Merge pull request #74 from Infectious-Disease-Modeling-Hubs/split-hu…

…butils Split hubutils - Release v0.0.1
hubverse-org · Mar 6, 2024 · e6aaba6 · e6aaba6
2 parents 2eb6b10 + 7f6dc2a
commit e6aaba6
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -41,7 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::tzdb
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hubValidations
 Title: Testing framework for hubverse hub validations
-Version: 0.0.0.9008
+Version: 0.0.1
 Authors@R: c(
     person(
         given = "Anna", 
@@ -37,7 +37,9 @@ Imports:
     dplyr,
     fs,
     gh,
-    hubUtils (>= 0.0.0.9016),
+    hubAdmin,
+    hubData,
+    hubUtils (>= 0.0.1),
     jsonlite,
     jsonvalidate,
     lubridate,
@@ -58,13 +60,15 @@ Suggests:
     testthis,
     withr
 Remotes:
-    Infectious-Disease-Modeling-Hubs/hubUtils,
+    Infectious-Disease-Modeling-Hubs/hubUtils#143,
+    Infectious-Disease-Modeling-Hubs/hubData#1,
+    Infectious-Disease-Modeling-Hubs/hubAdmin#1,
     assignUser/octolog
 Config/testthat/edition: 3
-Config/Needs/website:pkgdown, Infectious-Disease-Modeling-Hubs/hubStyle
+Config/Needs/website: pkgdown, Infectious-Disease-Modeling-Hubs/hubStyle
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations,
     https://infectious-disease-modeling-hubs.github.io/hubValidations/
 BugReports: https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations/issues

diff --git a/R/check_config_hub_valid.R b/R/check_config_hub_valid.R
@@ -6,7 +6,7 @@
 #'
 #' @export
 check_config_hub_valid <- function(hub_path) {
-  valid_config <- hubUtils::validate_hub_config(hub_path) %>%
+  valid_config <- hubAdmin::validate_hub_config(hub_path) %>%
     suppressMessages() %>%
     suppressWarnings()
 

diff --git a/R/check_metadata_file_exists.R b/R/check_metadata_file_exists.R
@@ -2,7 +2,7 @@
 #'
 #' @param file_path character string. Path to the file being validated relative to
 #' the hub's model-metadata directory.
-#' @inheritParams hubUtils::connect_hub
+#' @inheritParams hubData::connect_hub
 #'
 #' @inherit check_valid_round_id return
 #'

diff --git a/R/check_tbl_col_types.R b/R/check_tbl_col_types.R
@@ -13,7 +13,7 @@
 check_tbl_col_types <- function(tbl, file_path, hub_path) {
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
 
-  schema <- hubUtils::create_hub_schema(config_tasks,
+  schema <- hubData::create_hub_schema(config_tasks,
     partitions = NULL,
     r_schema = TRUE
   )[names(tbl)]

diff --git a/R/check_tbl_colnames.R b/R/check_tbl_colnames.R
@@ -7,7 +7,7 @@
 #' @param round_id character string. The round identifier.
 #' @param file_path character string. Path to the file being validated relative to
 #' the hub's model-output directory.
-#' @inheritParams hubUtils::connect_hub
+#' @inheritParams hubData::connect_hub
 #' @return
 #' Depending on whether validation has succeeded, one of:
 #' - `<message/check_success>` condition class object.

diff --git a/R/check_tbl_value_col.R b/R/check_tbl_value_col.R
@@ -9,11 +9,11 @@
 check_tbl_value_col <- function(tbl, round_id, file_path, hub_path) {
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
 
-  tbl[, names(tbl) != "value"] <- hubUtils::coerce_to_character(
+  tbl[, names(tbl) != "value"] <- hubData::coerce_to_character(
     tbl[, names(tbl) != "value"]
   )
 
-  full <- hubUtils::expand_model_out_val_grid(
+  full <- hubData::expand_model_out_val_grid(
     config_tasks,
     round_id = round_id,
     required_vals_only = FALSE,

diff --git a/R/check_tbl_values.R b/R/check_tbl_values.R
@@ -11,7 +11,7 @@ check_tbl_values <- function(tbl, round_id, file_path, hub_path) {
   # working with larger files but currently arrow does not match NAs as dplyr
   # does, returning false positives for mean & median rows which contain NA in
   # output type ID column.
-  accepted_vals <- hubUtils::expand_model_out_val_grid(
+  accepted_vals <- hubData::expand_model_out_val_grid(
     config_tasks = config_tasks,
     round_id = round_id,
     all_character = TRUE

diff --git a/R/check_tbl_values_required.R b/R/check_tbl_values_required.R
@@ -8,15 +8,15 @@
 check_tbl_values_required <- function(tbl, round_id, file_path, hub_path) {
   tbl[["value"]] <- NULL
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
-  req <- hubUtils::expand_model_out_val_grid(
+  req <- hubData::expand_model_out_val_grid(
     config_tasks,
     round_id = round_id,
     required_vals_only = TRUE,
     all_character = TRUE,
     bind_model_tasks = FALSE
   )
 
-  full <- hubUtils::expand_model_out_val_grid(
+  full <- hubData::expand_model_out_val_grid(
     config_tasks,
     round_id = round_id,
     required_vals_only = FALSE,
@@ -41,7 +41,7 @@ check_tbl_values_required <- function(tbl, round_id, file_path, hub_path) {
   if (check) {
     details <- NULL
   } else {
-    missing_df <- hubUtils::coerce_to_hub_schema(missing_df, config_tasks)
+    missing_df <- hubData::coerce_to_hub_schema(missing_df, config_tasks)
     details <- cli::format_inline("See {.var missing} attribute for details.")
   }
 

diff --git a/R/hub_validations_methods.R b/R/hub_validations_methods.R
@@ -73,11 +73,6 @@ validate_internal_class <- function(x, class = c(
   invisible(TRUE)
 }
 
