A Python frontend to (Open Biomedical) Ontologies.
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Published by althonos over 4 years ago
threads
parameter to Ontology
constructor to control the number ofis_a
pseudo-relationshipOntology
.Term.subclasses()
and Term.superclasses()
. (#84)fastobo
to v0.8
, which reduce memory footprint of identifiers,Xref
instantiation.idspace
clauses in their headers.TermSet
.nanoset
depency, which was not useful anymore in Python 3.8 and causedPublished by althonos over 4 years ago
Published by althonos over 4 years ago
Ontology
to outlive allTerm
s created from it.Term.id
property missing a return type annotation.Term.equivalent_to
not returning a TermSet
but a set of strings.SubclassesIterator
andSuperclassesIterator
to make both use the interal subclassing cache.Term.is_leaf
use internal subclassing cache to make it run inPublished by althonos over 4 years ago
TermSet.subclasses
and TermSet.superclasses
methods to query allTerm
.TermSet
class to the top-level pronto
module.Ontology
class.Term.consider
, Term.union_of
and Term.intersection_of
.cache
keyword argument for the Ontology
.SuperclassesIterator.to_set
being named to_self
because of a typo.fastobo
-backed serializer.Published by althonos over 4 years ago
with_self
to disable reflexivity of Term.subclasses
andTerm.superclasses
iterators.TermSet
class which stores a set of terms efficiently while providingTerm.subclasses
and Term.superclasses
to a dedicatedpronto.logic
submodule.contexter
requirement.Synonym.type
setter leading to a potential bug whentype
is None
.mypy
.fastobo
serializer crashing on namespace clauses because of a typefastobo
parsers using data version clauses as format version clauses.Published by althonos almost 5 years ago
fastobo
to v0.7.0
, switching parser implementation to usePublished by althonos almost 5 years ago
FastoboParser
.OboSerializer
occasionaly missing lines between term and typedef frames.Entity
properties.Published by althonos almost 5 years ago
RdfXMLParser
crashing on entities with rdf:label
elementsPublished by althonos almost 5 years ago
pronto.serializers
module not being embedded in Wheel distribution.Published by althonos about 5 years ago
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
.Entity
subclasses now store their id
directly to improve performance.Term.subclasses
and Term.superclasses
use collections.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%Ontology
.SynonymType
comparison implementation.Synonym.type
getter crashing on type
not being None
.RdfXMLParser
crashing on synonymtypedefs without scope specifiers.Published by althonos about 5 years ago
FastoboSerializer
.Ontology.create_term
and Ontology.create_relationship
not raising ValueError
BaseSerializer.dump
to remove encoding
argument.__slots__
in Entity
in non-typechecking runtime.fastobo
requirement to v0.6.0
.Published by althonos about 5 years ago
oboInOwl:consider
annotation in RdfXMLParser
.oboInOwl:savedBy
annotation in RdfXMLParser
.subsetdef
and synonymtypedef
as annotation properties inRdfXMLParser
.doap:Version
instead of owl:VersionIri
for specificationPropertyValue
classes, based on the lexicographic orderOntology.dump
and Ontology.dumps
methods to serialize an ontology inMetadata
not storing optional description of ID spaces if any.RelationshipData.equivalent_to_chain
.networkx
in Term.subclasses
.fastobo
-derived parsers will not create a new entity if one exists in thepronto.warnings
and the complete warnings hierarchy.Published by althonos about 5 years ago
OwlXMLParser
.RelationshipData.synonyms
attribute.Published by althonos about 5 years ago
3.6
.fastobo
.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.fastobo
.mypy
type hints.__debug__
mode.repr
implementation that should roundtrip most of the time.Term.rchildren
and Term.rparents
and stop making direction assumptions on relationships.Published by althonos almost 7 years ago
Published by althonos almost 7 years ago
sdist
format to release a zip filePublished by althonos almost 7 years ago
OwlXMLTargetParser
Description
class inheriting from string to hold xrefs__init__.py
: import pronto
will failOntology
test
and dev
extrasPublished by althonos about 7 years ago