add gh actions

.github/workflows/lint.yaml

@@ -0,0 +1,34 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: main
+  pull_request:
+    branches: main
+
+name: lint
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

R/imports-hubValidations.R

@@ -108,8 +108,8 @@ check_tbl_rows_unique <- function(tbl, file_path, hub_path) {
 #' @importFrom purrr imap
 check_tbl_value_col <- function(tbl, round_id, file_path, hub_path) {
   config_tasks <- read_config(hub_path, "tasks")
-  tbl <- dplyr::mutate(tbl, dplyr::across(-dplyr::contains("value"),
-                                          as.character))
+  tbl <- dplyr::mutate(tbl,
+                       dplyr::across(-dplyr::contains("value"), as.character))
   details <- split(tbl, f = tbl$output_type) |>
     purrr::imap(
       \(.x, .y) {

R/validate_submission.R

@@ -47,6 +47,7 @@ run_all_validation <- function(df, path, js_def0, js_def, round_id, hub_path,
     all <- merge_sample_id(df, req_colnames, merge_sample_col,  js_def0, js_def,
                            checks, partition = partition, verbose = TRUE,
                            verbose_col = verbose_col)
+    gc()
     df <- all$df
     pair <- all$msg
     if (!is.null(pair) && verbose)
@@ -82,8 +83,10 @@ run_all_validation <- function(df, path, js_def0, js_def, round_id, hub_path,
                                                                       "tasks"),
                                            output_type_id_datatype =
                                            "from_config")
+  gc()
   tbl_chr <- dplyr::mutate_all(df, as.character)
 
+  gc()
   checks$valid_vals <-
     try_check(check_tbl_values(tbl_chr, round_id = round_id,
                                file_path = file_path, hub_path = hub_path),
@@ -92,26 +95,31 @@ run_all_validation <- function(df, path, js_def0, js_def, round_id, hub_path,
     return(checks)
   }
 
+  gc()
   checks$rows_unique <-
     try_check(check_tbl_rows_unique(tbl_chr, file_path = file_path,
                                     hub_path = hub_path), path)
 
+  gc()
   checks$req_vals <-
     try_check(check_df_values_required(df, js_def, file_path = file_path), path)
   # -- slow
+  gc()
   checks$value_col_valid <-
     try_check(check_tbl_value_col(df, round_id = round_id,
                                   file_path = file_path, hub_path = hub_path),
               path)
-
+  gc()
   checks$value_col_non_desc <-
     try_check(check_tbl_value_col_ascending(tbl_chr, file_path = file_path,
                                             hub_path = hub_path,
                                             round_id = round_id,
                                             derived_task_ids = NULL), path)
   # -- slow
+  gc()
   checks <- sample_test(checks, tbl_chr, round_id, file_path, hub_path,
                         path, pair, js_def)
+  gc()
   checks <- value_test(df, checks, file_path, n_decimal = n_decimal, pop = pop,
                        obs = obs)
 

tests/testthat/test_submission.R

@@ -1,8 +1,18 @@
 test_that("Test validation process", {
 
-  obs <- "../exp/target-data/time-series.csv"
-  hub_path <- "../exp/"
-  pop_path <- "../exp/auxiliary-data/location_census/locations.csv"
+  hub_path0 <- tempdir()
+  hub_path <- paste0(hub_path0, "/exp/")
+  all_dir <- c(hub_path,
+               grep("\\.", paste0(hub_path, dir("../exp", recursive = TRUE,
+                                                include.dirs = TRUE)),
+                    value = TRUE, invert = TRUE))
+  purrr::map(all_dir, dir.create, showWarnings = FALSE)
+  file.copy(dir("../exp", full.names = TRUE, recursive = TRUE),
+            gsub("^../exp", hub_path, dir("../exp", full.names = TRUE,
+                                          recursive = TRUE)))
+
+  obs <- paste0(hub_path, "target-data/time-series.csv")
+  pop_path <- paste0(hub_path, "auxiliary-data/location_census/locations.csv")
   merge_sample_col <- c("run_grouping", "stochastic_run")
   partition <- round_id <- r_schema <- NULL
   n_decimal <- 1
@@ -463,4 +473,7 @@ test_that("Test validation process", {
                          merge_sample_col = merge_sample_col))
   expect_contains(attr(check$result$spl_compound_tid, "class"),
                   c("error", "check_error"))
+
+  unlink(hub_path0, recursive = TRUE)
+
 })