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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.15.2 - 2023-05-04

Changed

  • Bump darling derive dependency to v0.20.
  • Bump syn derive dependency to v2.0.

v0.15.1 - 2022-02-15

Added

  • IntoIterator trait implementation for &QualifierList and &mut QualifierList.
  • fastobo::syntax::pest re-exporting the pest crate to use with fastobo::syntax.

Changed

  • Bump smartstring dependency to v1.0.
  • Bump obofoundry test dependency to v0.10.
  • Bump fastobo-syntax to v0.7.4.
  • Bump darling derive dependency to v0.14.
  • Bump ordered-float dependency to v3.4.0.

v0.15.0 - 2022-02-15

Added

  • as_id and as_id_mut methods to Ident newtype wrappers.
  • as_prefixed, as_unprefixed and as_url methods to destructurate Ident variants.

Changed

  • Shorten Frame and EntityFrame methods by removing the _frame suffix where applicable.

v0.14.2 - 2022-02-11

Added

  • Conversion traits to build a TermClause or TypedefClause from a Synonym or PropertyValue.
  • Unescaping of IRI containing OBO-escaped path components.

Fixed

  • Parsing of Url identifiers with a scheme different of HTTP.

v0.14.1 - 2022-01-11

Fixed

  • Rendering of documentation on docs.rs.

v0.14.0 - 2022-01-11

Added

  • IsoDate and IsoTime to manage individuals components of an IsoDateTime.
  • CreationDate to store the date declared in a creation_date clause.
  • Display and Orderable trait implementations for ast::Frame.

Changed

  • Bump fastobo-syntax dependency to v0.7.1.
  • Use string interning for all identifier types allowing reference counting for common strings.
  • fastobo::parser::FromPair trait now takes a cache argument for interning strings.
  • XrefList::from_pair and QualifierList::from_pair will now use Xref::from_pair and Qualifier::from_pair instead of FromStr::from_str like before.

Fixed

  • OboDoc.assign_namespaces will not raise a CardinalityError on documents where all entities already have a namespace clause.
  • OboDoc.sort will not clone identifiers anymore before comparing entities.

v0.13.2 - 2022-01-11

Fixed

  • fastobo::to_writer not writing newlines between entity frames.

v0.13.1 - 2021-03-30

Added

  • Missing implementation of fastobo::ast::PrefixedIdent::is_canonical.

Fixed

  • Curly braces not being escaped from fastobo::ast::UnquotedString.

v0.13.0 - 2021-02-18

Changed

  • Make PrefixedIdent store both ID components contiguously and make it immutable.
  • Bumped outdated dependencies.
  • Replaced err-derive with thiserror to derive std::error::Error on error types.

Fixed

  • Compilation issues caused by latest version of syn.

Removed

  • fastobo::ast::id::local module.

v0.12.0 - 2020-09-29

Added

  • fastobo::ast::Url struct replacing url::Url to store URL identifiers.

Changed

  • Removed url crate dependency.
  • Bumped fastobo-syntax dependency to v0.6.2 to fix parsing of some URLs with empty paths lacking a trailing slash (e.g. http://example.com).

v0.11.2 - 2020-09-04

Fixed

  • Serialization of SynonymTypedef header clauses not using the correct tag. (pronto#97).

v0.11.1 - 2020-08-31

Changed

v0.11.0 - 2020-08-29

Added

  • Derived Default implementation for QuotedString and UnquotedString types.
  • PropertyValue variants now have actual corresponding structs fastobo::ast::ResourcePropertyValue and fastobo::ast::LiteralPropertyValue.
  • Definition struct to store text and xrefs of a definition clause.
  • EntityFrame.definition (and corresponding method for all entity frames) to get the definition of an entity frame if it is unique.

Changed

  • Enum types use boxed fields to reduce the memory footprint of their variant.
  • Bumped fastobo-syntax dependency to v0.6.1 to allow any datatype identifier for literal property values instead of XML Schema ones previously.
  • Made some optional fields of structs heap-allocated to further reduce memory consumption.

Removed

  • Dependency on opaque-typedef, which was pulling an outdated syn version in the dependencies and greatly increasing build time.

v0.10.0 - 2020-07-24

Added

  • smartstring feature to enable using the smartstring crate to store strings instead of std::string::String.
  • Additional blanket implementations for visit::Visit and visit::VisitMut traits using the blanket crate.
  • fastobo::parser::Parser to factor common operations on available OBO parsers.

Changed

  • Bumped fastobo-syntax dependency to v0.4.0 to support line comments.
  • Moved fastobo-syntax re-exports to fastobo::syntax.
  • Renamed fastobo::parser structs.

v0.9.0 - 2020-06-14

Removed

  • fastobo::share module.

Changed

  • IdentPrefix and IdentLocal do not store whether they are canonical or not to reduce the global memory footprint.

v0.8.4 - 2020-06-12

Changed

  • Relax exact version requirement for pest dependency.

