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Fix release names in CHANGELOG.md [ci skip]
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althonos committed Jul 12, 2022
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122 changes: 61 additions & 61 deletions CHANGELOG.md
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Expand Up @@ -7,49 +7,49 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pronto/compare/v2.4.6...HEAD

## [2.4.7]
[2.4.7]: https://github.com/althonos/pronto/compare/v2.4.6...v2.4.7
## [v2.4.7]
[v2.4.7]: https://github.com/althonos/pronto/compare/v2.4.6...v2.4.7
### Fixed
- Serialization of `is_class_level` properties with `fastobo`-based serializers ([#178](https://github.com/althonos/pronto/issues/178)).
- Parsing of `SynonymTypeProperty` elements in RDF/XML without a label attribute ([#176](https://github.com/althonos/pronto/issues/176)).

## [2.4.6] - 2022-06-18
[2.4.6]: https://github.com/althonos/pronto/compare/v2.4.5...v2.4.6
## [v2.4.6] - 2022-06-18
[v2.4.6]: https://github.com/althonos/pronto/compare/v2.4.5...v2.4.6
### Added
- Setters for the `holds_over_chain` and `equivalent_to_chain` properties of `Relationship` objects.
### Fixed
- Serialization of `holds_over_chain` properties with `fastobo`-based serializers ([#175](https://github.com/althonos/pronto/issues/175)).

## [2.4.5] - 2022-04-21
[2.4.5]: https://github.com/althonos/pronto/compare/v2.4.4...v2.4.5
## [v2.4.5] - 2022-04-21
[v2.4.5]: https://github.com/althonos/pronto/compare/v2.4.4...v2.4.5
### Fixed
- Serialization of *metadata tag* relationships by `fastobo` ([#164](https://github.com/althonos/pronto/issues/164)).

## [2.4.4] - 2022-01-24
[2.4.4]: https://github.com/althonos/pronto/compare/v2.4.3...v2.4.4
## [v2.4.4] - 2022-01-24
[v2.4.4]: https://github.com/althonos/pronto/compare/v2.4.3...v2.4.4
### Added
- `OwlFunctionalSerializer` to dump an `Ontology` to OWL Functional-style syntax.
### Changed
- Bumped `fastobo` dependency to `v0.11.1`.
- Make `FastoboParser` raise a `SyntaxWarning` when encoutering creation dates that are not `datetime.datetime`.

## [2.4.3] - 2021-08-02
[2.4.3]: https://github.com/althonos/pronto/compare/v2.4.2...v2.4.3
## [v2.4.3] - 2021-08-02
[v2.4.3]: https://github.com/althonos/pronto/compare/v2.4.2...v2.4.3
### Added
- Missing documentation for the `pronto.Entity.relationships` property.
### Fixed
- RDX/XML parser crashing on files containing a relationship and a term with the same ID ([#138](https://github.com/althonos/pronto/pull/138)).

## [2.4.2] - 2021-05-26
[2.4.2]: https://github.com/althonos/pronto/compare/v2.4.1...v2.4.2
## [v2.4.2] - 2021-05-26
[v2.4.2]: https://github.com/althonos/pronto/compare/v2.4.1...v2.4.2
### Added
- Support for `chardet` version `4.0` (in addition to older `3.0`).
### Fixed
- Serialization of `Ontology` failing with non-empty `idspaces`.
- Typo in OWL2 URL in `README.md` ([#130](https://github.com/althonos/pronto/issues/130)).

## [2.4.1] - 2021-02-19
[2.4.1]: https://github.com/althonos/pronto/compare/v2.4.0...v2.4.1
## [v2.4.1] - 2021-02-19
[v2.4.1]: https://github.com/althonos/pronto/compare/v2.4.0...v2.4.1
### Changed
- `pronto.pv.PropertyValue` is now an abstract class.
- `pronto.parsers.RdfXmlParser` now ignores synonym Xrefs not in
Expand All @@ -65,8 +65,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Implicit injection of `lxml` instead of `xml.etree`, which caused
issues with `RdfXmlParser`.

## [2.4.0] - 2021-02-18
[2.4.0]: https://github.com/althonos/pronto/compare/v2.3.2...v2.4.0
## [v2.4.0] - 2021-02-18
[v2.4.0]: https://github.com/althonos/pronto/compare/v2.3.2...v2.4.0
### Added
- Deprecation warnings for the retrieval of relationships via
indexing, to be deprecated in `v3`.
Expand All @@ -78,8 +78,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
caused multiple issues ([#120](https://github.com/althonos/pronto/issues/120),
[#126](https://github.com/althonos/pronto/issues/126)).

## [2.3.2] - 2020-12-17
[2.3.2]: https://github.com/althonos/pronto/compare/v2.3.1...v2.3.2
## [v2.3.2] - 2020-12-17
[v2.3.2]: https://github.com/althonos/pronto/compare/v2.3.1...v2.3.2
### Added
- Support for path-like objects when creating an `Ontology`
([#108](https://github.com/althonos/pronto/pull/108)).
Expand All @@ -88,13 +88,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
encoded when creating an `Ontology`
([#110](https://github.com/althonos/pronto/pull/110)).