-summary.hub_validations <- function(x, ...) {
-  # TODO
-  NULL
-}
-
 # TODO: Code to consider implementing more hierarchical printing of messages.
 # Currently not implemented as pr_hub_validations class not implemented.
 #' Print results of `validate_pr()` function as a bullet list

diff --git a/R/opt_check_metadata_team_max_model_n.R b/R/opt_check_metadata_team_max_model_n.R
@@ -14,7 +14,7 @@ opt_check_metadata_team_max_model_n <- function(file_path, hub_path, n_max = 2L)
     file_path,
     file_type = "model_metadata"
   )$team_abbr
-  all_model_meta <- hubUtils::load_model_metadata(hub_path)
+  all_model_meta <- hubData::load_model_metadata(hub_path)
 
   team_models <- all_model_meta[["model_abbr"]][all_model_meta[["team_abbr"]] == team_abbr]
   n_models <- length(team_models)

diff --git a/R/opt_check_tbl_col_timediff.R b/R/opt_check_tbl_col_timediff.R
@@ -19,7 +19,7 @@ opt_check_tbl_col_timediff <- function(tbl, file_path, hub_path,
   checkmate::assert_choice(t1_colname, choices = names(tbl))
 
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
-  schema <- hubUtils::create_hub_schema(config_tasks,
+  schema <- hubData::create_hub_schema(config_tasks,
     partitions = NULL,
     r_schema = TRUE
   )

diff --git a/R/opt_check_tbl_horizon_timediff.R b/R/opt_check_tbl_horizon_timediff.R
@@ -25,7 +25,7 @@ opt_check_tbl_horizon_timediff <- function(tbl, file_path, hub_path, t0_colname,
   checkmate::assert_choice(horizon_colname, choices = names(tbl))
 
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
-  schema <- hubUtils::create_hub_schema(config_tasks,
+  schema <- hubData::create_hub_schema(config_tasks,
     partitions = NULL,
     r_schema = TRUE
   )

diff --git a/R/read_model_out_file.R b/R/read_model_out_file.R
@@ -42,25 +42,25 @@ read_model_out_file <- function(file_path, hub_path = ".",
     parquet = {
       if (coerce_types == "hub") {
         arrow::read_parquet(full_path) %>%
-          hubUtils::coerce_to_hub_schema(
+          hubData::coerce_to_hub_schema(
             config_tasks = hubUtils::read_config(hub_path, "tasks")
           )
       } else if (coerce_types == "chr") {
         arrow::read_parquet(full_path) %>%
-          hubUtils::coerce_to_character()
+          hubData::coerce_to_character()
       } else {
         arrow::read_parquet(full_path)
       }
     },
     arrow = {
       if (coerce_types == "hub") {
         arrow::read_feather(full_path) %>%
-          hubUtils::coerce_to_hub_schema(
+          hubData::coerce_to_hub_schema(
             config_tasks = hubUtils::read_config(hub_path, "tasks")
           )
       } else if (coerce_types == "chr") {
         arrow::read_feather(full_path) %>%
-          hubUtils::coerce_to_character()
+          hubData::coerce_to_character()
       } else {
         arrow::read_feather(full_path)
       }
@@ -72,7 +72,7 @@ read_model_out_file <- function(file_path, hub_path = ".",
 create_model_out_schema <- function(hub_path,
                                     col_types = c("hub", "chr")) {
   col_types <- rlang::arg_match(col_types)
-  schema <- hubUtils::create_hub_schema(
+  schema <- hubData::create_hub_schema(
     config_tasks = hubUtils::read_config(hub_path, "tasks"),
     partitions = NULL
   )

diff --git a/man/check_config_hub_valid.Rd b/man/check_config_hub_valid.Rd
diff --git a/man/check_file_exists.Rd b/man/check_file_exists.Rd
diff --git a/man/check_file_format.Rd b/man/check_file_format.Rd
diff --git a/man/check_file_read.Rd b/man/check_file_read.Rd
diff --git a/man/check_metadata_file_exists.Rd b/man/check_metadata_file_exists.Rd
diff --git a/man/check_metadata_file_name.Rd b/man/check_metadata_file_name.Rd
diff --git a/man/check_metadata_matches_schema.Rd b/man/check_metadata_matches_schema.Rd
diff --git a/man/check_metadata_schema_exists.Rd b/man/check_metadata_schema_exists.Rd
diff --git a/man/check_submission_metadata_file_exists.Rd b/man/check_submission_metadata_file_exists.Rd
diff --git a/man/check_submission_time.Rd b/man/check_submission_time.Rd
diff --git a/man/check_tbl_col_types.Rd b/man/check_tbl_col_types.Rd
diff --git a/man/check_tbl_colnames.Rd b/man/check_tbl_colnames.Rd
diff --git a/man/check_tbl_match_round_id.Rd b/man/check_tbl_match_round_id.Rd
diff --git a/man/check_tbl_rows_unique.Rd b/man/check_tbl_rows_unique.Rd
diff --git a/man/check_tbl_unique_round_id.Rd b/man/check_tbl_unique_round_id.Rd
diff --git a/man/check_tbl_value_col.Rd b/man/check_tbl_value_col.Rd