Adapt to new SMILES names at PubChem

This may break some code using the old smiles names "PubChem_Canonical"
and "PubChem_Isomeric" instead of the new smiles names "PubChem"
(including isotopic and stereochemical information) and
"PubChem_Connectivity" (only containing connectivity, but still
canonical).

Further changes in this commit:
- A fix to the test target in the makefile
- Use markdown syntax for link to objects from other packages in the
  documentation
- Adapt the tests
- Increase test coverage a bit

1 files changed, 4 insertions, 0 deletions

diff --git a/NEWS.md b/NEWS.md
index f935343..07af04e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+## version 0.4.0
+
+- R/chent.R: PubChem has changed the names of the SMILES codes they provide. The former isomeric smiles that was incorporated in our chent objects as "Pubchem_Isomeric" is now simply calles SMILES, and is incorporated in our objects as "PubChem". The SMILES code formerly given as "canonical" is now termed "connectivity SMILES" because it does not contain isotopic or stereochemical specifications. In the chents object, it is now available under the name "PubChem_Connectivity". This is a breaking change, so objects generated with versions < 0.4.0 may produce errors when used with current versions.
+
 ## version 0.3.7
 
 - R/chent.R: Do not attempt to load a chyaml file per default, as the format of such a file and the resulting chyaml list object is not documented and would need to be inferred from its use in the pfm package.