## [2.3.1] - 2020-09-21
[2.3.1]: https://github.com/althonos/pronto/compare/v2.3.0...v2.3.1
## [v2.3.1] - 2020-09-21
[v2.3.1]: https://github.com/althonos/pronto/compare/v2.3.0...v2.3.1
### Fixed
- `pronto.entity` package not being included in source distribution.

## [2.3.0] - 2020-09-21 - **YANKED**
[2.3.0]: https://github.com/althonos/pronto/compare/v2.2.4...v2.3.0
## [v2.3.0] - 2020-09-21 - **YANKED**
[v2.3.0]: https://github.com/althonos/pronto/compare/v2.2.4...v2.3.0
### Added
- Retrieval of entities via their alternate IDs on the source `Ontology`.
- Direct edition of entity relationships via the `Relationships` view.
Expand All @@ -120,18 +120,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- 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 [2.2.2].
- Various type annotations not updated since version [v2.2.2].

## [2.2.4] - 2020-09-11
[2.2.4]: https://github.com/althonos/pronto/compare/v2.2.3...v2.2.4
## [v2.2.4] - 2020-09-11
[v2.2.4]: https://github.com/althonos/pronto/compare/v2.2.3...v2.2.4
### 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.

## [2.2.3] - 2020-07-31
[2.2.3]: https://github.com/althonos/pronto/compare/v2.2.2...v2.2.3
## [v2.2.3] - 2020-07-31
[v2.2.3]: https://github.com/althonos/pronto/compare/v2.2.2...v2.2.3
### Changed
- Replaced `frozendict` with `immutabledict` ([#90](https://github.com/althonos/pronto/pull/90)).
- Bumped `fastobo` dependency to `v0.9.0` to support inline comments.
Expand All @@ -140,17 +140,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Argument type checking in view layer is now disabled during the parsing
phase to reduce overhead.

## [2.2.2] - 2020-07-18
[2.2.2]: https://github.com/althonos/pronto/compare/v2.2.1...v2.2.2
## [v2.2.2] - 2020-07-18
[v2.2.2]: https://github.com/althonos/pronto/compare/v2.2.1...v2.2.2
### 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.

## [2.2.1] - 2020-06-17
[2.2.1]: https://github.com/althonos/pronto/compare/v2.2.0...v2.2.1
## [v2.2.1] - 2020-06-17
[v2.2.1]: https://github.com/althonos/pronto/compare/v2.2.0...v2.2.1
### Fixed
- Extraction of subclasses/superclasses hierarchy from nested imports.
- Serialization of OBO frames not being done in order.
Expand All @@ -159,8 +159,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `ResourceWarning` when creating `Ontology` from file-handles not mapping
to a filesystem location.

## [2.2.0] - 2020-06-17
[2.2.0]: https://github.com/althonos/pronto/compare/v2.1.0...v2.2.0
## [v2.2.0] - 2020-06-17
[v2.2.0]: https://github.com/althonos/pronto/compare/v2.1.0...v2.2.0
### Added
- `threads` parameter to `Ontology` constructor to control the number of
threads used by parsers supporting multithreading (OBO and OBO JSON at
Expand All @@ -183,8 +183,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `nanoset` depency, which was not useful anymore in Python 3.8 and caused
issues with multithreading when processing OBO frames in parallel.

## [2.1.0] - 2020-03-23
[2.1.0]: https://github.com/althonos/pronto/compare/v2.0.1...v2.1.0
## [v2.1.0] - 2020-03-23
[v2.1.0]: https://github.com/althonos/pronto/compare/v2.0.1...v2.1.0
### 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))
Expand All @@ -200,8 +200,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `FastoboSerializer` crashing when encountering a relationship with
at least one `replaced_by` clause.

## [2.0.1] - 2020-02-19
[2.0.1]: https://github.com/althonos/pronto/compare/v2.0.0...v2.0.1
## [v2.0.1] - 2020-02-19
[v2.0.1]: https://github.com/althonos/pronto/compare/v2.0.0...v2.0.1
### Fixed
- Internal handling of ontology data forcing an `Ontology` to outlive all
of the `Term`s created from it.
Expand All @@ -213,8 +213,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Make `Term.is_leaf` use internal subclassing cache to make it run in
constant time.

## [2.0.0] - 2020-02-14
[2.0.0]:https://github.com/althonos/pronto/compare/v1.2.0...v2.0.0
## [v2.0.0] - 2020-02-14
[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`.
Expand All @@ -227,8 +227,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `SuperclassesIterator.to_set` being named `to_self` because of a typo.
- Several bugs affecting the `fastobo`-backed serializer.

## [1.2.0] - 2020-02-10
[1.2.0]: https://github.com/althonos/pronto/compare/v1.1.5...v1.2.0
## [v1.2.0] - 2020-02-10
[v1.2.0]: https://github.com/althonos/pronto/compare/v1.1.5...v1.2.0
### Added
- Parameter `with_self` to disable reflexivity of `Term.subclasses` and
`Term.superclasses` iterators.
Expand All @@ -246,40 +246,40 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
issue.
- `fastobo` parsers using data version clauses as format version clauses.

