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Module Map

The module tree should teach responsibility by meaning, not by local lore. The practical question is simple: if a visible surface changes, which part of the repository is supposed to explain, govern, or rebuild it?

This page is not a directory dump. It is a responsibility map for moving from one question to the right owner quickly.

Lifecycle Owners

  • command_line/ owns parsing, dispatch, and the durable command registry
  • data_downloader/pipeline/, data_downloader/sources/, data_downloader/intake/, and data_downloader/exports/ own source-family collection, workbook intake, and context artifact writing
  • adna/ owns animal aDNA intake, sample extraction, locality recovery, chronology recovery, coordinate provenance, normalization, and validation
  • analysis/review/ owns candidate-site ranking reviews and sensitivity surfaces
  • evidence/ owns atlas evidence and scientific review surfaces
  • reporting/adna/, reporting/bundles/, reporting/context/, reporting/map_document/, reporting/presentation/, reporting/rendering/, and reporting/review/ own publication assembly, presentation helpers, governed report reviews, and public artifact writing
  • foundation/ owns architecture contracts, ownership maps, repository-truth builders, and release posture
  • core/ remains intentionally small: files, text, geojson, HTTP, time, and geo-distance primitives

Those boundaries matter because public outputs are only trustworthy when they can be traced back through a stable ownership path.

Fast Route By Question

  • if the question is about commands, entrypoints, or argument handling, start with command_line/
  • if the question is about where a source family came from or how raw material entered the repository, start with data_downloader/
  • if the question is about animal sample extraction, chronology, coordinates, or species review, start with adna/
  • if the question is about how evidence became a visible report, bundle, or map, start with reporting/
  • if the question is about posture, refusal, ownership, or truth language, start with foundation/
  • if the question is about small shared mechanics such as files, text, time, or geometry helpers, start with core/

Animal aDNA Ownership

If a question is about project intake, paper linkage, supplement capture, sample extraction, locality resolution, chronology evidence, coordinate provenance, species review, or atlas-ready animal rows, the answer should usually trace back into src/bijux_pollenomics/adna/.

If a question is about how those animal rows become country bundles, atlas bundles, or repository-truth reviews, the path should continue into reporting/adna/, reporting/bundles/, reporting/review/, and foundation/.

What The Tree Refuses

  • data_downloader/shared/ and reporting/shared/ remain compatibility shims, not canonical ownership areas
  • pollenomics is an alias distribution, not a second runtime
  • bijux-pollenomics-dev is maintainer tooling, not a home for runtime scientific logic

How To Use This Page

Use this page in this order when you need orientation:

  1. start from the public question, not from the directory name
  2. locate the lifecycle owner that governs that question
  3. only then drill into the narrower modules and files underneath that owner

If a page forces you to guess whether you need reporting/, adna/, data_downloader/, or foundation/, the module map is not doing its job well enough.