Description of work
Since the release of Numpy 2.0.0, the MDANSE unit tests have been producing large numbers of DeprecationWarnings. This PR corrects this. There are still errors output by rdkit, but they don't seem to cause immediate problems, and we expect them to be solved by rdkit developers eventually.
closes #479
Fixes
Removed the __array_wrap__ from IOutputVariable.
Replaced numpy.row_stack with numpy.vstack.
Corrected the code in MoleculeFinder which tried to access the trajectory HDF5 file directly, and not by using the methods of the Trajectory wrapper class.
To test
All tests should pass without producing warnings.
Try running MoleculeFinder on a trajectory without molecule labels, to see if the InChI strings are assigned as molecule labels by rdkit.
Description of work Since the release of Numpy 2.0.0, the MDANSE unit tests have been producing large numbers of DeprecationWarnings. This PR corrects this. There are still errors output by rdkit, but they don't seem to cause immediate problems, and we expect them to be solved by rdkit developers eventually.
closes #479
Fixes
To test All tests should pass without producing warnings. Try running MoleculeFinder on a trajectory without molecule labels, to see if the InChI strings are assigned as molecule labels by rdkit.