Fix check for rdkit availability

Also remove python-rdkit from the travis config as its version is too
old on travis (Ubuntu trusty)

6 files changed, 116 insertions, 80 deletions

diff --git a/.travis.yml b/.travis.yml
index 4aca61b..862f118 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,5 +3,3 @@ cache: packages
 r:
   - release
   - devel
-apt_packages:
-  - python-rdkit
diff --git a/ChangeLog b/ChangeLog
index 65505cd..e371d83 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,24 @@
+commit aa80ce4f46f9ff1a2851ba9ba873a55a8f6ebc6d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-02-19 17:17:48 +0100
+
+    Change package URL to github to get source code links
+
+commit f21038189af44e9dcea8458a66ce00bbf9b6b570
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-02-19 17:03:58 +0100
+
+    Add python-rdkit to travis configuration
+
+commit 87f9c5315c751896c2eef1fdbe8f93c5b151577e
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-02-19 16:02:19 +0100
+
+    Start using travis and update a test
+    
+    It seems the canonical SMILES for glyphosate on PubChem has dropped the
+    designation of the two charges
+
 commit b3d9bf2e5571cf506b924a6fc9cbcc366c82e340
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2018-09-27 18:57:55 +0200
diff --git a/R/chent.R b/R/chent.R
index 941b430..6a5abc7 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2016,2017,2018  Johannes Ranke
+# Copyright (C) 2016-2019  Johannes Ranke
 # Contact: jranke@uni-bremen.de
 # This file is part of the R package chents
 
@@ -88,7 +88,7 @@ chent <- R6Class("chent",
       }
 
       if (rdkit) {
-        if(requireNamespace("PythonInR", quietly = TRUE)) {
+        if(rdkit_available()) {
           if (is.null(self$smiles)) {
             message("RDKit would need a SMILES code")
           } else {
@@ -99,6 +99,8 @@ chent <- R6Class("chent",
             self$mw <- self$rdkit$mw
             attr(self$mw, "source") <- "rdkit"
           }
+        } else {
+          message("RDKit is not available via PythonInR")
         }
       }
 
@@ -162,62 +164,54 @@ chent <- R6Class("chent",
       }
     },
     get_rdkit = function(template = NULL) {
-      if (!requireNamespace("PythonInR"))
-        stop("PythonInR can not be loaded")
-      id <- names(self$identifier)
-      if (!PythonInR::pyIsConnected()) {
-        PythonInR::pyConnect()
+      if(!rdkit_available()) {
+        stop("RDKit is not available via PythonInR")
       }
-      try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"))
-      if (inherits(try_rdkit, "try-error")) {
-        message("Could not import RDKit in Python session")
-      } else {
-        self$rdkit <- list()
-        PythonInR::pyImport("Descriptors", from = "rdkit.Chem")
-        PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')"))
-        self$rdkit$mw <- PythonInR::pyExecg("mw = Descriptors.MolWt(mol)", "mw")
-        if (!is.null(self$mw)) {
-          if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {
-            message("RDKit mw is ", self$rdkit$mw)
-            message("mw is ", self$mw)
-          }
+      self$rdkit <- list()
+      PythonInR::pyImport("Descriptors", from = "rdkit.Chem")
+      PythonInR::pyExec(paste0("mol = Chem.MolFromSmiles('", self$smiles[1], "')"))
+      self$rdkit$mw <- PythonInR::pyExecg("mw = Descriptors.MolWt(mol)", "mw")
+      if (!is.null(self$mw)) {
+        if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {
+          message("RDKit mw is ", self$rdkit$mw)
+          message("mw is ", self$mw)
         }
+      }
 
-        # Create an SVG representation
-        PythonInR::pyImport("Draw", from = "rdkit.Chem")
-        PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw")
-        PythonInR::pyImport("rdDepictor", from = "rdkit.Chem")
-        PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)")
-        if (!is.null(template)) {
-          PythonInR::pyImport("AllChem", from = "rdkit.Chem")
-          PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')"))
-          PythonInR::pyExec("AllChem.Compute2DCoords(template)")
-          PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)")
-        }
-        PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)")
-        PythonInR::pyExec("d2d.DrawMolecule(mol)")
-        PythonInR::pyExec("d2d.FinishDrawing()")
-        self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
+      # Create an SVG representation
+      PythonInR::pyImport("Draw", from = "rdkit.Chem")
+      PythonInR::pyImport("rdMolDraw2D", from = "rdkit.Chem.Draw")
+      PythonInR::pyImport("rdDepictor", from = "rdkit.Chem")
+      PythonInR::pyExec("rdDepictor.Compute2DCoords(mol)")
+      if (!is.null(template)) {
+        PythonInR::pyImport("AllChem", from = "rdkit.Chem")
+        PythonInR::pyExec(paste0("template = Chem.MolFromSmiles('", template, "')"))
+        PythonInR::pyExec("AllChem.Compute2DCoords(template)")
+        PythonInR::pyExec("AllChem.GenerateDepictionMatching2DStructure(mol, template)")
+      }
+      PythonInR::pyExec("d2d = rdMolDraw2D.MolDraw2DSVG(400,500)")
+      PythonInR::pyExec("d2d.DrawMolecule(mol)")
+      PythonInR::pyExec("d2d.FinishDrawing()")
+      self$svg <- PythonInR::pyGet("d2d.GetDrawingText()")
 
