Merge pull request #438 from mrc-ide/optional-duckdb

Make duckdb an optional dependency

.github/workflows/pkgdown.yaml

@@ -27,7 +27,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mrc-ide.r-universe.dev/bin/linux/jammy/4.3
+          extra-repositories: https://mrc-ide.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

DESCRIPTION

@@ -26,7 +26,6 @@ Imports:
     brio,
     data.tree,
     dplyr (>= 1.1.0),
-    duckdb (>= 0.10.0),
     eppasm (>= 0.7.1),
     gt,
     first90 (>= 1.6.1),
@@ -60,6 +59,7 @@ Suggests:
     DiagrammeR,
     covr,
     datamodelr,
+    duckdb (>= 0.10.0),
     here,
     knitr,
     lubridate,

NEWS.md

@@ -1,3 +1,7 @@
+# naomi 2.9.28
+
+* Make duckdb an optional dependency
+
 # naomi 2.9.27
 
 * Show calibration plot ratio values to nearest 0.1. 

R/outputs.R

@@ -1355,6 +1355,7 @@ read_hintr_output <- function(path) {
 }
 
 read_duckdb <- function(path) {
+  assert_package_installed("duckdb")
   con <- DBI::dbConnect(duckdb::duckdb(dbdir = path, read_only = TRUE))
   on.exit(DBI::dbDisconnect(con, shutdown = TRUE))
   DBI::dbGetQuery(con, sprintf("SELECT * from %s", DUCKDB_OUTPUT_TABLE_NAME))

R/run-model.R

@@ -157,6 +157,7 @@ hintr_save <- function(obj, file) {
       stop(paste("Trying to save invalid object as duckdb database.",
               "Only data frames can be saved as database."))
     }
+    assert_package_installed("duckdb")
     con <- DBI::dbConnect(duckdb::duckdb(dbdir = file))
     on.exit(DBI::dbDisconnect(con, shutdown = TRUE))
     DBI::dbWriteTable(con, DUCKDB_OUTPUT_TABLE_NAME, obj)

R/utils.R

@@ -100,3 +100,15 @@ vlapply <- function(X, FUN, ...) {
 is_empty <- function(x) {
   length(x) == 0 || is.null(x) || is.na(x) || !nzchar(x)
 }
+
+
+assert_package_installed <- function(package_name) {
+  if (!requireNamespace(package_name, quietly = TRUE)) {
+    stop(
+      sprintf("Package '%s' must be installed to use this function.",
+              package_name),
+      call. = FALSE
+    )
+  }
+  invisible(TRUE)
+}

tests/testthat/test-01-run-model.R

@@ -689,6 +689,7 @@ test_that("trying to calibrate incompatible model output returns error", {
 })
 
 test_that("calibration plot data can be saved as duckdb database", {
+  testthat::skip_if_not_installed("duckdb")
 
   ## Calibration makes no modification of existing files.
   output_hash <- tools::md5sum(a_hintr_output$model_output_path)

tests/testthat/test-hintr-plot-data.R

@@ -54,6 +54,8 @@ test_that("there is metadata for every indicator in comparison data", {
 })
 
 test_that("hintr data can be saved and read as qs or duckdb type", {
+  testthat::skip_if_not_installed("duckdb")
+
   t_qs <- tempfile(fileext = ".qs")
   t_db <- tempfile(fileext = ".duckdb")
   t_rds <- tempfile(fileext = ".rds")

tests/testthat/test-utils.R

@@ -26,3 +26,12 @@ test_that("is_empty", {
   expect_true(is_empty(c()))
   expect_false(is_empty(c("things")))
 })
+
+test_that("can assert optional package is installed", {
+  expect_true(assert_package_installed("testthat"))
+
+  expect_error(
+    assert_package_installed("my.fake.pkg"),
+    "Package 'my.fake.pkg' must be installed to use this function.",
+    fixed = TRUE)
+})