Pronto

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.

Added
- `Synonym.xrefs` now has a setter. ([70](https://github.com/althonos/pronto/issues/70))
- `pickle` support for `Ontology`. ([66](https://github.com/althonos/pronto/issues/66))
- `RdfXmlParser` support for `owl:inverseOf` and `rdfs:subPropertyOf`.
Changed
- `Synonym.xrefs` now returns a mutable set that can be used to add
`Xref` to the synonym directly.
Fixed
- `SynonymType.type` setter does not consider all synonym types as
undeclared anymore. ([71](https://github.com/althonos/pronto/issues/71))
- `RdfXmlParser` crashing on synonym types definition without a label
like in Uberon. ([67](https://github.com/althonos/pronto/issues/67))
- `FastoboSerializer` crashing when encountering a relationship with
at least one `replaced_by` clause.

Fixed
- Internal handling of ontology data forcing an `Ontology` to outlive all
of the `Term`s created from it.
- `Term.id` property missing a return type annotation.
- `Term.equivalent_to` not returning a `TermSet` but a set of strings.
Changed
- Refactored implementation of `SubclassesIterator` and
`SuperclassesIterator` to make both use the interal subclassing cache.
- Make `Term.is_leaf` use internal subclassing cache to make it run in
constant time.

[v2.0.0]:https://github.com/althonos/pronto/compare/v1.2.0...v2.0.0
Added
- `TermSet.subclasses` and `TermSet.superclasses` methods to query all
the subclasses / superclasses of all `Term`.
- `TermSet` class to the top-level `pronto` module.
- Dynamic management of subclassing cache for the `Ontology` class.
- Setters for `Term.consider`, `Term.union_of` and `Term.intersection_of`.
Removed
- `cache` keyword argument for the `Ontology`.
Fixed
- `SuperclassesIterator.to_set` being named `to_self` because of a typo.
- Several bugs affecting the `fastobo`-backed serializer.

Added
- Parameter `with_self` to disable reflexivity of `Term.subclasses` and
`Term.superclasses` iterators.
- `TermSet` class which stores a set of terms efficiently while providing
some useful shortcuts to access the underlying data.
Changed
- Moved code of `Term.subclasses` and `Term.superclasses` to a dedicated
iterator class in the `pronto.logic` submodule.
- Dropped `contexter` requirement.
Fixed
- Fix a typo in `Synonym.type` setter leading to a potential bug when
the given `type` is `None`.
- Fix miscellaneous bugs found with `mypy`.
- `fastobo` serializer crashing on namespace clauses because of a type
issue.
- `fastobo` parsers using data version clauses as format version clauses.

Changed
- Bumped `fastobo` to `v0.7.0`, switching parser implementation to use
multi-threading in order to speedup the parser process.