Improve test coverage and use testthat 3rd editionHEADmain

3 files changed, 39 insertions, 38 deletions

diff --git a/tests/testthat/_snaps/chent.md b/tests/testthat/_snaps/chent.md
new file mode 100644
index 0000000..b214852
--- /dev/null
+++ b/tests/testthat/_snaps/chent.md
@@ -0,0 +1,18 @@
+# We can initialise an object and add information
+
+    Code
+      print(oct)
+    Output
+      <chent>
+      Identifier $identifier 1-octanol 
+      InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
+      SMILES string $smiles:
+             user     PubChem 
+      "CCCCCCCCO" "CCCCCCCCO" 
+      Molecular weight $mw: 130.2 
+      PubChem synonyms (up to 10):
+       [1] "1-octanol"             "Octan-1-ol"            "111-87-5"             
+       [4] "N-octanol"             "Octyl alcohol"         "caprylic alcohol"     
+       [7] "n-Octyl alcohol"       "Heptyl carbinol"       "1-Hydroxyoctane"      
+      [10] "Primary octyl alcohol"
+
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 4546423..1f4a186 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -1,29 +1,21 @@
-context("Generation of chent objects")
-
 # Check if we can use RDKit
 skip_if_no_rdkit <- function() {
   if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
 }
 
-oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
-
-test_that("We can initialise an object only with identifier and SMILES code", {
+test_that("We can initialise an object and add information", {
+  oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
   expect_equal(oct$identifier, c(X1.octanol = "1-octanol")) # The name of the identifier is generated using make.names()
   expect_equal(oct$inchikey, structure(NA, source = "user"))
   expect_equal(oct$smiles, c(user = "CCCCCCCCO"))
-})
-
-test_that("We can generate a chent object from SMILES using RDKit", {
-  skip_if_no_rdkit()
-  oct$get_rdkit()
-  expect_equivalent(round(oct$mw, 2), 130.23)
-})
-
-test_that("We can add information retrieved from PubChem via webchem", {
-  expect_warning(oct$try_pubchem(), "Overwriting uninitialized InChIKey")
-  expect_equivalent(round(oct$mw, 2), 130.23)
-  ik = "KBPLFHHGFOOTCA-UHFFFAOYSA-N"
-  attr(ik, "source") <- "pubchem"
-  expect_equal(oct$inchikey, ik)
+  oct$try_pubchem() |> 
+    expect_message("Querying PubChem for name 1-octanol") |> 
+    expect_warning("Overwriting uninitialized InChIKey")
+  expect_equal(oct$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")
+  expect_equal(round(oct$mw, 2), structure(130.23, source = "pubchem"))
+  expect_snapshot(print(oct))
 })
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index f38672d..0d5264a 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -1,25 +1,16 @@
-# For manual use of this file
-require(chents)
-require(testthat)
-
-context("Generation of pai objects")
-
 test_that("a pai object is correctly generated", {
   skip_on_travis() # server certificate verification failed in curl_fetch_memory()
-  glyphosate <- pai$new("glyphosate")
+  {glyphosate <- pai$new("glyphosate")} |> 
+    expect_message("Querying BCPC for glyphosate") |> 
+    expect_message("Querying PubChem for inchikey ") |> 
+    expect_message("Get chemical information from RDKit using PubChem SMILES")
   
-  # This did not give results at BCPC in previous times, so it was used to test
-  # the corresponding warning.
-  #bc <- pai$new("benzalkonium chloride") 
-
-  expect_equivalent(glyphosate$bcpc$cas, "1071-83-6")
-  expect_equivalent(glyphosate$bcpc$formula, "C3H8NO5P")
-  expect_equivalent(glyphosate$bcpc$iupac_name, "N-(phosphonomethyl)glycine")
+  expect_equal(glyphosate$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")
   ik = "XDDAORKBJWWYJS-UHFFFAOYSA-N"
-  attr(ik, "source") <- c("bcpc", "pubchem")
-  expect_equal(glyphosate$inchikey, ik)
-  expect_equivalent(round(glyphosate$mw, 2), 169.07)
-  smiles <- "C(C(=O)O)NCP(=O)(O)O"
-  expect_equal(glyphosate$smiles[["PubChem"]], smiles)
+  expect_equal(glyphosate$inchikey, structure("XDDAORKBJWWYJS-UHFFFAOYSA-N", source = c("bcpc", "pubchem")))
+  expect_equal(round(glyphosate$mw, 2), structure(169.07, source = "pubchem"))
+  expect_equal(glyphosate$smiles[["PubChem"]], "C(C(=O)O)NCP(=O)(O)O")
 })