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authorJohannes Ranke <jranke@uni-bremen.de>2021-11-19 00:18:22 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-11-19 00:18:22 +0100
commit0056584e5168df75bca159ddf3469aa07457b77d (patch)
tree12fae625ede19eba2776a3c5e3d9b3d8f9fd41c5
parentd032fb8ba7b0827bb896b6d9a07d6449d88cf511 (diff)
Update tests and logs
-rw-r--r--ChangeLog27
-rw-r--r--DESCRIPTION2
-rw-r--r--R/zzz.R12
-rw-r--r--test.log17
-rw-r--r--tests/testthat/test_chent.R2
-rw-r--r--tests/testthat/test_pai.R8
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"

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