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Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

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* Deprecation: planned removal of .message() and .getMessage() methods

* Deprecation: planned removal of old MolHash code

* document deprecations

* output the diffs when the psql tests fail

* remove .message() from SWIG wrappers

note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway

* typo
This commit is contained in:
Greg Landrum
2020-04-01 14:30:07 +02:00
committed by GitHub
parent cf031c2f7e
commit 5712176605
126 changed files with 1172 additions and 22492 deletions
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18
Contrib/ConformerParser/test.cpp
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@@ -15,7 +15,8 @@
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
@@ -52,14 +53,15 @@
using namespace RDKit;
using namespace RDKit::ConformerParser;
void test1(){
void test1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test ConformerParser." << std::endl;
ROMol *mol = SmilesToMol("CCC");
std::vector<std::vector<double> > coords;
std::vector<std::vector<double>> coords;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Contrib/ConformerParser/test_data/water_coords_bad.trx";
std::string fName =
rdbase + "/Contrib/ConformerParser/test_data/water_coords_bad.trx";
bool ok = false;
try {
readAmberTrajectory(fName, coords, mol->getNumAtoms());
@@ -73,7 +75,7 @@ void test1(){
try {
readAmberTrajectory(fName, coords, mol->getNumAtoms());
} catch (ValueErrorException &e) {
//std::cout << e.message() << std::endl;
// std::cout << e.what() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
@@ -103,18 +105,16 @@ void test1(){
TEST_ASSERT(coords[1].size() == 9);
res = addConformersFromList(*mol, coords);
TEST_ASSERT((*mol).getNumConformers() == 2);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
int main() {
RDLog::InitLogs();
#if 1
test1();
#endif
}