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SynBioDex / pySBOL3

Native python implementation of SBOL 3.0 specification
MIT License
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Support rdflib 6.0 #279

Closed bbartley closed 3 years ago

bbartley commented 3 years ago

The 6.0 release of rdflib has some breaking changes in the graph.serialize method. Notably the method now returns a regular string rather than a bytestring. This breaks pysbol's Document.write_string method.

See this build log for an example of this failure mode: https://github.com/SynBioDex/sbol_factory/runs/3135729743?check_suite_focus=true#step:5:124

tcmitchell commented 3 years ago

Version 1.0b5 contains a workaround for this issue. It pins the RDFlib dependency at version 5.

tcmitchell commented 3 years ago

See https://github.com/RDFLib/rdflib/issues/1376 for a minor issue with rdflib 6.0.

tcmitchell commented 3 years ago

And see https://github.com/RDFLib/rdflib/issues/1376#issuecomment-885741449 for a workaround

tcmitchell commented 3 years ago

See https://github.com/RDFLib/OWL-RL/issues/44 for an issue about warnings emitted by owlrl which is a dependency of pyshacl. These will bother users in interactive tutorials that use pySBOL3 because pySBOL3 depends on pyshacl and these warnings show up in an interactive python interpreter after import sbol3.