Repository Layout¶

Canonical Layout¶

src/genomics/
  cli.py
  workspace.py
  doctor.py            # genomics doctor / the visualizer's System page
  core/
  visualizer/
  workflows/
    alphagenome/       # local_server.py (setup/start/check), model_server.py (runs in the server env)
  predictors/
  converters/

configs/
  genomes_analyzer/
  predictors/
    genotype_based/
    variant_transformer/
    snp_ancestry/
  workflows/
    non_longevous_dataset/
    longevity_dataset/
    alphagenome/
  converters/
    vcf_to_23andme/

docs/
  components/
  concepts/
  getting-started/
  guides/
  historical/
    alphagenome/
    1000-genomes/
  operations/
    monster.md
    scripts.md
  reference/

legacy/
  neural_ancestry_predictor_deprecated/
  neural_longevity_dataset/

scripts/
  env/
  ops/
  maintenance/
  diagnostics/
  experiments/
  dev/

native/
  genes_difference_count/

third_party/
  FROGAncestryCalc/

Rules¶

Active Python package code lives under src/genomics/.
New commands should be exposed through genomics ....
Shared code belongs in src/genomics/core/.
Canonical configs belong under configs/.
Legacy-only neural ancestry configs belong under legacy/neural_ancestry_predictor_deprecated/configs/, not under configs/.
Historical reproducibility code belongs under legacy/.
Historical notes and migration records belong under docs/historical/.
External modified code belongs under third_party/.
Native non-Python tools belong under native/.
Root-level wrappers and old package directories should not be reintroduced.