Prevent reticulate error when between = is given as a named list

bodkan · Apr 7, 2023 · 7965e4f · 7965e4f
1 parent f234fbf
commit 7965e4f
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Showing 2 changed files with 14 additions and 5 deletions.
diff --git a/R/tree-sequences.R b/R/tree-sequences.R
@@ -1619,7 +1619,7 @@ ts_ibd <- function(ts, coordinates = FALSE, within = NULL, between = NULL,
   if (!is.null(within))
     within <- unlist(purrr::map(within, ~ get_node_ids(ts, .x)))
   else if (!is.null(between)) {
-    between <- purrr::map(between, ~ get_node_ids(ts, .x))
+    between <- unname(purrr::map(between, ~ get_node_ids(ts, .x)))
     # another bug in reticulate? if the list has names, Python gives us:
     #   Error in py_call_impl(callable, dots$args, dots$keywords):
     #     TypeError: '<' not supported between instances of 'numpy.ndarray' and 'int'

diff --git a/tests/testthat/test-ibd.R b/tests/testthat/test-ibd.R
@@ -43,10 +43,19 @@ test_that("`within =` argument of ts_ibd() does what it is supposed to", {
 })
 
 test_that("`between =` argument of ts_ibd() does what it is supposed to", {
-  ibd_totals <- ts_ibd(ts, coordinates = FALSE, minimum_length = 100000,
-                       between = list(pop1_samples, pop2_samples))
-  expect_true("POP1" == unique(unlist(ibd_totals$pop1)))
-  expect_true("POP2" == unique(unlist(ibd_totals$pop2)))
+  # individual names in a named list
+  ibd_totals1 <- ts_ibd(ts, coordinates = FALSE, minimum_length = 100000,
+                        between = list(x = pop1_samples, y = pop2_samples))
+  expect_true("POP1" == unique(unlist(ibd_totals1$pop1)))
+  expect_true("POP2" == unique(unlist(ibd_totals1$pop2)))
+
+  # individual names in an unnamed list
+  ibd_totals2 <- ts_ibd(ts, coordinates = FALSE, minimum_length = 100000,
+                        between = list(pop1_samples, pop2_samples))
+  expect_true("POP1" == unique(unlist(ibd_totals2$pop1)))
+  expect_true("POP2" == unique(unlist(ibd_totals2$pop2)))
+
+  expect_true(all(ibd_totals1 == ibd_totals2))
 })
 
 test_that("IBD of a given minimum length is returned", {