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.
2.2.0 - 2020-06-17¶
Added¶
threads
parameter toOntology
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 ownerOntology
.Support for subclass/superclass edition directly from the objects returned by
Term.subclasses()
andTerm.superclasses()
. (#84)
Changed¶
Updated
fastobo
tov0.8
, 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.
2.1.0 - 2020-03-23¶
Added¶
Changed¶
Synonym.xrefs
now returns a mutable set that can be used to addXref
to the synonym directly.
2.0.1 - 2020-02-19¶
Fixed¶
Internal handling of ontology data forcing an
Ontology
to outlive all of theTerm
s created from it.Term.id
property missing a return type annotation.Term.equivalent_to
not returning aTermSet
but a set of strings.
Changed¶
Refactored implementation of
SubclassesIterator
andSuperclassesIterator
to make both use the interal subclassing cache.Make
Term.is_leaf
use internal subclassing cache to make it run in constant time.
2.0.0 - 2020-02-14¶
Added¶
TermSet.subclasses
andTermSet.superclasses
methods to query all
the subclasses / superclasses of allTerm
.TermSet
class to the top-levelpronto
module.Dynamic management of subclassing cache for the
Ontology
class.Setters for
Term.consider
,Term.union_of
andTerm.intersection_of
.
Removed¶
cache
keyword argument for theOntology
.
Fixed¶
SuperclassesIterator.to_set
being namedto_self
because of a typo.Several bugs affecting the
fastobo
-backed serializer.
1.2.0 - 2020-02-10¶
Added¶
Parameter
with_self
to disable reflexivity ofTerm.subclasses
andTerm.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
andTerm.superclasses
to a dedicated iterator class in thepronto.logic
submodule.Dropped
contexter
requirement.
Fixed¶
Fix a typo in
Synonym.type
setter leading to a potential bug when the giventype
isNone
.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.
1.1.5 - 2020-01-25¶
Changed¶
Bumped
fastobo
tov0.7.0
, switching parser implementation to use multi-threading in order to speedup the parser process.
1.1.3 - 2019-11-10¶
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¶
Fixed¶
RdfXMLParser
crashing on entities withrdf:label
elements without literal content.
1.1.0 - 2019-10-24¶
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.Ontology
caches subclassing relationships to greatly improve performance ofTerm.subclasses
.
Changed¶
Entity
subclasses now store theirid
directly to improve performance.Term.subclasses
andTerm.superclasses
usecollections.deque
instead ofqueue.Queue
as a LIFO structure since thread-safety is not needed.chardet
result is now used even when prediction confidence is under 100% to detect encoding of the handle passed toOntology
.
Fixed¶
SynonymType
comparison implementation.Synonym.type
getter crashing ontype
not beingNone
.RdfXMLParser
crashing on synonymtypedefs without scope specifiers.
1.0.0 - 2019-10-11¶
Fixed¶
Issues with typedef serialization in
FastoboSerializer
.Ontology.create_term
andOntology.create_relationship
not raisingValueError
when given an identifier already in the knowledge graph.Signature of
BaseSerializer.dump
to removeencoding
argument.Missing
__slots__
inEntity
in non-typechecking runtime.
Changed¶
Bumped
fastobo
requirement tov0.6.0
.
1.0.0-alpha.3 - 2019-10-10¶
Added¶
Extraction of
oboInOwl:consider
annotation inRdfXMLParser
.Extraction of
oboInOwl:savedBy
annotation inRdfXMLParser
.Extraction of
subsetdef
andsynonymtypedef
as annotation properties inRdfXMLParser
.Support for
doap:Version
instead ofowl:VersionIri
for specification of ontology data version.Proper comparison of
PropertyValue
classes, based on the lexicographic order of their serialization.Ontology.dump
andOntology.dumps
methods to serialize an ontology in obo or obojson format.
Fixed¶
Metadata
not storing optional description of ID spaces if any.Wrong type hints in
RelationshipData.equivalent_to_chain
.
Changed¶
Added type checking to some more property setters.
Avoid using
networkx
inTerm.subclasses
.fastobo
-derived parsers will not create a new entity if one exists in the graph of dependencies already.Exposed
pronto.warnings
and the complete warnings hierarchy.
1.0.0-alpha.2 - 2019-10-03¶
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¶
Changed¶
Dropped support for Python earlier than
3.6
.Brand new data model that follow the OBO 1.4 object model.
Partial OWL XML parser implementation using the OBO 1.4 semantics.
New OBO parser implementation based on
fastobo
.Imports are properly separated from the top-level ontology.
Ontology.__getitem__
can also access entities from imports.Term
,Relationship
,Xref
,SynonymType
compare only based on their ID.Subset
,Definition
compare only based on their textual value.
Added¶
Support for OBO JSON parser based on
fastobo
.Provisional
mypy
type hints.Type checking for most properties in
__debug__
mode.Proper
repr
implementation that should roundtrip most of the time.Detection of file format and encoding based on buffer content.
Removed¶
OBO and JSON serialization support (for now).
Term.rchildren
andTerm.rparents
and stop making direction assumptions on relationships.