-CMD-check-devel.yaml b/.github/workflows/R-CMD-check-devel.yaml
@@ -20,11 +20,11 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.7"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           http-user-agent: "release"
           use-public-rspm: true
 

diff --git a/.github/workflows/R-CMD-check-hard.yaml b/.github/workflows/R-CMD-check-hard.yaml
@@ -27,7 +27,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/R-CMD-check-strict.yaml b/.github/workflows/R-CMD-check-strict.yaml
@@ -40,7 +40,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -27,11 +27,11 @@ jobs:
 
           #- { os: windows-latest, r: "devel" }
           - { os: windows-latest, r: "release" }
-          - { os: windows-latest, r: "oldrel-1" }
+          #- { os: windows-latest, r: "oldrel-1" }
 
           #- { os: ubuntu-latest, r: "devel" }
           - { os: ubuntu-latest, r: "release" }
-          - { os: ubuntu-latest, r: "oldrel-1" }
+          #- { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -42,7 +42,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-all-examples.yaml b/.github/workflows/check-all-examples.yaml
@@ -30,7 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/check-link-rot.yaml b/.github/workflows/check-link-rot.yaml
@@ -21,11 +21,11 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/check-random-test-order.yaml b/.github/workflows/check-random-test-order.yaml
@@ -18,7 +18,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/check-readme.yaml b/.github/workflows/check-readme.yaml
@@ -30,7 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.7"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-spelling.yaml b/.github/workflows/check-spelling.yaml
@@ -21,7 +21,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-test-warnings.yaml b/.github/workflows/check-test-warnings.yaml
@@ -22,7 +22,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/check-vignette-warnings.yaml b/.github/workflows/check-vignette-warnings.yaml
@@ -22,11 +22,11 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.7"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/html-5-check.yaml b/.github/workflows/html-5-check.yaml
@@ -19,7 +19,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "devel"
+          #r-version: "devel"
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -38,7 +38,8 @@ jobs:
         run: |
           options(crayon.enabled = TRUE)
           library(lintr)
-          lint_package(linters = linters_with_defaults(
+          lint_package(linters = linters_with_tags(
+            tags = NULL,
             absolute_path_linter = NULL,
             assignment_linter = NULL,
             commented_code_linter = NULL,
@@ -59,8 +60,7 @@ jobs:
             undesirable_function_linter = NULL,
             undesirable_operator_linter = NULL,
             unnecessary_concatenation_linter(allow_single_expression = FALSE),
-            unused_import_linter = NULL,
-            defaults = linters_with_tags(tags = NULL)
+            unused_import_linter = NULL
           ))
         shell: Rscript {0}
         env:

diff --git a/.github/workflows/pkgdown-no-suggests.yaml b/.github/workflows/pkgdown-no-suggests.yaml
@@ -25,7 +25,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.9"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -24,7 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.7"
+          pandoc-version: "3.1.11.1"
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -46,7 +46,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.3
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           branch: gh-pages
           folder: docs
diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
@@ -24,7 +24,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.9"
           architecture: "x64"

diff --git a/.github/workflows/styler.yaml b/.github/workflows/styler.yaml
@@ -29,7 +29,7 @@ jobs:
             local::.
             r-lib/pkgapi
             r-lib/styler
-            r-lib/roxygen2
+            any::roxygen2
             anthonynorth/roxyglobals
           needs: |
             styler

diff --git a/.lintr b/.lintr
@@ -1,9 +1,8 @@
-linters: linters_with_defaults(
+linters: all_linters(
     absolute_path_linter = NULL,
     assignment_linter = NULL,
     commented_code_linter = NULL,
     cyclocomp_linter(25L),
-    extraction_operator_linter = NULL,
     if_not_else_linter(exceptions = character(0L)),
     implicit_integer_linter = NULL,
     library_call_linter = NULL,
@@ -19,6 +18,5 @@ linters: linters_with_defaults(
     undesirable_function_linter = NULL,
     undesirable_operator_linter = NULL,
     unnecessary_concatenation_linter(allow_single_expression = FALSE),
-    unused_import_linter = NULL,
-    defaults = linters_with_tags(tags = NULL)
+    unused_import_linter = NULL
   )
diff --git a/.ls-lint.yml b/.ls-lint.yml
@@ -0,0 +1,6 @@
+ls:
+    .R: kebab-case
+
+# package name can't be changed to follow kebab-case
+ignore:
+    - '**/statsExpressions*'
diff --git a/CITATION.cff b/CITATION.cff
@@ -110,7 +110,7 @@ references:
     given-names: Jeffrey N.
     email: [email protected]
   year: '2023'
-  version: '>= 0.9.12-4.5'
+  version: '>= 0.9.12-4.6'
 - type: software
   title: correlation
   abstract: 'correlation: Methods for Correlation Analysis'
@@ -201,7 +201,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4777-038X
   year: '2023'
-  version: '>= 1.1.3'
+  version: '>= 1.1.4'
 - type: software
   title: effectsize
   abstract: 'effectsize: Indices of Effect Size'
@@ -255,7 +255,7 @@ references:
   abstract: 'insight: Easy Access to Model Information for Various Model Objects'
   notes: Imports
   url: https://easystats.github.io/insight/
-  repository: https://easystats.r-universe.dev
+  repository: https://CRAN.R-project.org/package=insight
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -290,7 +290,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9271-5075
   year: '2023'
-  version: '>= 0.19.6'
+  version: '>= 0.19.7'
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
@@ -336,13 +336,13 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2023'
-  version: '>= 0.21.2'
+  version: '>= 0.21.3'
 - type: software
   title: performance
   abstract: 'performance: Assessment of Regression Models Performance'
   notes: Imports
   url: https://easystats.github.io/performance/
-  repository: https://CRAN.R-project.org/package=performance
+  repository: https://easystats.r-universe.dev
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -537,6 +537,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2023'
+  version: '>= 0.13.1'
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -706,7 +707,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2023'
-  version: '>= 3.2.0'
+  version: '>= 3.2.1'
 - type: software
   title: utils
   abstract: 'R: A Language and Environment for Statistical Computing'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,15 +26,15 @@ Depends:
     R (>= 4.1.0)
 Imports:
     afex (>= 1.3-0),
-    BayesFactor (>= 0.9.12-4.5),
+    BayesFactor (>= 0.9.12-4.6),
     correlation (>= 0.8.4),
     datawizard (>= 0.9.0),
-    dplyr (>= 1.1.3),
+    dplyr (>= 1.1.4),
     effectsize (>= 0.8.6),
     glue,
-    insight (>= 0.19.6),
+    insight (>= 0.19.7),
     magrittr,
-    parameters (>= 0.21.2),
+    parameters (>= 0.21.3),
     performance (>= 0.10.8),
     PMCMRplus,
     purrr (>= 1.0.2),
@@ -46,7 +46,7 @@ Imports:
     WRS2,
     zeallot
 Suggests:
-    bayestestR,
+    bayestestR (>= 0.13.1),
     ggplot2,
     knitr,
     metaBMA,
@@ -55,7 +55,7 @@ Suggests:
     rmarkdown,
     rstantools,
     survival,
-    testthat (>= 3.2.0),
+    testthat (>= 3.2.1),
     utils
 VignetteBuilder: 
     knitr
@@ -66,7 +66,7 @@ Roxygen: list(
     markdown = TRUE,
     roclets = c("collate", "namespace", "rd", "pkgapi::api_roclet", "roxyglobals::global_roclet")
   )
-RoxygenNote: 7.2.3.9000
+RoxygenNote: 7.3.0
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/check: anthonynorth/roxyglobals