Merge pull request #71 from HighlanderLab:issues_69_and_70

Fixing edge cases in tests

Author: gregorgorjanc

RcppTskit/tests/testthat/test_TableCollection.R

@@ -131,8 +131,7 @@ test_that("TableCollection and TreeSequence round-trip works", {
 
   tc <- ts$dump_tables()
   expect_true(is(tc, "TableCollection"))
-  expect_output(tc$print(), NA) # non-interactive mode
-  p <- tc$print()
+  tmp <- capture.output(p <- tc$print())
   expect_equal(
     p,
     list(
@@ -178,8 +177,9 @@ test_that("TableCollection and TreeSequence round-trip works", {
 
   ts2 <- tc$tree_sequence()
   expect_true(is(ts2, "TreeSequence"))
-  expect_output(ts$print(), NA) # non-interactive mode
-  expect_equal(ts$print(), ts2$print())
+  tmp <- capture.output(ts_print <- ts$print())
+  tmp <- capture.output(ts2_print <- ts2$print())
+  expect_equal(ts_print, ts2_print)
 
   # Edge cases
   expect_error(

RcppTskit/tests/testthat/test_get_tskit_py.R

@@ -1,4 +1,16 @@
+skip_if_offline_or_on_cran <- function() {
+  if (!(requireNamespace("covr", quietly = TRUE) && covr::in_covr())) {
+    # We need internet connection for get_tskit_py()
+    skip_if_offline()
+
+    # The tests below take quite a bit of time since they pull in installation of
+    # Python modules, hence skipping on CRAN due to time limits on CRAN
+    skip_on_cran()
+  }
+}
+
 test_that("get_tskit_py() works", {
+  skip_if_offline_or_on_cran()
   # Testing that get_tskit_py() fails with a non-module object
   # Next two lines ensure that testthat is looking into the global environment
   # as is get_tskit_py()
@@ -9,15 +21,6 @@ test_that("get_tskit_py() works", {
     regexp = "Object 'rubbish' exists in the global environment but is not a reticulate Python module"
   )
 
-  if (!covr::in_covr()) {
-    # To get_tskit_py() we need internet connection
-    skip_if_offline()
-
-    # The tests below take quite a bit of time since they pull in installation of
-    # Python modules, hence skipping on CRAN due to time limits on CRAN
-    skip_on_cran()
-  }
-
   # Uncomment the below to explore test behaviour, but note that the removal
   # doesn't work when you try to run the tests multiple times in the same session!
   # Hence we are commenting this next line out.
@@ -59,6 +62,7 @@ test_that("get_tskit_py() works", {
 })
 
 test_that("check_tskit_py() validates reticulate Python module objects", {
+  skip_if_offline_or_on_cran()
   expect_message(
     expect_false(check_tskit_py(1)),
     "object must be a reticulate Python module object!"

RcppTskit/tests/testthat/test_load_summary_and_dump.R

@@ -13,7 +13,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   )
   expect_no_error(tc_load(ts_file, skip_tables = TRUE))
   check_empty_tables <- function(ts) {
-    p <- ts$print()
+    tmp <- capture.output(p <- ts$print())
     expect_true(all(p$tables$number == 0))
   }
   ts <- ts_load(ts_file, skip_tables = TRUE)
@@ -50,7 +50,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   )
   expect_no_error(tc_load(ts_file, skip_tables = TRUE))
   check_empty_tables <- function(tc) {
-    p <- tc$print()
+    tmp <- capture.output(p <- tc$print())
     expect_true(all(p$tables$number == 0))
   }
   tc <- tc_load(ts_file, skip_tables = TRUE)
@@ -225,7 +225,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
     regexp = "ts must be an object of externalptr class!"
   )
   p_ptr <- ts_ptr_print(ts_ptr)
-  p <- ts$print()
+  tmp <- capture.output(p <- ts$print())
   expect_equal(
     p,
     list(
@@ -276,7 +276,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
     regexp = "tc must be an object of externalptr class!"
   )
   p_ptr <- tc_ptr_print(tc_ptr)
-  p <- tc$print()
+  tmp <- capture.output(p <- tc$print())
   expect_equal(
     p,
     list(
@@ -549,7 +549,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   expect_equal(m_ptr, m)
 
   p_ptr <- ts_ptr_print(ts_ptr)
-  p <- ts$print()
+  tmp <- capture.output(p <- ts$print())
   expect_equal(
     p_ptr,
     list(
@@ -630,7 +630,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   expect_equal(m_ptr_tc, m_ptr_ts)
 
   p_ptr <- tc_ptr_print(tc_ptr)
-  p <- tc$print()
+  tmp <- capture.output(p <- tc$print())
   expect_equal(
     p_ptr,
     list(

RcppTskit/tests/testthat/test_r_to_py_and_py_to_r.R

@@ -1,6 +1,6 @@
 skip_if_no_tskit_py <- function() {
-  if (!covr::in_covr()) {
-    # To get_tskit_py() we need internet connection
+  if (!(requireNamespace("covr", quietly = TRUE) && covr::in_covr())) {
+    # We need internet connection for get_tskit_py()
     skip_if_offline()
   }
   if (!reticulate::py_module_available("tskit")) {
@@ -142,8 +142,9 @@ test_that("ts_r_to_py() and ts_py_to_r() work", {
   expect_equal(length(ts2_py$tables$mutations$metadata), m2$mutations)
 
   expect_true(is(ts2_r, "TreeSequence"))
-  expect_output(ts2_r$print(), NA) # non-interactive mode
-  expect_equal(ts2_r$print(), ts_ptr_print(ts_ptr2_r))
+  tmp <- capture.output(ts2_r_print <- ts2_r$print())
+  tmp <- capture.output(ts_ptr2_r_print <- ts_ptr_print(ts_ptr2_r))
+  expect_equal(ts2_r_print, ts_ptr2_r_print)
 })
 
 test_that("tc_r_to_py() and tc_py_to_r() work", {
@@ -263,6 +264,7 @@ test_that("tc_r_to_py() and tc_py_to_r() work", {
   expect_equal(length(tc2_py$mutations$metadata), m2$mutations)
 
   expect_true(is(tc2_r, "TableCollection"))
-  expect_output(tc2_r$print(), NA) # non-interactive mode
-  expect_equal(tc2_r$print(), tc_ptr_print(tc_ptr2_r))
+  tmp <- capture.output(tc2_r_print <- tc2_r$print())
+  tmp <- capture.output(tc_ptr2_r <- tc_ptr_print(tc_ptr2_r))
+  expect_equal(tc2_r_print, tc_ptr2_r)
 })