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Releases: althonos/pronto

v0.6.0

10 Nov 14:59
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  • 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

v0.5.0

10 Nov 14:58
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  • 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)

v0.4.2

10 Nov 14:57
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  • Fix obo export with utf-8 chars

v0.4.1

10 Nov 14:55
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  • Fix owl parser
  • Fix obo export on headerless ontology files

v0.4.0

19 Sep 12:17
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  • 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

v0.3.3

12 Aug 16:41
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  • Attempted compatibility patch for multiprocessing to work with
    Mac OS X

v0.3.2

27 Jul 09:33
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  • Improved Python2/3 compatibility & performance using six

v0.3.1

27 Jul 09:33
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  • Added a stricter timeout to ontology opening to avoid waiting ages for each imports

v0.3.0

27 Jul 09:32
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  • Increased multiprocessing support
  • Made all pronto types pickable (protocol >=2 required)
  • Fix many performance issues

v0.2.1

16 Jul 21:22
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  • Fix Relationships other than predefined ones not extracting
  • Moved Relationship class properties bottomup and topdown to class methods