Merge branch 'main' into more_uniform_data_extraction

IndrajeetPatil · Sep 22, 2023 · 560fc51 · 560fc51
2 parents 109aeb2 + de77bdc
commit 560fc51
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Showing 63 changed files with 517 additions and 611 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,6 +7,7 @@
 ^CRAN-RELEASE$
 ^CRAN-SUBMISSION$
 ^LICENSE\.md$
+^Makefile$
 ^Meta$
 ^NEWS$
 ^README-.*\.png$
@@ -48,4 +49,5 @@
 hextools
 publication/*
 references.bib
+shell
 tests\^spelling
diff --git a/.github/workflows/R-CMD-check-devel.yaml b/.github/workflows/R-CMD-check-devel.yaml
@@ -16,11 +16,11 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/R-CMD-check-hard.yaml b/.github/workflows/R-CMD-check-hard.yaml
@@ -23,11 +23,11 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - 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
@@ -34,11 +34,11 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -35,11 +35,11 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-all-examples.yaml b/.github/workflows/check-all-examples.yaml
@@ -26,7 +26,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-link-rot.yaml b/.github/workflows/check-link-rot.yaml
@@ -17,11 +17,11 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-random-test-order.yaml b/.github/workflows/check-random-test-order.yaml
@@ -14,7 +14,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-readme.yaml b/.github/workflows/check-readme.yaml
@@ -26,11 +26,11 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-spelling.yaml b/.github/workflows/check-spelling.yaml
@@ -13,11 +13,11 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-styling.yaml b/.github/workflows/check-styling.yaml
@@ -15,7 +15,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/check-test-warnings.yaml b/.github/workflows/check-test-warnings.yaml
@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/check-vignette-warnings.yaml b/.github/workflows/check-vignette-warnings.yaml
@@ -18,11 +18,11 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/html-5-check.yaml b/.github/workflows/html-5-check.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
@@ -12,7 +12,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -26,21 +26,41 @@ jobs:
             any::purrr
           needs: check
 
-      - name: Add lintr options
-        run: |
-          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
-        shell: Rscript {0}
-
       - name: Install package
         run: R CMD INSTALL .
 
       - name: Extract and lint files changed by this PR
         run: |
+          options(crayon.enabled = TRUE)
+          library(lintr)
           files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
           changed_files <- purrr::map_chr(files, "filename")
           all_files <- list.files(recursive = TRUE)
           exclusions_list <- as.list(setdiff(all_files, changed_files))
-          lintr::lint_package(exclusions = exclusions_list)
+          lint_package(linters = linters_with_defaults(
+            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,
+            line_length_linter(120L),
+            namespace_linter = NULL,
+            nonportable_path_linter = NULL,
+            object_name_linter = NULL,
+            object_length_linter(50L),
+            object_usage_linter = NULL,
+            string_boundary_linter = NULL,
+            strings_as_factors_linter = NULL,
+            todo_comment_linter = NULL,
+            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)
+          ), exclusions = exclusions_list)
         shell: Rscript {0}
         env:
           LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -18,7 +18,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -32,27 +32,36 @@ jobs:
             local::.
           needs: lint
 
+      # TODO: Revisit to remove some of these allowances after more important lints
+      # have been removed.
       - name: Lint
         run: |
+          options(crayon.enabled = TRUE)
           library(lintr)
           lint_package(linters = linters_with_defaults(
             absolute_path_linter = NULL,
+            assignment_linter = NULL,
             commented_code_linter = NULL,
-            cyclocomp_linter(20L),
+            cyclocomp_linter(25L),
             extraction_operator_linter = NULL,
+            if_not_else_linter(exceptions = character(0L)),
             implicit_integer_linter = NULL,
+            library_call_linter = NULL,
             line_length_linter(120L),
+            namespace_linter = NULL,
+            nonportable_path_linter = NULL,
             object_name_linter = NULL,
             object_length_linter(50L),
             object_usage_linter = NULL,
-            nonportable_path_linter = NULL,
             string_boundary_linter = NULL,
             strings_as_factors_linter = NULL,
             todo_comment_linter = NULL,
             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)
           ))
         shell: Rscript {0}
-        # env:
-        #   LINTR_ERROR_ON_LINT: true
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/pkgdown-no-suggests.yaml b/.github/workflows/pkgdown-no-suggests.yaml
@@ -21,11 +21,11 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -20,11 +20,11 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: "3.1.5"
+          pandoc-version: "3.1.7"
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
@@ -19,7 +19,7 @@ jobs:
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/styler.yaml b/.github/workflows/styler.yaml
@@ -13,7 +13,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -30,6 +30,7 @@ jobs:
             r-lib/pkgapi
             r-lib/styler
             r-lib/roxygen2
+            anthonynorth/roxyglobals
           needs: |
             styler
             roxygen2

diff --git a/.github/workflows/test-coverage-examples.yaml b/.github/workflows/test-coverage-examples.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.lintr b/.lintr
@@ -1,18 +1,24 @@
 linters: linters_with_defaults(
     absolute_path_linter = NULL,
+    assignment_linter = NULL,
     commented_code_linter = NULL,
-    cyclocomp_linter = cyclocomp_linter(20),
+    cyclocomp_linter(25L),
     extraction_operator_linter = NULL,
+    if_not_else_linter(exceptions = character(0L)),
     implicit_integer_linter = NULL,
-    line_length_linter(120),
+    library_call_linter = NULL,
+    line_length_linter(120L),
+    namespace_linter = NULL,
+    nonportable_path_linter = NULL,
     object_name_linter = NULL,
-    object_length_linter(50),
+    object_length_linter(50L),
     object_usage_linter = NULL,
-    nonportable_path_linter = NULL,
+    todo_comment_linter = NULL,
     string_boundary_linter = NULL,
     strings_as_factors_linter = NULL,
-    todo_comment_linter = NULL,
     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)
   )