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Open Protocol Interface Language beta 3

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@bbartley bbartley released this 01 Mar 20:53
· 32 commits to master since this release
v1.0b3
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Learn about vigilant mode.

This version allows the opil module to be run as an executable with commandline options for generating documentation.

This versions also corrects a parser bug that prevented round-tripping files that contain SampleSet objects.

Breaking changes

OPIL Documents generated using previous versions of OPIL will not parse correctly with this version. This is because the namespace for OPIL has changed from http://bbn.com/synbio/opil# to http://bioprotocols.org/opil/v1#. While this will not break existing code, it does mean that OPIL serializations will need to be regenerated.

This version also includes some updates to property cardinalities that may result in breaking changes, specifically all of the following properties no longer accepted unbounded lists, rather they only accept a singleton value.

  • TimeInterval.min_time
  • TimeInterval.max_time
  • StringValue.value_of, IntegerValue.value_of, BooleanValue.value_of, EnumeratedValue.value_of, MeasureValue.value_of
  • MeasureValue.has_measure
  • SampleSet.replicates

These breaking changes will manifest with an error:

TypeError: Expecting {type}, got <class 'list'>
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