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.

v0.12.2 - 2022-12-06

Added

  • Explicit support for Python 3.11.

  • Pre-built wheels for MacOS aarch64 platforms.

Changed

  • Bump pyo3 to v0.17.3.

  • Bump fastobo to v0.15.1.

  • Bump fastobo-graphs to v0.4.8.

v0.12.1 - 2022-07-08

Changed

  • Stop releasing the GIL when loading an ontology from a file to fix Windows compilation.

v0.12.0 - 2022-07-08

Changed

  • Improve handling of exceptions in Rust code.

  • Bump pyo3 dependency to v0.16.

  • Intern constant strings returned by raw_tag methods of clause objects.

Fixed

  • Compilation of fastobo extension with newer setuptools-rust versions (#300).

Removed

  • Support for Python 3.6.

v0.11.1 - 2022-01-23

Fixed

  • Extraction of date argument when creating a CreationDateClause.

  • Skip displaying empty xrefs in fastobo.typedef.DefClause.__repr__.

v0.11.0 - 2022-01-23

Added

  • fastobo.exceptions module with dedicated exception types to report specific errors.

  • fastobo.dump_owl to convert and write an OBO document to an OWL ontology (using fastobo-owl and horned-owl) in Functional-style syntax (using horned-functional).

Changed

  • Bumped fastobo to v0.14.0.

  • Bumped fastobo-graphs to v0.4.4.

  • DateClause may now store a datetime.date instead of a datetime.datetime if the source document contains a date without time specifier.

  • PyPI source distribution now contains vendored Rust sources, allowing compilation without network access.

Fixed

  • setup.py script not auto-installing the Rust compiler in latest setuptools_rust versions.

v0.10.2-post1 - 2021-09-19

Added

  • Aarch64 wheels built from GitHub Actions and deployed to PyPI (#245).

v0.10.2 - 2021-08-02

Changed

  • Bumped pyo3 dependency to v0.14.1.

Fixed

  • fastobo.iter erroneously wrapping SyntaxError raised in the header into a TypeError.

v0.10.1 - 2021-03-30

Changed

  • Bumped fastobo dependency to v0.13.1.

Fixed

  • Curly braces not being properly escaped when writing unquoted strings.

v0.10.0 - 2021-02-19

Added

  • __hash__ implementation to fastobo.id.BaseIdent subclasses.

  • __init__ method to classes missing one in fastobo.header.

Changed

  • Bumped pyo3 dependency to v0.13.2.

  • Bumped fastobo dependency to v0.13.0.

Fixed

  • Broken __repr__ implementation for some types.

Removed

  • unsafe blocks in derive macros implementation of IntoPyObject for OBO clauses.

  • Support for Python 3.5.

  • fastobo.id.IdentPrefix and fastobo.id.IdentLocal classes.

v0.9.3 - 2020-12-04

Fixed

  • setup.py crashing when compiling from source on a platform with stable Rust as the default toolchain (#182, thanks to @alexhenrie).

v0.9.2 - 2020-09-04

Changed

  • Bumped fastobo to v0.11.2.

v0.9.1 - 2020-08-15

Added

  • Wheel compilation for older OSX versions.

  • Automatic download on UNIX platforms for platforms without rustc installing from source distribution.

v0.9.0 - 2020-07-29

Changed

  • Bumped fastobo to v0.10.0 to support comment lines.

  • Bumped pyo3 to v0.11.1.

Fixed

  • fastobo.id.parse will chain the eventual SyntaxError to the ValueError raised if the identifier is invalid.

  • Python threads are now released during intensive operations running only on the Rust side.

v0.8.2 - 2020-06-16

Fixed

  • OboDoc not implementing list methods (.append, etc.).

v0.8.1 - 2020-06-14

Changed

  • Bumped fastobo to v0.9.0.

  • Bumped fastobo-graphs to v0.3.0.

Added

  • fastobo.id.is_valid function to check whether or not a string is a valid OBO identifier.

v0.8.0 - 2020-06-12

Changed

  • Bumped fastobo to v0.8.4.

  • Bumped pyo3 to v0.10.1.

  • Removed occurences of unsafe code for Python type management.

  • Reduced number of GIL acquisition where possible.

  • Changed implementation of file wrappers to use PyAny where applicable.

Added

  • Configuratble support for multithreading in fastobo.iter, fastobo.load and fastobo.loads using the threads keyword argument.

v0.7.2 - 2020-02-12

Changed

  • Bumped fastobo to v0.8.3 to fix Display implementation of fastobo::ast::IsoDateTime.

v0.7.1 - 2020-02-11

Changed

  • Bumped fastobo to v0.8.2 to fix Display implementation of HeaderClause::Unreserved variant.

