lingyuzeng/macrolactone-toolkit
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1e36e52112d145aa3e08b0e65af00496e7e08549
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Author SHA1 Message Date
lingyuzeng
1e36e52112 feat(validation): add stratified sampling by ring size 2026-03-19 10:28:38 +08:00
lingyuzeng
2e3b52d049 feat(validation): add isotope tagging utilities 2026-03-19 10:28:03 +08:00
lingyuzeng
d18133ce16 feat(validation): add SQLModel database models and fix relationships 2026-03-19 10:27:20 +08:00
lingyuzeng
d0cdf50ed5 feat(validation): add SQLModel database models 2026-03-19 10:23:47 +08:00
lingyuzeng
c0ead42384 feat(toolkit): add classification and migration 
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.
 2026-03-18 23:56:41 +08:00
lingyuzeng
9ccbcfcd04 chore(repo): ignore project worktrees 2026-03-18 23:35:56 +08:00
lingyuzeng
5e7b236f31 feat(toolkit): ship macro_lactone_toolkit package 
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
 2026-03-18 22:06:45 +08:00
hotwa
a768d26e47 Move project docs to docs/project-docs and update references 
- Move AGENTS.md, CLEANUP_SUMMARY.md, DOCUMENTATION_GUIDE.md,
  IMPLEMENTATION_SUMMARY.md, QUICK_COMMANDS.md to docs/project-docs/
- Update AGENTS.md to include splicing module documentation
- Update mkdocs.yml navigation to include project-docs section
- Update .gitignore to track docs/ directory
- Add docs/plans/ splicing design documents

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-18 17:56:03 +08:00
hotwa
68f171ad1d Add splicing module and related tests 
- 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>
 2026-03-18 17:47:00 +08:00
hotwa
0ced0fa816 Add AGENTS.md and ring numbering test 
- 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>
 2026-01-23 09:53:27 +08:00
hotwa
0d99f7d12c first add 2025-11-14 20:34:58 +08:00