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¶
v0.12.3 - 2023-12-06¶
Added¶
Explicit support for Python 3.12.
Changed¶
Bump
pyo3
tov0.19.2
.Make
DisconnectedChannelError
inherit fromRuntimeError
instead ofChildProcessError
.
v0.12.2 - 2022-12-06¶
Added¶
Explicit support for Python 3.11.
Pre-built wheels for MacOS
aarch64
platforms.
Changed¶
Bump
pyo3
tov0.17.3
.Bump
fastobo
tov0.15.1
.Bump
fastobo-graphs
tov0.4.8
.
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 tov0.16
.Intern constant strings returned by
raw_tag
methods of clause objects.
Fixed¶
Compilation of
fastobo
extension with newersetuptools-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 (usingfastobo-owl
andhorned-owl
) in Functional-style syntax (usinghorned-functional
).
Changed¶
Bumped
fastobo
tov0.14.0
.Bumped
fastobo-graphs
tov0.4.4
.DateClause
may now store adatetime.date
instead of adatetime.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 latestsetuptools_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 tov0.14.1
.
Fixed¶
fastobo.iter
erroneously wrappingSyntaxError
raised in the header into aTypeError
.
v0.10.1 - 2021-03-30¶
Changed¶
Bumped
fastobo
dependency tov0.13.1
.
Fixed¶
Curly braces not being properly escaped when writing unquoted strings.
v0.10.0 - 2021-02-19¶
Added¶
__hash__
implementation tofastobo.id.BaseIdent
subclasses.__init__
method to classes missing one infastobo.header
.
Changed¶
Bumped
pyo3
dependency tov0.13.2
.Bumped
fastobo
dependency tov0.13.0
.
Fixed¶
Broken
__repr__
implementation for some types.
Removed¶
unsafe
blocks in derive macros implementation ofIntoPyObject
for OBO clauses.Support for Python 3.5.
fastobo.id.IdentPrefix
andfastobo.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
tov0.11.2
.
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
tov0.10.0
to support comment lines.Bumped
pyo3
tov0.11.1
.
Fixed¶
fastobo.id.parse
will chain the eventualSyntaxError
to theValueError
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
tov0.9.0
.Bumped
fastobo-graphs
tov0.3.0
.
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
tov0.8.4
.Bumped
pyo3
tov0.10.1
.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
andfastobo.loads
using thethreads
keyword argument.
v0.7.2 - 2020-02-12¶
Changed¶
Bumped
fastobo
tov0.8.3
to fixDisplay
implementation offastobo::ast::IsoDateTime
.
v0.7.1 - 2020-02-11¶
Changed¶
Bumped
fastobo
tov0.8.2
to fixDisplay
implementation ofHeaderClause::Unreserved
variant.Bumped
built
build-dependency tov0.4.0
.
v0.7.0 - 2020-01-24¶
Changed¶
Bumped
fastobo
tov0.8.1
to use multi-threaded parser implementation.Added
ordered
keyword argument to top-levelfastobo
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
tov0.7.5
, 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 infastobo.typdef
submodule.fastobo.id
module performing unneeded string allocation.
v0.6.0 - 2019-10-08¶
Added¶
__init__
to all classes offastobo.typedef
.
Changed¶
Renamed
term
field offastobo.typedef.Relationship
totarget
.
v0.5.4 - 2019-10-08¶
Added¶
__init__
implementation forfastobo.doc.OboDoc
.__init__
implementation forfastobo.term.ConsiderClause
.__init__
implementation forfastobo.term.IsObsoleteClause
.Add constructor signatures to classes in
fastobo.term
andfastobo.header
.
Changed¶
Bumped
pyo3
dependency tov0.8.1
.
Fixed¶
Automatic generation of
pyproject.toml
insdist
.
v0.5.3 - 2019-10-06¶
Added¶
__init__
anddate
getter toCreationDateClause
in bothfastobo.term
andfastobo.typedef
with proper timezone support.
v0.5.2 - 2019-09-28¶
Added¶
Getters for
ReplacedByClause
infastobo.typedef
.
Fixed¶
PyFileGILRead
(used infastobo.iter
) should now be thread safe.
v0.5.1 - 2019-09-19¶
Added¶
Getters for
ExpandExpressionToClause
andExpandAssertionToClause
infastobo.typedef
.
Fixed¶
Missing
NamespaceIdRuleClause
class is now a member offastobo.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 forError
.
Changed¶
OboDoc
cannot be subclassed anymore.
v0.4.2 - 2019-09-16¶
Added¶
Getters for
IsClassLevelClause
andIsMetadataTag
infastobo.typedef
.Getters for
RelationshipClause
infastobo.term
.
Changed¶
Inconsistent naming for
PropertyValueClause
betweenfastobo.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 forfastobo.term.DefClause
__init__
implementation forfastobo.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
TypeError
s.Enabled
extension-module
feature ofpyo3
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 tofastobo.id.PrefixedIdent
.
Changed¶
Bumped Rust dependencies to latest PyO3 version.
v0.3.1 - 2019-08-08¶
Fixed¶
PyFile.write
callingwrite
with two arguments causing duck typing check to fail all the time indump_graph
.
v0.3.0 - 2019-08-08¶
Added¶
load_graph
anddump_graph
functions to read and write OBO JSON files.
Changed¶
Updated to
fastobo
v0.7.1.
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¶
Updated to
fastobo
v0.6.0.
Fixed¶
Parser now accepts ISO 8601 dates with fractional second.
v0.2.0 - 2019-07-22¶
Changed¶
Updated to
fastobo
v0.5.0.
Added¶
Support for OBO graph deserialization using
fastobo-graphs
.Limited support for instance frames in
fastobo.instance
module.Methods
OboDoc.compact_ids
andOboDoc.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.