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PyAutoMemory — Agent Guidance

PyAutoMemory is the Memory organ of the PyAuto organism: long-term knowledge — what the science says. Literature wikis, concepts, entities, bibliographies. (The organs and boundaries are defined once in PyAutoBrain/ORGANISM.md.)

The read contract

Memory is pull-only, on demand — no agent queries it automatically. Consult it when the work is scientific or a plan names a domain (lensing, SMBH, CTI/Euclid, inference methods, galaxy evolution); skip it entirely for packaging, tooling, and workflow tasks.

When you do read:

  1. Index first. Start at index.md, then the relevant sub-wiki's own index.md (wiki/lensing/, wiki/smbh/, wiki/cti/, wiki/methods/, wiki/galaxies/).
  2. Then at most 2–3 pages. Read only the concept/entity/source pages the index points you to. Never bulk-load a sub-wiki.
  3. Do not couple to the internal layout — reach pages through the indexes, not hard-coded paths.

The write contract (layout rules)

The repo has exactly two content homes, enforced by make validate-structure (CI runs it on every push/PR):

  • wiki/<domain>/ — every sub-wiki, following the shared schema in wiki/CLAUDE.md. New sub-wikis are added beside the existing ones, never at the repo root.
  • bibliography/ — the only place BibTeX lives. One canonical file (pyautomemory.bib) plus bibkey_aliases.yaml; never add loose .bib files anywhere else.

Source PDFs live off-repo. Never commit a paper (PDF/HTML, with or without a file extension) — read it, stub it in the right wiki/<domain>/sources/*.md, add its canonical entry to bibliography/, and run make validate. Unrecognised top-level files/folders fail the lint; the allowlist is in scripts/validate_structure.py.

What does NOT live here

  • Operational history — what the organism did (prior tasks, decisions, failed approaches) lives in PyAutoMind (complete.md, GitHub issues), not here. Memory = what the science says; Mind = what the organism did.
  • Workflow state, health, execution — Mind / Heart / Build respectively.

This repo is personal

PyAutoMemory contains personal research material. Never reference or copy PyAutoMemory content into public or user-facing repos (libraries, workspaces, tutorials, assistants).

Never rewrite history

Never rewrite pushed history on any repo with a remote — no git init over a tracked repo, no force-push to main, no fresh-start "Initial commit", no filter-repo / filter-branch / rebase -i on pushed branches. To get a clean tree: git fetch origin && git reset --hard origin/main && git clean -fd.