Add a public numbering module and route fragmenting, validation,
and scaffold preparation through the canonical numbering entry.
Rewrite the repository entry docs around the fixed numbering
contract, add MkDocs landing pages, and document the mirror
mapping used for medicinal-chemistry comparisons.
Also refresh the validation analysis reports to explain the
canonical-versus-mirrored numbering relationship.
Keep key validation outputs and analysis tables tracked directly,
package analysis plot PNGs into a small tar.gz backup, and add
analysis scripts plus tests so the stored results remain
reproducible without flooding git with large image trees.
- skip fused/shared/multi-anchor side systems during extraction
- add fragment library schema and fragment_library.csv export
- make scaffold prep strict for non-spliceable positions
- Add MacrolactoneDB filtered datasets
- Add ring12_20 and ring16 subdirectories with processed data
- Add ml_id column as unique identifier (ML00000001 format)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implement the standard/non-standard/not-macrolactone classification layer
and integrate it into analyzer, fragmenter, and CLI outputs.
Port the remaining legacy package capabilities into new visualization and
workflow modules, restore batch/statistics/SDF scripts on top of the flat
CSV workflow, and update active docs to the new package API.
Unify macrolactone detection, numbering, fragmentation, and
splicing under the installable macro_lactone_toolkit package.
- replace legacy src.* modules with the new package layout
- add analyze/number/fragment CLI entrypoints and pixi tasks
- migrate tests, README, and scripts to the new package API
- Add src/splicing/ module with scaffold_prep, fragment_prep, and engine
- Add tylosin_splicer.py entry script
- Add unit tests for splicing components
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add AGENTS.md with AI assistant guidelines for the project
- Add tests/test_ring_numbering.py to verify ring numbering consistency
- Test confirms atom numbering is fixed and reproducible
Co-Authored-By: Claude <noreply@anthropic.com>
