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Updated the assemblies loop to have less code, condensed and redid how we added to the sets
Luke Dysart Update to bug with assembly after attempted push
Luke update to run_sbol2 assembly, working on push in git
…ON and kwargs, and added `run_sbol2assembly_with_params.py` script for SBOL loop assembly with custom parameters.
…ical feasibility of assemblies and updated `run_sbol2assembly_with_params.py` to include revised advanced parameters.
…ement and updated `run_sbol2assembly_with_params.py` to utilize this feature.
…and introduced `run_sbol2transformation_with_params.py` for transformation protocols with enhanced customization.
…N and kwargs, and added `run_sbol2plating_with_params.py` script for plating protocols with enhanced customization.
…ssembly_data` and `assemblies`, added `Optional` type hints, and improved error handling for assembly initialization.
…ly, transformation, and plating, with support for JSON-based input, metadata customization, and automatic protocol type detection.
…simulation, improved DNA and combination naming consistency for downstream protocols.
…`assembly.py` and removed redundant initialization in constructor.
Logic error fix
…rator improvements
transformation.py:
- Introduce self.plasmid_name_to_wells (name → [well_obj, ...]) populated at
load time, replacing all positional/enumeration-based DNA well lookups
- Introduce self.location_replicates derived from plasmid_locations, unifying
96-well plate and temp module code paths into a single loop structure
- Rewrite _transfer_competent_cells with sequential well_index counter and
per-chassis chassis_reaction_count dict for correct tube selection across
multiple chassis types
- Rewrite _transfer_DNA as a unified single method with no plate/temp module
branching; uses self.transformations as ground truth throughout
- _load_dna_into_dna_plate / _load_dna_into_temp_module now populate
plasmid_name_to_wells instead of returning DNA_wells
- _load_reagents_96plate / _load_reagents_temp_module return 2-tuple;
_validate_protocol accounts for location_replicates in reaction counts
- Add strain as first entry in dict_of_parts_in_thermocycler per well
- Rewrite Transformation base class docstring to match current parameters;
add comprehensive HeatShockTransformation docstring for all subclass params
generate_protocol.py:
- Add generate_param_reference() to append a commented parameter table and
full docstrings to every generated protocol for last-minute editing
- Add --plasmid-locations CLI flag and plasmid_locations support throughout
- Raise line-length threshold from 80 to 100 for single-line list formatting
- Improve transformation protocol auto-detection for bare list format
assembly.py:
- Initialize self.product_uri_to_wells = {}
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…ta` format and inlined advanced parameters for improved clarity and consistency.
…ly-class-for-markdown-protocol-generation Add ManualAssembly to render Golden Gate manual protocols as Markdown
Removed outdated notes and updated instructions for thermocycler iterations and DNA part concentrations.
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