Change Log

From v3.4.4 to v3.4.5

Fixes

Fixed a bug in calculation of the Pareto fronts (fronts are now calculated for maximization of objectives instead of objective minimization).
Patch a bug that that caused a crash when an invalid smiles was encountered in the fragment generation step. This
bug was introduced in v3.4.4, now invalid smiles are skipped and a warning is printed to the log.

Installation of pip package with pyproject.toml instead of setup.cfg.
Methods cpu_non_dominated_sort and gpu_non_dominated_sort have been replace by get_Pareto_fronts.
Improve calculation of crowding distance.
The rewards module is refactored and the RankingStrategy class was replace by ParetoRankingScheme class.
- The final reward calcuation for ParetoRankingScheme-based methods is now directly the scaled rank of the molecules.
- The ParetoTanimotoDistance now has a attribute distance_metric which can be "min", "mean" or "mutual" instead of attribute ranking.
DrugEx is now compatible with the latest version of qsprpred v2.0.1, previous versions of qsprpred are no longer supported.
drugex.generate CLI environment arguments are no longer overwritten by environment variables from generator.

None.

When installing package with pip, the commit hash and date of the installation is saved into qsprpred._version
Added an automated Docker runner for tests that can run on GPUs. See testing/runner/README.md for more information.
When installing package with pip, the commit hash and date of the installation is saved into drugex._version. This information is also used as a basis of a new dynamic versioning scheme for the package. The version number is generated automatically upon installation of the package and saved to drugex.__version__.
QSPRPred is now available as an optional dependency that can be installed with DrugEx using the [qsprpred] option.