DAT-1820: update files to reflect dependency version changes and remove deprecated imports

.github/workflows/lint.yaml

@@ -24,7 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: lintr@3.2.0, any::pkgload, local::.
+          extra-packages: any::lintr, any::pkgload, local::.
           needs: lint
 
       - name: Lint

DESCRIPTION

@@ -18,32 +18,29 @@ License: MIT + file LICENSE
 URL: https://databrary.github.io/databraryr/,
     https://github.com/databrary/databraryr
 BugReports: https://github.com/databrary/databraryr/issues
+Depends:
+    R (>= 4.3.0)
 Imports:
     assertthat (>= 0.2.1),
     dplyr (>= 1.1.4),
-    getPass (>= 0.2.4),
-    httr2 (>= 1.0.0),
-    keyring (>= 1.3.2),
+    getPass (>= 0.2-4),
+    httr2 (>= 1.2.1),
+    keyring (>= 1.4.1),
     lifecycle (>= 1.0.4),
-    magrittr,
-    methods (>= 4.3.2),
-    options (>= 0.2.0),
-    purrr (>= 1.0.2),
-    stringr (>= 1.5.1),
+    magrittr (>= 2.0.0),
+    openssl (>= 2.0.0),
+    options (>= 0.3.1),
+    purrr (>= 1.1.0),
+    stringr (>= 1.5.2),
     stats,
-    tibble (>= 3.2.1)
+    tibble (>= 3.3.0)
 Suggests:
-    av (>= 0.9.0),
-    covr (>= 3.6.0),
-    ggplot2,
-    knitr,
-    lintr (>= 3.0.0),
-    openssl,
-    readr,
-    rmarkdown (>= 2.26),
-    testthat (>= 3.0.0),
-    withr (>= 2.5.0),
-    xml2 (>= 1.3.0)
+    covr (>= 3.6.5),
+    knitr (>= 1.45),
+    lintr (>= 3.3.0),
+    rmarkdown (>= 2.31),
+    testthat (>= 3.2.3),
+    withr (>= 3.0.2)
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -113,6 +113,5 @@ export(update_session_file)
 export(update_volume_record)
 export(upload_file)
 export(whoami)
-importFrom(lifecycle,deprecated)
+importFrom(lifecycle,badge)
 importFrom(magrittr,"%>%")
-importFrom(methods,is)

R/databraryr-package.R

@@ -2,7 +2,6 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom lifecycle deprecated
-#' @importFrom methods is
+#' @importFrom lifecycle badge
 ## usethis namespace: end
 NULL

R/get_institution_avatar.R

@@ -78,9 +78,9 @@ get_institution_avatar <- function(institution_id = 1,
   }
 
   # Build the request with the avatar URL
-  req <- req %>%
-    httr2::req_url(full_url) %>%
-    httr2::req_method("GET") %>%
+  req <- req |>
+    httr2::req_url(full_url) |>
+    httr2::req_method("GET") |>
     httr2::req_error(
       is_error = function(resp) {
         FALSE

R/get_institution_by_id.R

@@ -45,6 +45,6 @@ get_institution_by_id <- function(institution_id = 12,
     latitude = institution$latitude,
     longitude = institution$longitude,
     manual_coordinates = institution$manual_coordinates
-  ) %>%
+  ) |>
     as.list()
 }

R/get_user_by_id.R

@@ -47,6 +47,6 @@ get_user_by_id <- function(user_id = 6,
     affiliation_id = institution_id,
     is_authorized_investigator = user$is_authorized_investigator,
     has_avatar = user$has_avatar
-  ) %>%
+  ) |>
     as.list()
 }

R/list_asset_formats.R

@@ -32,8 +32,8 @@ list_asset_formats <- function(vb = options::opt("vb")) {
   transcodable <- NULL
 
   if (!is.null(db_constants$format)) {
-    purrr::map(db_constants$format, as.data.frame) %>%
-      purrr::list_rbind() %>%
+    purrr::map(db_constants$format, as.data.frame) |>
+      purrr::list_rbind() |>
       dplyr::rename(format_id = id,
                     format_mimetype = mimetype,
                     format_extension = extension,
@@ -42,6 +42,6 @@ list_asset_formats <- function(vb = options::opt("vb")) {
   } else {
     if (vb)
       message("No format information retrieved.")
-    return(NULL)
+    NULL
   }
 }

R/list_folder_assets.R

@@ -96,7 +96,7 @@ list_folder_assets <- function(folder_id = 9807,
     )
   })
 
-  file_rows %>%
+  file_rows |>
     dplyr::mutate(
       folder_id = folder_id,
       vol_id = vol_id,

R/list_session_assets.R

@@ -99,7 +99,7 @@ list_session_assets <- function(session_id = 9807,
     )
   })
 
-  asset_rows %>%
+  asset_rows |>
     dplyr::mutate(
       session_id = session_id,
       vol_id = vol_id,

R/list_user_volumes.R

@@ -48,11 +48,11 @@ list_user_volumes <- function(user_id = 6,
       vol_access_level = entry$access_level,
       vol_sharing_level = entry$sharing_level
     )
-  }, .progress = TRUE) %>%
-    purrr::list_rbind() %>%
+  }, .progress = TRUE) |>
+    purrr::list_rbind() |>
     dplyr::mutate(user_id = user_df$id,
                   user_prename = user_df$prename,
                   user_sortname = user_df$sortname,
-                  user_affiliation = user_df$affiliation) %>%
+                  user_affiliation = user_df$affiliation) |>
     dplyr::arrange(vol_id)
 }

R/list_volume_assets.R

@@ -79,9 +79,9 @@ list_volume_assets <- function(vol_id = 1,
         session_date = session$source_date,
         session_release = session$release_level
       )
-    }, .progress = TRUE) %>%
+    }, .progress = TRUE) |>
       purrr::list_rbind()
-  }) %>%
+  }) |>
     purrr::list_rbind()
 
   if (is.null(files) || nrow(files) == 0) {

R/list_volume_funding.R

@@ -68,7 +68,7 @@ list_volume_funding <- function(vol_id = 1,
       rows <- dplyr::mutate(rows, vol_id = id)
     }
     rows
-  }) %>%
+  }) |>
     purrr::list_rbind()
 
   if (is.null(out) || nrow(out) == 0L) {

R/list_volume_info.R

@@ -39,7 +39,7 @@ list_volume_info <-
 
     volume <- databraryr::get_volume_by_id(vol_id = vol_id, vb = vb, rq = rq)
     if (is.null(volume)) {
-      return(NULL)
+      NULL
     } else {
       if (vb) message("Summarising volume detail...")
 

R/list_volume_session_assets.R

@@ -102,7 +102,7 @@ list_volume_session_assets <-
         session_name = session$name,
         session_release = session$release_level
       )
-    }) %>%
+    }) |>
       purrr::list_rbind()
 
     asset_rows

R/list_volume_sessions.R

@@ -82,7 +82,7 @@ list_volume_sessions <-
         vb = vb
       )
 
-      df <- df %>%
+      df <- df |>
         dplyr::mutate(
           vol_id = volume$id,
           vol_name = volume$title,

R/make_login_client.R

@@ -123,8 +123,8 @@ make_login_client <- function(email = NULL,
   if (is.null(rq))
     rq <- make_default_request()
 
-  rq <- rq %>%
-    httr2::req_url(LOGIN) %>%
+  rq <- rq |>
+    httr2::req_url(LOGIN) |>
     httr2::req_body_json(list(email = email, password = password))
 
   resp <- tryCatch(