Do not depend on RDKit in pai test

This hopefully addresses test failures observed on R-Universe.
Update coverage report.

3 files changed, 12 insertions, 9 deletions

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
new file mode 100644
index 0000000..fb55272
--- /dev/null
+++ b/tests/testthat/setup.R
@@ -0,0 +1,4 @@
+# Check if we can use RDKit
+skip_if_no_rdkit <- function() {
+  if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
+}
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 1f4a186..76af7aa 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -1,8 +1,3 @@
-# Check if we can use RDKit
-skip_if_no_rdkit <- function() {
-  if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
-}
-
 test_that("We can initialise an object and add information", {
   oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
   expect_equal(oct$identifier, c(X1.octanol = "1-octanol")) # The name of the identifier is generated using make.names()
@@ -13,6 +8,7 @@ test_that("We can initialise an object and add information", {
     expect_warning("Overwriting uninitialized InChIKey")
   expect_equal(oct$inchikey, structure("KBPLFHHGFOOTCA-UHFFFAOYSA-N", source = "pubchem"))
   expect_equal(oct$smiles[["PubChem"]], "CCCCCCCCO")
+
   skip_if_no_rdkit()
   oct$get_rdkit() |> 
     expect_message("Get chemical information from RDKit using user SMILES")
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index 0d5264a..9d73b58 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -1,14 +1,17 @@
 test_that("a pai object is correctly generated", {
-  skip_on_travis() # server certificate verification failed in curl_fetch_memory()
-  {glyphosate <- pai$new("glyphosate")} |> 
+
+  {glyphosate <- pai$new("glyphosate", rdkit = FALSE)} |> 
     expect_message("Querying BCPC for glyphosate") |> 
-    expect_message("Querying PubChem for inchikey ") |> 
-    expect_message("Get chemical information from RDKit using PubChem SMILES")
+    expect_message("Querying PubChem for inchikey ")
   
+  # Check BCPC results
   expect_equal(glyphosate$bcpc$cas, "1071-83-6")
   expect_equal(glyphosate$bcpc$formula, "C3H8NO5P")
   expect_equal(glyphosate$bcpc$iupac_name, "N-(phosphonomethyl)glycine")
+  
   expect_equal(names(glyphosate$identifier), "glyphosate")
+
+  # Check PubChem results
   ik = "XDDAORKBJWWYJS-UHFFFAOYSA-N"
   expect_equal(glyphosate$inchikey, structure("XDDAORKBJWWYJS-UHFFFAOYSA-N", source = c("bcpc", "pubchem")))
   expect_equal(round(glyphosate$mw, 2), structure(169.07, source = "pubchem"))