refactor: remove deprecated functions

R/add_physicochemical_properties_to_HMMER_tbl.R

@@ -83,15 +83,16 @@ add_physicochemical_properties_to_HMMER_tbl <- function(data, colname = "hits.fu
     data %>%
         dplyr::group_by(!!group_var) %>%
         dplyr::group_split() %>%
-        purrr::map_dfr(function(x) {
+        purrr::map(\(x) {
             x %>% dplyr::bind_cols(inner_function(x[[colname]][[1]]))
-        })
+        }) %>%
+        dplyr::bind_rows()
 }
 
 calculate_peptides <- function(y) { # nolint
     Peptides::aaComp(y) %>%
-        purrr::map_dfr(~ {
-            as.data.frame(.x) %>%
+        purrr::map(\(x) {
+            as.data.frame(x) %>%
                 tibble::rownames_to_column("properties") %>%
                 dplyr::rename("Percentage" = "Mole%") %>%
                 dplyr::select(c("Percentage", "properties")) %>%
@@ -100,7 +101,8 @@ calculate_peptides <- function(y) { # nolint
                     values_from = c("Percentage")
                 ) %>%
                 dplyr::mutate(
-                    dplyr::across(where(is.numeric), ~ .x / 100)
+                    dplyr::across(tidyselect::where(is.numeric), ~ .x / 100)
                 )
-        })
+        }) %>%
+        dplyr::bind_rows()
 }

R/add_sequences_to_hmmer_tbl.R

@@ -27,14 +27,11 @@ add_sequences_to_hmmer_tbl <- function(data, extension = "fullfasta", max_times
         }
     )
     group_var <- rlang::sym("uuid")
-    data %>%
+    data <- data %>%
         dplyr::group_by(!!group_var) %>%
         dplyr::group_split() %>%
-        purrr::map_dfr(inner_function) %>%
-        delete_na_rows()
-}
-
-delete_na_rows <- function(data) {
+        purrr::map(inner_function) %>%
+        purrr::bind_rows()
     data[rowSums(is.na(data)) <= nrow(data), ]
 }
 

R/add_taxa_to_hmmer_tbl.R

@@ -32,5 +32,6 @@ add_taxa_to_hmmer_tbl <- function(data, mode = "remote", rank_vc = NULL) { # nol
     data %>%
         dplyr::group_by(!!group_var) %>%
         dplyr::group_split() %>%
-        purrr::map_dfr(~ purrr::possibly(inner_function, .)(.))
+        purrr::map(~ purrr::possibly(inner_function, .)(.)) %>%
+        purrr::bind_rows()
 }

R/read_hmmer_from_json.R

@@ -23,5 +23,6 @@ read_hmmer_from_json <- function(file) { # nolint
                 parse_results_into_tbl()
         }
     )
-    purrr::map_dfr(.x = file, .id = "file", .f = inner_function)
+    purrr::map(.x = file, .id = "file", .f = inner_function) %>%
+        dplyr::bind_rows()
 }

R/search_hmmsearch.R

@@ -32,10 +32,9 @@ search_hmmsearch <- function(aln, seqdb = "swissprot", timeout = 180, verbose =
     hmmsearch <- purrr::possibly(search_in_hmmer, otherwise = NULL) # nolint
     # all combinations of inputs
     seq <- ifelse(is.list(aln), aln, list(aln)) %>%
-        purrr::map_chr(function(x) {
-            Biostrings::unmasked(x) %>%
-                format_AAStringSet_into_hmmer_string()
-        })
+        purrr::map(\(x) Biostrings::unmasked(x) %>%
+            format_AAStringSet_into_hmmer_string()) %>%
+        as.character()
     tidyr::expand_grid(seq, seqdb, algorithm = "hmmsearch") %>%
         dplyr::rowwise() %>%
         purrr::pmap(

R/utils.R

@@ -7,14 +7,14 @@ download_file <- function(url) { # nolint
     return(temp)
 }
 
-check_if_url <- function(urls) {
-    purrr::map_lgl(
+check_if_url <- function(urls) { # nolint
+    purrr::map(
         urls,
         purrr::possibly(
             Negate(httr::http_error),
             otherwise = FALSE
         )
-    )
+    ) %>% as.logical()
 }
 
 convert_input_seq <- function(seq) {

tests/testthat/test-pairwise_aligment.R

@@ -1,12 +1,13 @@
-testthat::test_that("Test that pairwise_alignment_sequence_identity works with missing values", {
-  phmmer_2abl$hits.fullfasta %>%
-    pairwise_alignment_sequence_identity() %>%
-    expect_snapshot_value(style = "deparse")
-})
+"Test that pairwise_alignment_sequence_identity works with missing values" %>%
+  testthat::test_that({
+    phmmer_2abl$hits.fullfasta %>%
+      pairwise_alignment_sequence_identity() %>%
+      expect_snapshot_value(style = "deparse")
+  })
 
 testthat::test_that("Test that pairwise plots work", {
-  phmmer_2abl$hits.fullfasta %>%
-    pairwise_alignment_sequence_identity() -> data
+  data <- phmmer_2abl$hits.fullfasta %>%
+    pairwise_alignment_sequence_identity()
   hist_plot <- pairwise_sequence_identity_histogram(data)
   vdiffr::expect_doppelganger("Base graphics histogram", hist_plot)
   heatmap_plot <- pairwise_sequence_identity_heatmap(data)