Added

  • SequentialParser.into_inner method allowing to retrieve inner BufRead from a SequentialParser instance.

v0.8.3 - 2020-02-12

Fixed

  • IsoDateTime formatting in DD-MM-YYYY format instead of YYYY-MM-DD format when serialized to xsd:datetime.

v0.8.2 - 2020-02-11

Fixed

  • Display implementation for the HeaderClause::Unreserved variant.

v0.8.1 - 2020-01-24

Added

  • FrameReader.ordered method to make the reader preserve the order of the frames as they appear in the source document.
  • TryFrom<&mut FrameReader> implementation for OboDoc (allows giving a mutable reference and not only taking ownership of the source reader).

v0.8.0 - 2020-01-23

Added

  • Parallel FrameReader implementation compiled under the threading feature gate.

Fixed

  • Location of syntax errors not being reported properly in most cases.

Changed

  • Interface of fastobo::parser::FrameReader to be more intuitive to use.
  • Bumped fastobo-syntax to 0.3.8 to support indentation within files.

v0.7.5 - 2020-01-18

Changed

  • Bumped fastobo-syntax to 0.3.7 to support Windows-style line breaks.

v0.7.4 - 2019-10-05

Changed

  • Bumped fastobo-syntax to 0.3.6 to fix an edge-case bug when parsing a Synonym.

Added

  • IsoDateTime.timezone accessor to get the underlying IsoTimeZone.

v0.7.3 - 2019-09-17

Added

  • FrameReader.as_ref and FrameReader.as_mut to get a reference to the underlying BufRead.

v0.7.2 - 2019-08-27

Changed

  • Bumped syn and quote to version 1.0 in derive macros.

Added

  • Added BOSC 2019 poster reference to README.md.

v0.7.1 - 2019-08-08

Changed

  • Updated documentation.

v0.7.0 - 2019-08-06

Added

  • Line.as_inner_mut method (alias for Line.as_mut).
  • OboDoc.is_empty method to check if an ontology is empty.
  • fastobo::from_file, fastobo::from_reader, fastobo::from_str, fastobo::to_writer and fastobo::to_file.
  • AsRef<Ident> implementation for Ident.

Changed

  • Require exact pest version 2.1.1 because of unsafe hack to access PestError fields.

Removed

  • OboDoc::from_file and OboDoc::from_stream methods (replaced with fastobo::from_file and fastobo::from_reader).

Fixed

  • Serialization of UnquotedString not escaping ! characters.

v0.6.1 - 2019-07-24

Changed

  • Bumped internal url dependency to v2.0.0.

v0.6.0 - 2019-07-23

Added

  • fraction method to Iso8601DateTime.

Fixed

  • Iso8601DateTime now support parsing ISO datetimes with fractional seconds.

v0.5.0 - 2019-07-15

Changed

  • Transitioned to err-derive for error management instead of failure.

v0.4.4 - 2019-07-08

Added

  • fastobo::visit::IdCompactor and fastobo::visit::IdDecompactor to handle url to prefixed ident conversion in OBO documents.

v0.4.3 - 2019-06-17

Fixed

  • HeaderFrame.sort to avoid shuffling OwlAxiom header clauses.

Added

  • HeaderFrame.merge_owl_axioms method to merge OWL axioms in a header frame.

v0.4.2 - 2019-06-13

Fixed

  • Cardinality::to_error not returning an error for ZeroOrOne clauses present twice in a frame.

v0.4.1 - 2019-06-13

Fixed

  • TermClause::PropertyValue having invalid ZeroOrOne cardinality

v0.4.0 - 2019-06-12

Added

  • Parsing iterator implementation in fastobo::parser::FrameReader
  • fastobo-derive-internal proc-macros to reduce code boilerplate.
  • OboClause and OboFrame traits with common operations for all clauses/frames in an OBO document.
  • Cardinality enum which can be retrieved from any OboClause variant with the cardinality method.
  • OboDoc.is_fully_labeled semantic check.

Changed

  • Decomposed errors into smaller errors: the main Error now wraps CardinalityError, IOError and SyntaxError which can be accessed independently.

Removed

  • Removed OboSemantics trait and added functions to OboDoc directly.

Fixed

  • Bug causing XrefList to be parsed incorrectly when having a comma in their quote-enclosed description.

v0.3.0 - 2019-05-27

Changed

  • Renamed variants of PropertyValue and PropVal enums.

v0.2.1 - 2019-05-24

Fixed

  • InstanceFrame::from_pair_unchecked being implemented but not used in EntityFrame::from_pair_unchecked, causing a panic when parsing an OBO document with instance frames.

v0.2.0 - 2019-05-14

Added

  • Orderable trait for syntax structs that must be serialized in a particular order (e.g. EntityFrame, XrefList, OboDoc, ...).
  • Identified trait for syntax structs that have an identifier (e.g. EntityFrame, Qualifier, ...).
  • Support for is_asymmetric typedef clause.

Fixed

  • Error::IOError and Error::ParserError will now return their inner error when calling the Fail.cause method.

v0.1.1 - 2019-05-10

Added

  • PartialOrd implementation for header clauses, identifiers, Synonym and PropertyValue.

Fixed

  • Removed missing docs feature from docs.rs build metadata.
  • Changed links to refer to the new outsourced repository fastobo/fastobo.

v0.1.0 - 2019-05-08

Initial release.