  • Bumped built build-dependency to v0.4.0.

v0.7.0 - 2020-01-24

Changed

  • Bumped fastobo to v0.8.1 to use multi-threaded parser implementation.

  • Added ordered keyword argument to top-level fastobo function to disable requirement to parse the document in order-preserving mode.

v0.6.2 - 2020-01-18

Added

  • Compilation of Python 3.8, PyPy 3.5 and PyPy 3.6 wheels for OSX.

Fixed

  • Bumped fastobo to v0.7.5, which should finally support Windows style line-endings.

v0.6.1 - 2019-11-19

Added

  • Compilation of Python 3.8 wheels for Linux and Windows (#67).

Fixed

  • BaseTypedefClause not being declared in fastobo.typdef submodule.

  • fastobo.id module performing unneeded string allocation.

v0.6.0 - 2019-10-08

Added

  • __init__ to all classes of fastobo.typedef.

Changed

  • Renamed term field of fastobo.typedef.Relationship to target.

v0.5.4 - 2019-10-08

Added

  • __init__ implementation for fastobo.doc.OboDoc.

  • __init__ implementation for fastobo.term.ConsiderClause.

  • __init__ implementation for fastobo.term.IsObsoleteClause.

  • Add constructor signatures to classes in fastobo.term and fastobo.header.

Changed

  • Bumped pyo3 dependency to v0.8.1.

Fixed

  • Automatic generation of pyproject.toml in sdist.

v0.5.3 - 2019-10-06

Added

  • __init__ and date getter to CreationDateClause in both fastobo.term and fastobo.typedef with proper timezone support.

v0.5.2 - 2019-09-28

Added

  • Getters for ReplacedByClause in fastobo.typedef.

Fixed

  • PyFileGILRead (used in fastobo.iter) should now be thread safe.

v0.5.1 - 2019-09-19

Added

  • Getters for ExpandExpressionToClause and ExpandAssertionToClause in fastobo.typedef.

Fixed

  • Missing NamespaceIdRuleClause class is now a member of fastobo.header.

v0.5.0 - 2019-09-18

Added

  • fastobo.iter function to iterate over the entity frames of an OBO document.

  • From<std::io::Error> impl for Error.

Changed

  • OboDoc cannot be subclassed anymore.

v0.4.2 - 2019-09-16

Added

  • Getters for IsClassLevelClause and IsMetadataTag in fastobo.typedef.

  • Getters for RelationshipClause in fastobo.term.

Changed

  • Inconsistent naming for PropertyValueClause between fastobo.header and other submodules.

Fixed

  • Bug with fastobo.header.ImportClause.reference returning the whole clause serialization instead.

v0.4.1 - 2019-09-15

Added

  • Precompiled wheels for CPython 3.5, 3.6 and 3.7 on Windows x86-64.

v0.4.0 - 2019-09-14

Added

  • __init__ implementation for fastobo.term.DefClause

  • __init__ implementation for fastobo.syn.Synonym

  • Precompiled wheels for PyPy3 on OSX and Linux.

Fixed

  • XrefList.__repr__ implementation entering infinite recursion.

  • Derive macros generating weird error messages for some TypeErrors.

  • Enabled extension-module feature of pyo3 to allow static linking to Python interpreter.

  • Inconsistent error-chaining in Python causing issues with try/except blocks.

v0.3.3 - 2019-09-10

Changed

  • Use stable PyO3 release (v0.8.0).

  • Add back __build__ attribute to check build variables.

v0.3.2 - 2019-08-29

Added

  • Added BOSC 2019 poster reference to README.md.

  • Added __richcmp__ implementation to fastobo.id.PrefixedIdent.

Changed

  • Bumped Rust dependencies to latest PyO3 version.

v0.3.1 - 2019-08-08

Fixed

  • PyFile.write calling write with two arguments causing duck typing check to fail all the time in dump_graph.

v0.3.0 - 2019-08-08

Added

  • load_graph and dump_graph functions to read and write OBO JSON files.

Changed

v0.2.2 - 2019-07-24

Changed

  • Updated to fastobo v0.6.1.

  • Updated to url v2.0.0.

v0.2.1 - 2019-07-23

Changed

Fixed

  • Parser now accepts ISO 8601 dates with fractional second.

v0.2.0 - 2019-07-22

Changed

Added

  • Support for OBO graph deserialization using fastobo-graphs.

  • Limited support for instance frames in fastobo.instance module.

  • Methods OboDoc.compact_ids and OboDoc.decompact_ids to create semantically equivalent OBO document with compacted/decompacted identifiers.

v0.1.1 - 2019-06-28

Fixed

  • PyPI release not being uploaded because of older development release.

v0.1.0 - 2019-06-28

Initial release.