## [1.1.5] - 2020-01-25
[1.1.5]: https://github.com/althonos/pronto/compare/v1.1.4...v1.1.5
## [v1.1.5] - 2020-01-25
[v1.1.5]: https://github.com/althonos/pronto/compare/v1.1.4...v1.1.5
### Changed
- Bumped `fastobo` to `v0.7.0`, switching parser implementation to use
multi-threading in order to speedup the parser process.

## [1.1.4] - 2020-01-21
[1.1.4]: https://github.com/althonos/pronto/compare/v1.1.3...v1.1.4
## [v1.1.4] - 2020-01-21
[v1.1.4]: https://github.com/althonos/pronto/compare/v1.1.3...v1.1.4
### Added
- Explicit support for Python 3.8.
- Support for Windows-style line endings
([#53](https://github.com/althonos/pronto/issues/53))

## [1.1.3] - 2019-11-10
[1.1.3]: https://github.com/althonos/pronto/compare/v1.1.2...v1.1.3
## [v1.1.3] - 2019-11-10
[v1.1.3]: https://github.com/althonos/pronto/compare/v1.1.2...v1.1.3
### Fixed
- Handling of some clauses in `FastoboParser`.
- `OboSerializer` occasionaly missing lines between term and typedef frames.
### Added
- Missing docstrings to some `Entity` properties.

## [1.1.2] - 2019-10-30
[1.1.2]: https://github.com/althonos/pronto/compare/v1.1.1...v1.1.2
## [v1.1.2] - 2019-10-30
[v1.1.2]: https://github.com/althonos/pronto/compare/v1.1.1...v1.1.2
### Fixed
- `RdfXMLParser` crashing on entities with `rdf:label` elements
without literal content.

## [1.1.1] - 2019-10-29
[1.1.1]: https://github.com/althonos/pronto/compare/v1.1.0...v1.1.1
## [v1.1.1] - 2019-10-29
[v1.1.1]: https://github.com/althonos/pronto/compare/v1.1.0...v1.1.1
### Fixed
- `pronto.serializers` module not being embedded in Wheel distribution.

## [1.1.0] - 2019-10-24
[1.1.0]: https://github.com/althonos/pronto/compare/v1.0.0...v1.1.0
## [v1.1.0] - 2019-10-24
[v1.1.0]: https://github.com/althonos/pronto/compare/v1.0.0...v1.1.0
### Added
- `Entity.add_synonym` method to create a new synonym and add it to an entity.
- `@roundrepr` now adds a minimal docstring to the generated `__repr__` method.
Expand All @@ -296,8 +296,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `Synonym.type` getter crashing on `type` not being `None`.
- `RdfXMLParser` crashing on synonymtypedefs without scope specifiers.

## [1.0.0] - 2019-10-11
[1.0.0]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.3...v1.0.0
## [v1.0.0] - 2019-10-11
[v1.0.0]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.3...v1.0.0
### Fixed
- Issues with typedef serialization in `FastoboSerializer`.
- `Ontology.create_term` and `Ontology.create_relationship` not raising `ValueError`
Expand All @@ -307,8 +307,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### Changed
- Bumped `fastobo` requirement to `v0.6.0`.

## [1.0.0-alpha.3] - 2019-10-10
[1.0.0-alpha.3]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.2...v1.0.0-alpha.3
## [v1.0.0-alpha.3] - 2019-10-10
[v1.0.0-alpha.3]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.2...v1.0.0-alpha.3
### Added
- Extraction of `oboInOwl:consider` annotation in `RdfXMLParser`.
- Extraction of `oboInOwl:savedBy` annotation in `RdfXMLParser`.
Expand All @@ -330,15 +330,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
graph of dependencies already.
- Exposed `pronto.warnings` and the complete warnings hierarchy.

## [1.0.0-alpha.2] - 2019-10-03
[1.0.0-alpha.2]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.1...v1.0.0-alpha.2
## [v1.0.0-alpha.2] - 2019-10-03
[v1.0.0-alpha.2]: https://github.com/althonos/pronto/compare/v1.0.0-alpha.1...v1.0.0-alpha.2
### Added
- Support for extraction of relationships from OWL/XML files to `OwlXMLParser`.
### Fixed
- Type hints of `RelationshipData.synonyms` attribute.

## [1.0.0-alpha.1] - 2019-10-02
[1.0.0-alpha.1]: https://github.com/althonos/pronto/compare/v0.12.2...v1.0.0-alpha.1
## [v1.0.0-alpha.1] - 2019-10-02
[v1.0.0-alpha.1]: https://github.com/althonos/pronto/compare/v0.12.2...v1.0.0-alpha.1
### Changed
- Dropped support for Python earlier than `3.6`.
- Brand new data model that follow the OBO 1.4 object model.
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