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Level 2 assembly, transformation, and test suite - #102

Merged

Gonza10V merged 114 commits into

mainfrom

assembly_lvl2

Jul 11, 2026

Merged

Level 2 assembly, transformation, and test suite#102
Gonza10V merged 114 commits into
mainfrom
assembly_lvl2

Commits on Mar 26, 2026
- established missing implementation warning framework
  doublergreer
  committed
  a70c7a5
Commits on Mar 31, 2026
- incorrect draft of lvl2
  doublergreer
  committed
  2653177
- resolving original plasmid part overwrite issue in digestion
  doublergreer
  committed
  8f8c624
Commits on Apr 1, 2026
- unique objects for each lvl1 + passing in final doc for continuity
  doublergreer
  committed
  6083612
- only grab first and last fusion site from new composite
  doublergreer
  committed
  7f68281
Commits on Apr 2, 2026
- codex check
  doublergreer
  committed
  53716c0
Commits on Apr 3, 2026
- linking xml to json and json to protocol
  Gonza10V
  committed
  c2fc5c3
Commits on Apr 4, 2026
- Revise README for clarity and add project purpose
  Gonza10V
  authored
  5438141
- Rename project and update metadata in pyproject.toml
  Gonza10V
  authored
  45d1a26
- Delete SBOL2Build.ipynb
  Gonza10V
  authored
  74fe1d8
Commits on Apr 6, 2026
- backbone now listed last in product
  doublergreer
  committed
  1ad96f2
Commits on Apr 7, 2026
- Enhance README with project details and workflow
  Gonza10V
  authored
  0a2aa91
- Add PRODUCT.md for BuildCompiler overview
  Gonza10V
  authored
  56173d9
- Add Developer Guide for AI Agents
  Gonza10V
  authored
  813f7d5
- type correction on ligation products
  doublergreer
  committed
  fd65c9a
- function to simplify complex plasmid part representation to a scar-TU-scar-bb representation
  doublergreer
  committed
  ee7451f
Commits on Apr 8, 2026
- intermediate w/ annos not working
  doublergreer
  committed
  5640cd8
Commits on Apr 9, 2026
- Implement BuildCompiler transformation orchestration stage
  Gonza10V
  committed
  f4a8701
Commits on Apr 14, 2026
Commits on Apr 21, 2026
- remove todo
  doublergreer
  committed
  2747758
- ligase and RE flow optimized + domestication added if not found
  doublergreer
  committed
  494ddcf
- definition->identity
  doublergreer
  committed
  69fea09
Commits on Apr 27, 2026
- lvl2 and multi-design lvl1 drafts
  doublergreer
  committed
  d9fbdf2
- docstring updates
  doublergreer
  committed
  88a3b44
Commits on Apr 28, 2026
- Add plating workflow with SBOL/protocol artifact generation
  Gonza10V
  committed
  6bce1f0
- Merge pull request #50 from MyersResearchGroup/codex/implement-buildcompiler.plating-method
  Gonza10V
  authored
  873ed74
- Implement full_build orchestration with manifest and packaging
  Gonza10V
  committed
  c75a283
- Add full_build quickstart notebook example
  Gonza10V
  committed
  fe3e9e7
- get referencing CD in extract toplevel definition
  doublergreer
  committed
  230f2ba
- ironing out iterative lvl1
  doublergreer
  committed
  de292b8
Commits on Apr 29, 2026
- better doc search in get_or_pull
  doublergreer
  committed
  a0f395c
- added combinatorial design support to lvl1
  doublergreer
  committed
  fb76b9c
Commits on Apr 30, 2026
Commits on May 5, 2026
Commits on May 6, 2026
Commits on May 7, 2026
- new tests for digestion and ligation
  doublergreer
  committed
  79b6b3a
- combinatorial test
  doublergreer
  committed
  e622941
Commits on May 8, 2026
- type and error handling adjustments
  doublergreer
  committed
  4e704fc
- adjusting backbone arg to allow for dictionary mapping design.displayId:backbone in multi-design assemblylvl1
  doublergreer
  committed
  a0bb9e0
- type correction
  doublergreer
  committed
  cc967fe
- Add local SBOL document indexing entry point
  Gonza10V
  committed
  b4fb2ca
Commits on May 12, 2026
- activity tests for digestion and ligation
  doublergreer
  committed
  4e9f961
- test buildcompiler draft
  doublergreer
  committed
  3dc25ee
- level 1 and first comb test complete
  doublergreer
  committed
  7d346cf
- removed superfluous prints
  doublergreer
  committed
  da38668
- new test suite
  doublergreer
  committed
  d2fe409
Commits on May 13, 2026
- synbiohub.org->api.synbiohub.org
  doublergreer
  committed
  feb64fa
- secret access for github job
  doublergreer
  committed
  3384148
- api for pulls only
  doublergreer
  committed
  cecf73f
- api for collections
  doublergreer
  committed
  26e638d
- revert api for collections
  doublergreer
  committed
  f91e490
- added server mode flag to add api. to canonical sbh registry uris
  doublergreer
  committed
  bb8d338
- notebooks for creating various implementations used in buildcompiler
  doublergreer
  committed
  776bc73
Commits on May 16, 2026
- decouple forward and reverse fusion site matching to fix skipped backbone match + composite numbering adjustment
  doublergreer
  committed
  767fa6b
- lvl2 working
  doublergreer
  committed
  0454cfe
Commits on May 17, 2026
- lvl2 test draft
  doublergreer
  committed
  307f61c
Commits on May 18, 2026
- lvl1 TU tests for lvl2 assembly
  doublergreer
  committed
  9cebf0d
- Fix local document indexing to avoid duplicate re-indexing
  Gonza10V
  committed
  769bd06
- Merge pull request #100 from MyersResearchGroup/codex/add-local-sbol-document-indexing-support
  Gonza10V
  authored
  fa0a2b5
- transformation test
  doublergreer
  committed
  207b68c
- notebook updates
  doublergreer
  committed
  1c67d56
- added transformation
  doublergreer
  committed
  2237123
Commits on Jul 9, 2026
- Merge branch 'full_build' into assembly_lvl2
  Gonza10V
  authored
  28cebdc
- Fix domestication BsaI implementation reference
  Gonza10V
  committed
  2ed6001
- Respect supplied level 2 backbone
  Gonza10V
  committed
  f10a5b4
- Select top-level design for lvl2 TU extraction
  Gonza10V
  committed
  de4387a

Commits

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Commits on Jul 9, 2026