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Changelog

0.2.0

Migration from 0.1.0

  • Pass shared decks with lab.compile(protocol, deck=deck, liquid_handler=...). A positional second argument is now reserved for a concrete target.
  • lab.compile(protocol) defaults to a manual target and writes a bundle to ~/.lab/<protocol>/<target>/. Use to=None to compile without writing, to=path to choose a directory, or LAB_HOME to change the default root. Recompilation replaces the files in that protocol/target bundle; Compilation.write() still refuses to replace different existing artifacts.
  • Replace the removed lab.protocols request and material API with the cloning experiment builders and lab.samples. Assembly and Transformation recipes take native sbol3.Component objects; pySBOL3 is now a core dependency.

Added

  • Sample identities, lineage, design references, and optional implementation references are preserved in the protocol snapshot. Declared outputs produce manifest.json and are available through Compilation.manifest.
  • Assembly, transformation, and plating examples carry native SBOL design identities through their planned outputs, with a separate example for computational design provenance.
  • An optional LabOP integration exports prospective protocol plans using upstream LabOP. It is installed from the checkout in a separate environment and is not imported by the core package.

Repository

  • Move the source repository to https://github.com/MyersResearchGroup/LabCompiler and update package URLs, README links, and publishing instructions. The PyPI package remains lab-compiler; the Python import remains lab.