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| role="dna", | ||
| replicate=location_index + 1, | ||
| source_sample_id=upstream.id if upstream else None, | ||
| initial_volume_ul=config.volume_dna, |
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When a plasmid is shared across enough reactions, every output draws transfer_volume_dna from the same sample, but that sample is always loaded with only volume_dna. For example, six reactions sharing one plasmid with the defaults create twelve 2 µL draws from a 20 µL aliquot, so the protocol runs the source dry. Validate cumulative consumption or allocate/load additional aliquots before rendering the protocol.
AGENTS.md reference: AGENTS.md:L48-L53
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| SamplePoint(sample_id=output.id) for _, output in group | ||
| ), | ||
| volume_ul=config.transfer_volume_competent_cell, | ||
| mix_before=(3, 50), |
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If tube_volume_competent_cell is configured below 50 µL, which current validation permits as long as it covers one transfer, every cell distribution still attempts to mix 50 µL from that tube. For example, a 20 µL tube with a 20 µL transfer compiles successfully but generates an impossible aspiration; reject such configurations or derive the mix volume from the available source volume.
AGENTS.md reference: AGENTS.md:L48-L53
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| volume_ul=config.transfer_volume_recovery_media, | ||
| air_gap_ul=10, |
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The recovery transfer is emitted without checking the final volume against the allocated nest_96_wellplate_100ul_pcr_full_skirt wells. A request with many plasmids, or otherwise valid custom cell/DNA/recovery volumes, can make cell + DNA transfers + recovery exceed 100 µL while compilation still succeeds, producing a protocol that overflows the reaction well; validate the aggregate volume before adding this step.
AGENTS.md reference: AGENTS.md:L48-L53
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Inspired by the functionality of PUDU's protocol, but looking to introduce a more robust software architecture, this PR introduces a
buildcompiler.protocolssubpackage which contains cloning workflows (currently: assembly, transformation, and plating) for the OpenTrons OT-2. The protocols can be rendered using the OpenTrons Python API or the OpenTrons JSON API.While the code is very different from PUDU (it is very much a derivative work), both of these output protocols are currently evaluated for functional equivalence with their PUDU counterparts and, as such, should behave identically to the current version of the PUDU protocols.