Update tests and logs

6 files changed, 45 insertions, 23 deletions

diff --git a/ChangeLog b/ChangeLog
index 69b201d..5daebcf 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,30 @@
+commit d032fb8ba7b0827bb896b6d9a07d6449d88cf511
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2021-11-18 23:52:32 +0100
+
+    We are on Xenial, no python3-rdkit...
+
+commit 368edcfe670c674391d79a27a5d0490fbc1a7ef2
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2021-11-18 23:48:41 +0100
+
+    Another attempt to get python3-rdkit on Travis
+
+commit f91a75460fbf756e27bd280b969284d043c5a451
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2021-11-18 23:22:32 +0100
+
+    Install python3-rdkit on Travis
+
+commit ae755fbb06c3dda0740e9bb9323fbdfe3f2788a4
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2021-11-18 23:03:16 +0100
+
+    Use reticulate instead of PythonInR, alanwood has moved
+    
+    Because the pesticide compendium at alanwood.net has moved to bcpc.org,
+    we need to depend on a development branch of webchem at the moment.
+
 commit 898d598bcbb022ac767e0105e868798130f2c74c
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2020-10-13 15:10:03 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 041999c..5793f4b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.3.1
-Date: 2021-11-18
+Date: 2021-11-19
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de"))
 Description: Utilities for dealing with chemical entities and associated
diff --git a/R/zzz.R b/R/zzz.R
index 19ca10d..5503a4a 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,13 +1,9 @@
 .onLoad = function(libname, pkgname) {
   rdkit_available <- FALSE
-  if(requireNamespace("reticulate", quietly = TRUE)) {
-    rdkit_module <- try(reticulate::import("rdkit"))
-    if (!inherits(rdkit_module, "try-error")) {
-      rdkit_available <- TRUE
-    }
+  rdkit_module <- try(reticulate::import("rdkit"), silent = TRUE)
+  if (!inherits(rdkit_module, "try-error")) {
+    rdkit_available <- TRUE
   }
   assign('rdkit_available', rdkit_available, envir = topenv())
-  if (rdkit_available) {
-    assign('rdkit_module', rdkit_module, envir = topenv())
-  }
+  assign('rdkit_module', rdkit_module, envir = topenv())
 }
diff --git a/test.log b/test.log
index 34cf63b..9817e02 100644
--- a/test.log
+++ b/test.log
@@ -1,12 +1,11 @@
 Loading required package: usethis
-Loading chents
+ℹ Loading chents
+ℹ Testing chents
+✔ | F W S  OK | Context
+✔ |         6 | Generation of chent objects [3.3s]
+✔ |         8 | Generation of pai objects [8.1s]
 
-Attaching package: ‘testthat’
+══ Results ═════════════════════════════════════════════════════════════════════
+Duration: 11.4 s
 
-The following object is masked from ‘package:devtools’:
-
-    test_file
-
-Testing chents
-✔ |  OK F W S | Context
-
⠏ |   0       | Generation of chent objects
⠋ |   1       | Generation of chent objects
\ No newline at end of file
+[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 094ff8b..4551cf7 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -2,7 +2,7 @@ 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 PythonInR")
+  if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
 }
 
 oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE, chyaml = FALSE)
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index 368876e..e22b6ae 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -8,12 +8,12 @@ test_that("a pai object is correctly generated from an ambiguous name", {
   glyphosate <- pai$new("glyphosate", chyaml = FALSE)
   expect_message(pai$new("benzalkonium chloride", chyaml = FALSE), "did not give results")
 
-  expect_equivalent(glyphosate$alanwood$cas, "1071-83-6")
-  expect_equivalent(glyphosate$alanwood$formula, "C3H8NO5P")
-  expect_equivalent(glyphosate$alanwood$iupac_name, "N-(phosphonomethyl)glycine")
+  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(names(glyphosate$identifier), "glyphosate")
   ik = "XDDAORKBJWWYJS-UHFFFAOYSA-N"
-  attr(ik, "source") <- c("alanwood", "pubchem")
+  attr(ik, "source") <- c("bcpc", "pubchem")
   expect_equal(glyphosate$inchikey, ik)
   expect_equivalent(round(glyphosate$mw, 2), 169.07)
   smiles <- "C(C(=O)O)NCP(=O)(O)O"