Skip to content

Latest commit

 

History

History
20 lines (18 loc) · 3.86 KB

changelog.md

File metadata and controls

20 lines (18 loc) · 3.86 KB
Raw

Change log for CPSign versions

2.0.0 RC4 :

  • Solved minor bug with swapped get[Min|Max]SplitIndex values for the LOOSplitter class.
  • Moved the encrypt-api to a separate project which simplifies and decouples that API vs the remaining code. Now the other components can rely on a fixed version (as it is not likely to change often or at all) and not have issues with incompatibility due to transitive dependencies to the parent project pom (i.e. encrypt-api would rely on e.g. the 2.0.0-rc3 version whilst the remaining cpsign modules will rely on a later version of the parent pom).
  • Added two callback interfaces for progress information and monitoring while running GridSearch jobs, one that only get information (ProgressCallback) and the other one (ProgressMonitor) that can choose to exit the grid search e.g. due to time-restraints. Note that these are synchronous calls at this point (CPSign is not multithreaded otherwise so no use adding that for this one task). Added an implementation tailored for the CLI so that information is printed in the terminal (e.g. " - Finished 2/10 grid points") to provide more feedback about the progress so e.g. too long jobs can be aborted earlier.

2.0.0 RC2 RC3 :

Note: due to a minor mistake in updating the encrypt-api version to the updated 2.0.1 version in the test-utils module, the build failed at GitHub and RC1 is amended directly by release candidate 3 (RC3).

  • Introduced a common ProgressTracker that is shared among the processing stack while loading and processing new data. This way a specific threshold of "number of allowed failures" can be adhered to instead of having individual thresholds for each level of processing. This trickles down into --early-termination of the CLI now stopping when it should.
  • Fixed bug where MolAndActivityConverter would stop when encountering the maximum specified number of conversion failures, and do it silently without causing the expected exception. This bug was also present when using the CLI precompute program - and is now solved.
  • Remove the possibility to use clustered POSIX flags to the CLI, which resulted in strange behaviour that was hard to find the cause of.
  • Update the Fuzzy matching logics to (hopefully) improve matching of parameters to the CLI.
  • Update dependency version of Picocli.
  • Added logics for trying to deduce the user error to improve error messages to CLI users, specifically for running precompute. Also streamlined the output to be more coherent among predict, predict-online and validate.
  • Extracted prediction logics of predict and predict-online into common utility class, again to streamline the behaviour seen by the user.
  • Added more information to the model-info program of the CLI, i.e. in case a model can be used for generating prediction images and the number of attributes/features used.
  • Added new interface ChemFilter that replaces the [set|get]MinHAC of a ChemDataset (API level). Added two implementations; HACFilter (allows to set both minimum and maximum HAC) and MolMassFilter (min/max molecular mass). At the CLI level the --min-hac is now deprecated and will give a deprecation message if used, and is replaced by the --chem-filters parameter that allows to set multiple filters. To keep consistent with earlier versions there is a default HACFilter using the same minimum heavy atom count of 5. In order to not apply any chemical filters the user can give --chem-filters none.
  • At CLI level there is a new explain chem-filters that give some general information as well as list the currently available filters and sub-parameters of these.
  • Improved aggregation of metrics from mulit-test splits (i.e. when computing mean +/- standard deviation), also improve output from CLI to the user (i.e. remove the wording "Calibration plot" when only having a single confidence level).