-        if (!requireNamespace("grConvert")) {
-          stop("grConvert is not available, self$Picture will not be created")
-        } else {
-          # Convert to PostScript, remembering size properties
-          svgfile <- tempfile(fileext = ".svg")
-          writeLines(self$svg, svgfile)
-          psfile <- tempfile(fileext = ".ps")
-          suppressMessages(grConvert::convertPicture(svgfile, psfile))
-          ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
-          ps_font_size <- gsub(" .*$", "", ps_font_line)
-          self$Pict_font_size = as.numeric(ps_font_size)
-
-          # Read in to create Picture
-          xmlfile <- tempfile(fileext = ".xml")
-          PostScriptTrace(psfile, outfilename = xmlfile)
-          unlink(paste0("capture", basename(psfile)))
-          self$Picture <- readPicture(xmlfile)
-          unlink(c(xmlfile, psfile, svgfile))
-        }
+      if (!requireNamespace("grConvert")) {
+        stop("grConvert is not available, self$Picture will not be created")
+      } else {
+        # Convert to PostScript, remembering size properties
+        svgfile <- tempfile(fileext = ".svg")
+        writeLines(self$svg, svgfile)
+        psfile <- tempfile(fileext = ".ps")
+        suppressMessages(grConvert::convertPicture(svgfile, psfile))
+        ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
+        ps_font_size <- gsub(" .*$", "", ps_font_line)
+        self$Pict_font_size = as.numeric(ps_font_size)
+
+        # Read in to create Picture
+        xmlfile <- tempfile(fileext = ".xml")
+        PostScriptTrace(psfile, outfilename = xmlfile)
+        unlink(paste0("capture", basename(psfile)))
+        self$Picture <- readPicture(xmlfile)
+        unlink(c(xmlfile, psfile, svgfile))
       }
     },
     get_chyaml = function(repo = c("wd", "local", "web"),
@@ -607,4 +601,24 @@ pp <- R6Class("pp",
     }
   )
 )
+
+rdkit_available <- function()
+{
+  if(requireNamespace("PythonInR", quietly = TRUE)) {
+    if (!PythonInR::pyIsConnected()) {
+      PythonInR::pyConnect()
+    }
+    sink(tempfile())
+    try_rdkit <- try(PythonInR::pyImport("Chem", from = "rdkit"), 
+                     silent = TRUE)
+    sink()
+    if (inherits(try_rdkit, "try-error")) {
+      return(FALSE)
+    } else {
+      return(TRUE)
+    }
+  } else {
+    return(FALSE)
+  }
+}
 # vim: set ts=2 sw=2 expandtab:
diff --git a/README.md b/README.md
index 75b9d7e..ffa9844 100644
--- a/README.md
+++ b/README.md
@@ -1,21 +1,9 @@
 # chents
 
-The R package **chents** provides some utilities for working with chemical 
-entities in R, made available under the GNU public license.
-This means:
-
-    This program is free software: you can redistribute it and/or modify it under
-    the terms of the GNU General Public License as published by the Free Software
-    Foundation, either version 3 of the License, or (at your option) any later
-    version.
-
-    This program is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-    details.
+[![Build Status](https://travis-ci.com/jranke/chents.svg?branch=master)](https://travis-ci.com/jranke/chents)
 
-    You should have received a copy of the GNU General Public License along with
-    this program. If not, see <http://www.gnu.org/licenses/>
+The R package **chents** provides some utilities for working with chemical 
+entities in R.
 
 ## Features
 
@@ -26,6 +14,8 @@ PythonInR, some additional chemical information is computed and a 2D graph can
 be plotted
 - Additional information can be read from a local .yaml file
 
+## Examples
+
 Some examples are available from the 
 [reference on jrwb.de](http://pkgdown.jrwb.de/chents/reference).
 
diff --git a/test.log b/test.log
index abb856b..9062ecc 100644
--- a/test.log
+++ b/test.log
@@ -1,13 +1,20 @@
 Loading chents
-Loading required package: testthat
+
+Attaching package: ‘testthat’
+
+The following objects are masked from ‘package:devtools’:
+
+    setup, test_file
+
 Testing chents
-Generation of chent objects: 
-Initialize Python Version 3.4.2 (default, Oct  8 2014, 10:47:48) 
-[GCC 4.9.1]
+✔ | OK F W S | Context
+
⠏ |  0       | Generation of chent objects
⠋ |  1       | Generation of chent objects
⠙ |  2       | Generation of chent objects
⠹ |  3       | Generation of chent objects
⠸ |  4       | Generation of chent objects
⠼ |  5       | Generation of chent objects
⠴ |  6       | Generation of chent objects
✔ |  6       | Generation of chent objects [2.8 s]
+
⠏ |  0       | Generation of pai objects
⠋ |  1       | Generation of pai objects
⠙ |  2       | Generation of pai objects
⠹ |  3       | Generation of pai objects
⠸ |  4       | Generation of pai objects
⠼ |  5       | Generation of pai objects
⠴ |  6       | Generation of pai objects
⠦ |  7       | Generation of pai objects
⠧ |  8       | Generation of pai objects
⠇ |  9       | Generation of pai objects
✔ |  9       | Generation of pai objects [6.4 s]
 
-Trying to get chemical information from RDKit using user SMILES
-CCCCCCCCO
-......
-Generation of pai objects: .........
+══ Results ═════════════════════════════════════════════════════════════════════
+Duration: 9.2 s
 
-DONE ===========================================================================
+OK:       15
+Failed:   0
+Warnings: 0
+Skipped:  0
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 28d120e..1fa0852 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -1,8 +1,14 @@
 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")
+}
+
 oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE, chyaml = FALSE)
 
 test_that("We can generate a chent object from SMILES using RDKit", {
+  skip_if_no_rdkit()
   expect_equivalent(round(oct$mw, 2), 130.23) 
   expect_equal(names(oct$identifier), "X1.octanol")
   expect_equal(oct$smiles[["user"]], "CCCCCCCCO")