Setup lintr and fix a few lints (#112)

* Setup `lintr` and fix a few lints * fix merge conflicts * put .lintr in buildignore --------- Co-authored-by: Beniamino Green <[email protected]>
beniaminogreen · Feb 14, 2024 · 090a56d · 090a56d
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commit 090a56d
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Showing 5 changed files with 17 additions and 13 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -20,3 +20,4 @@ src/rust/uncomment.sh
 ^CRAN-SUBMISSION$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.lintr
diff --git a/.lintr b/.lintr
@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+    line_length_linter = NULL,
+    indentation_linter = NULL,
+    commas_linter = NULL,
+    infix_spaces_linter = NULL
+  ) # see vignette("lintr")
+encoding: "UTF-8"
diff --git a/R/em_link.R b/R/em_link.R
@@ -63,7 +63,7 @@
 #' @export
 em_link <- function(X, g, tol = 10^-6, max_iter = 10^3) {
   stopifnot(
-    "There can be no NA's in X (but you can add NA as its own agreement level)" = !any(is.na(X))
+    "There can be no NA's in X (but you can add NA as its own agreement level)" = !anyNA(X)
   )
 
   stopifnot(

diff --git a/R/euclidean_join_core.R b/R/euclidean_join_core.R
@@ -20,7 +20,6 @@ multi_by_validate <- function(a, b, by) {
       by_a <- by
       by_b <- by
     }
-
     stopifnot(by_a %in% names(a))
     stopifnot(by_b %in% names(b))
   }
@@ -37,10 +36,10 @@ euclidean_join_core <- function(a, b, by = NULL, n_bands = 30, band_width = 10,
   by <- multi_by_validate(a, b, by)
   by_a <- by[[1]]
   by_b <- by[[2]]
-  stopifnot("There should be no NA's in by_a[1]" = !any(is.na(dplyr::pull(a, by_a[1]))))
-  stopifnot("There should be no NA's in by_a[2]" = !any(is.na(dplyr::pull(a, by_a[2]))))
-  stopifnot("There should be no NA's in by_b[1]" = !any(is.na(dplyr::pull(b, by_b[1]))))
-  stopifnot("There should be no NA's in by_b[2]" = !any(is.na(dplyr::pull(b, by_b[2]))))
+  stopifnot("There should be no NA's in by_a[1]" = !anyNA(a[[by_a[1]]]))
+  stopifnot("There should be no NA's in by_a[2]" = !anyNA(a[[by_a[2]]]))
+  stopifnot("There should be no NA's in by_b[1]" = !anyNA(b[[by_b[1]]]))
+  stopifnot("There should be no NA's in by_b[2]" = !anyNA(b[[by_b[2]]]))
 
   thresh_prob <- euclidean_probability(threshold, n_bands, band_width, r)
   if (thresh_prob < .95) {

diff --git a/R/jaccard_join_core.R b/R/jaccard_join_core.R
@@ -59,20 +59,17 @@ jaccard_join <- function(a, b, mode, by, salt_by, n_gram_width, n_bands,
       ") have only a ", round(thresh_prob * 100), "% chance of being compared.\n",
       "Please consider changing `n_bands` and `band_width`."
     )
-
     warning(str)
   }
 
-
-
   by <- simple_by_validate(a, b, by)
   by_a <- by[[1]]
   by_b <- by[[2]]
   stopifnot("'by' vectors must have length 1" = length(by_a) == 1)
   stopifnot("'by' vectors must have length 1" = length(by_b) == 1)
 
-  stopifnot("There should be no NA's in by_a" = !any(is.na(dplyr::pull(a, by_a))))
-  stopifnot("There should be no NA's in by_b" = !any(is.na(dplyr::pull(b, by_b))))
+  stopifnot("There should be no NA's in by_a" = !anyNA(a[[by_a]]))
+  stopifnot("There should be no NA's in by_b" = !anyNA(b[[by_b]]))
 
   salt_by_a <- NULL
   salt_by_b <- NULL
@@ -82,9 +79,9 @@ jaccard_join <- function(a, b, mode, by, salt_by, n_gram_width, n_bands,
     salt_by_a <- salt_by[[1]]
     salt_by_b <- salt_by[[2]]
     stopifnot("There should be no NA's in the blocking variables" = !
-    any(is.na(dplyr::select(a, dplyr::all_of(salt_by_a)))))
+    anyNA(a[, salt_by_a, drop = FALSE]))
     stopifnot("There should be no NA's in the blocking variables" = !
-    any(is.na(dplyr::select(b, dplyr::all_of(salt_by_b)))))
+    anyNA(b[, salt_by_b, drop = FALSE]))
   }
 
   # Clean strings that are matched on