Deeponto

Added

- [x] **Add** `set_seed()` method at `deeponto.utils`.

Changed

- [x] **Change** the layout of all utility methods by making them stand-alone instead of static methods.
- [x] **Change** the `.verbalise_class_expression()` method by adding an option to keep entity IRIs without verbalising them using `.vocabs` at `deeponto.onto.OntologyVerbaliser`.
- [x] **Change** default `apply_lowercasing` value to `False` for both `.get_annotations()` and `.build_annotation_index()` methods at `deeponto.onto.Ontology`.
- [x] **Change** the method `.get_owl_object_annotations()` to `.get_annotations()` at `deeponto.onto.Ontology`.
- [x] **Change** the LogMap debugger memory options for BERTMap's mapping repair.
- [x] **Change** the default jar command timeout to 1 hour.

Fixed

- [x] **Fix** duplicate logging in running BERTMap due to progapagation.

Added

- [x] **Add** specific check of `use_in_alignment` annotation in BERTMap for the OAEI.
- [x] **Add** OAEI utilities at `deeponto.align.oaei`.

Changed

- [x] **Change** the `read_table_mappings` method to allow `None` for threshold.

Fixed

- [x] **Fix** BERTMap error and add corresponding warning when an input ontology has no sibling class group, related to Issue 10.
- [x] **Fix** BERTMap error and add corresponding warning when an input ontology has some class with no label (annotation), related to Issue 10.

Changed

- [x] **Change** the mapping extension from using reasoner to direct assertions.
- [x] **Change** the name of pruning function in `deeponto.onto.OntologyPruner`.
- [x] **Change** the verbalisation function by setting quantifier words as optional (by default not adding).
- [x] **Change** sibing retrieval from using reasoner to direct assertions.

Fixed

- [x] **Fix** the minor bug for the `f1` and `MRR` method in `deeponto.align.evaluation.AlignmentEvaluator`.

Added

- [x] **Add** the ontology normaliser at `deeponto.onto.OntologyNormaliser`.
- [x] **Add** the ontology projector at `deeponto.onto.OntologyProjector`.

Changed

- [x] **Change** the dependency `transformers` to `transformers[torch]`.

Changed

- [x] **Change** Java dependencies from using `lib` from mowl to direct import.
- [x] **Change** `get_owl_object_annotations` by adding `uniqify` at the end to preserve the order.

Fixed

- [x] **Fix** BERTMap's non-synonym sampling when the class labels are not available using the try-catch block.

Added

- [x] **Add** the BERTSubs module at `deeponto.subs.bertsubs`; its inter-ontology setting is also imported at `deeponto.align.bertsubs`.

Changed

- [x] **Move** the pruning functionality into `deeponto.onto.OntologyPruner` as a separate module.
- [x] **Amend** JVM checking before displaying the JVM memory prompt from importing `deeponto.onto.Ontology`; if started already, skip this step.
- [x] **Change** the function `get_owl_object_annotations` at `deeponto.onto.Ontology` by preserving the relative order of annotation retrieval, i.e., create `set` first and use the `.add()` function instead of casting the `list` into `set` in the end.

Fixed

- [x] **Fix** the function `check_deprecated` at `deeponto.onto.Ontology` by adding a check for the $\texttt{owl:deprecated}$ annotation property -- if this property does not exist in the current ontology, return `False` (not deprecated).