pronto
A Python frontend to (Open Biomedical) Ontologies.
MIT License
Ecosystems:
Python
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pronto
- v0.6.1
Published by althonos almost 8 years ago
- Fix
requirements-test.txtnot being embedded in the wheelfile
pronto
- v0.6.0
Published by althonos almost 8 years ago
- Completely rewrote Parsers in a Pythonic, non-multiprocessed way
- Remove lxml from requirements. pronto now looks for any
available xml parser among (in that order): lxml,
xml.etree.cElementTree, xml.etree.ElementTree. - Added a second OwlXML parser using a TargetCollector instead of
building a tree, that is longer but less memory-hungry - Added a 'parser' kwarg to Ontology to force usage of a parser.
- Removed Parser being imported with 'from pronto import *'
- Implemented partial Unicode sandwich, at least in Relationship.
Complete use of unicode internals is a v1.0.0 requirement. - Added a try/except block to use enums if available to represent
the current section of the files parsers are exploring - Ensured PyPy support
- Add full support in Python3 and partial support in Python2 of
gzipped files parsing. - Refactored tests. Now all tests are run through the unittest
interface, even doctest. - Cleaned dead code
pronto
- v0.5.0
Published by althonos almost 8 years ago
- Use six functions when possible
- Add try/except blocks to pronto/init.py (will stop raising ImportError if six is not installed)
- Add support for obo defined relationships (typedef)
- Add support for gzipped ontology files
- Revert to nested loops in Ontology.reference (may improve performance in versions other than 3.5)
pronto
- v0.4.2
Published by althonos almost 8 years ago
- Fix obo export with utf-8 chars
pronto
- v0.4.1
Published by althonos almost 8 years ago
- Fix owl parser
- Fix obo export on headerless ontology files
pronto
- v0.4.0
Published by althonos about 8 years ago
- Changed Term obo export to be more compliant with the Obo File Format
- Added metadata extraction of Owl files (for now, only oboInOwl tags are supported, but more xml namespaces will be added
- Added obo export of metadata (Obo headers)
- Switched imports to absolute imports
- Reversed to the stdlib multiprocessing.queues.Queue implementation. This should fix both deadlocks and #4, but sometimes produces a BrokenPipeError in background processes after the end of the parsing...
- Enhanced API documentation
- Fixed occasional duplication of Terms in TermList
pronto
- v0.3.3
Published by althonos about 8 years ago
- Attempted compatibility patch for multiprocessing to work with
Mac OS X
pronto
- v0.2.1
Published by althonos over 8 years ago
- Fix Relationships other than predefined ones not extracting
- Moved Relationship class properties
bottomupandtopdownto class methods
pronto
- v0.2.0
Published by althonos over 8 years ago
- Relationship are now extracted as objects
- Children, parents, rchildren and rparents properties and methods of each Term are now memoized
- Relationship classes have a Lock class property to avoid data races when Relationship objects may be created at the same time they are iterated over
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