Pronto

Added
- Retrieval of entities via their alternate IDs on the source `Ontology`.
- Direct edition of entity relationships via the `Relationships` view.
- `__all__` attribute to all modules of the data model.
- `RelationshipSet` container like `TermSet` with shortcut attributes and
proxying of actual `Relationship` instances.
- `Relationship.subproperties` and `Relationship.superproperties` methods
to add, remove, clear and iterate over the subproperties and superproperties
of a `Relationship` instance.
- `Ontology.synonym_types` method to count (via `SizedIterator`) and iterate
over the synonym types of an ontology and all of its imports.
- `Ontology.get_synonym_type` method to retrieve a single synonym type by ID
from an ontology or one of its imports.
Changed
- Management of sub-properties / super-properties is now consistent with
the management of subclasses / superclasses.
- `consider`, `disjoint_from`, `disjoint_over`, `equivalent_to`, `replaced_by`
`transitive_over` and `union_of` properties of `Relationship` now return
a `RelationshipSet`.
Fixed
- Outdated documentation in `Term.subclasses` describing the performances of
the previous algorithm.
- Possible `AttributeError` with the setter of the `Entity.synonyms` property.
- Issue with synonym types declared in imported ontologies not being usable
with synonyms of the actual ontology.
- Various type annotations not updated since version [v2.2.2].

Changed
- Make `Entity.annotations` return a mutable set and add a setter.
Fixed
- `Term.relationship` erroneously updating the `Ontology._lineage` cache.
- Unneeded code in `pronto.serializers._fastobo` handling `is_a` clauses.

Changed
- Replaced `frozendict` with `immutabledict` ([90](https://github.com/althonos/pronto/pull/90)).
- Bumped `fastobo` dependency to `v0.9.0` to support inline comments.
- Parsers will now process their imports in parallel using a thread pool.
Fixed
- Argument type checking in view layer is now disabled during the parsing
phase to reduce overhead.

Added
- Extraction of basic relationships from RDF/XML documents.
Fixed
- Erroneous type annotations on `Term.subclasses` and `Term.superclasses`.
- Bug with `Term.equivalent_to` setter crashing with a `NameError`.
- Bug with `Entity.synonyms` setter not extracting synonym data.

Fixed
- Extraction of subclasses/superclasses hierarchy from nested imports.
- Serialization of OBO frames not being done in order.
- Parsing issue with `anti_symmetric` clauses in OBO typedefs.
- Xrefs not being extracted when declared as axioms in RDF/XML documents.
- `ResourceWarning` when creating `Ontology` from file-handles not mapping
to a filesystem location.

Added
- `threads` parameter to `Ontology` constructor to control the number of
threads used by parsers supporting multithreading (OBO and OBO JSON at
the moment).
- Deprecation warnings for suspected uses of the `is_a` pseudo-relationship
since subclasses/superclasses is now to be handled by the owner `Ontology`.
- Support for subclass/superclass edition directly from the objects returned
by `Term.subclasses()` and `Term.superclasses()`. ([84](https://github.com/althonos/pronto/issues/84))
Changed
- Updated `fastobo` to `v0.8`, which reduce memory footprint of identifiers,
and improves the parser speed.
- Improved OBO parser performance using threading plus zero-copy validation
of identifiers on `Xref` instantiation.
- Improved performance in debug mode by having the typechecker only extract
the wrapped function signature once.
Fixed
- OBO parser crashing on files containing `idspace` clauses in their headers.
- Reference management issue with binary operations of `TermSet`.
Removed
- `nanoset` depency, which was not useful anymore in Python 3.8 and caused
issues with multithreading when processing OBO frames in parallel.