From b3233c62979c3dcf541d2970bd6b80a30798c456 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Sat, 19 Sep 2026 13:47:51 +0100 Subject: [PATCH] maintenance: finish provider-neutral instructions and agent metadata --- AGENTS.md | 2 +- README.md | 2 +- bibliography/README.md | 2 +- index.md | 6 +- reading-queue.md | 2 +- scripts/board.py | 10 +- scripts/validate_wikilinks.py | 6 +- tests/test_board.py | 2 +- wiki/AGENTS.md | 167 +++++++++++++++++++++++++++++++++ wiki/CLAUDE.md | 168 +--------------------------------- wiki/cti/AGENTS.md | 50 +++++++++- wiki/cti/CLAUDE.md | 49 +--------- wiki/cti/index.md | 4 +- wiki/galaxies/AGENTS.md | 64 ++++++++++++- wiki/galaxies/CLAUDE.md | 63 +------------ wiki/galaxies/index.md | 4 +- wiki/lensing/AGENTS.md | 41 ++++++++- wiki/lensing/CLAUDE.md | 40 +------- wiki/lensing/index.md | 4 +- wiki/methods/AGENTS.md | 59 +++++++++++- wiki/methods/CLAUDE.md | 58 +----------- wiki/methods/index.md | 4 +- wiki/smbh/AGENTS.md | 57 +++++++++++- wiki/smbh/CLAUDE.md | 56 +----------- wiki/smbh/index.md | 4 +- 25 files changed, 467 insertions(+), 457 deletions(-) create mode 100644 wiki/AGENTS.md diff --git a/AGENTS.md b/AGENTS.md index 9011774..71acffd 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -28,7 +28,7 @@ The repo has exactly **two content homes**, enforced by `make validate-structure` (CI runs it on every push/PR): - **`wiki//`** — every sub-wiki, following the shared schema in - [`wiki/CLAUDE.md`](wiki/CLAUDE.md). New sub-wikis are added beside the + [`wiki/AGENTS.md`](wiki/AGENTS.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`); never add loose `.bib` files anywhere else. diff --git a/README.md b/README.md index 73bbbc9..dd4777a 100644 --- a/README.md +++ b/README.md @@ -79,7 +79,7 @@ and the claim support together, then passes `make validate` (CI-enforced on every push). The wiki schema is defined in -[`wiki/CLAUDE.md`](wiki/CLAUDE.md) and inherited by every +[`wiki/AGENTS.md`](wiki/AGENTS.md) and inherited by every sub-wiki. How agents should read this repo: [AGENTS.md](AGENTS.md). The organism this repo is the Memory of: [PyAutoBrain/ORGANISM.md](https://github.com/PyAutoLabs/PyAutoBrain/blob/main/ORGANISM.md), diff --git a/bibliography/README.md b/bibliography/README.md index bb2e3b7..d5e68ed 100644 --- a/bibliography/README.md +++ b/bibliography/README.md @@ -15,7 +15,7 @@ personal library in 2026-07 — the merge audit is in git history.) 2. Search `pyautomemory.bib` by DOI, arXiv ID, and title. Reuse the existing canonical key; otherwise add verified metadata under a unique, stable author-year key. 3. Add a compact section to the relevant `../wiki//sources/*.md` using the inherited - schema in [`../wiki/CLAUDE.md`](../wiki/CLAUDE.md). + schema in [`../wiki/AGENTS.md`](../wiki/AGENTS.md). 4. Add concept/entity links only where the paper materially supports existing text. 5. Run `make validate-literature-citations`. diff --git a/index.md b/index.md index 73b0d4c..f48f5f0 100644 --- a/index.md +++ b/index.md @@ -3,7 +3,7 @@ The PyAuto organism's long-term knowledge: a multi-domain knowledge base of accumulated scientific and project knowledge, organised as several Karpathy-style LLM wikis over a shared canonical bibliography. Each sub-wiki uses -the schema in [`wiki/CLAUDE.md`](wiki/CLAUDE.md). +the schema in [`wiki/AGENTS.md`](wiki/AGENTS.md). ## Sub-wikis @@ -62,8 +62,8 @@ the schema in [`wiki/CLAUDE.md`](wiki/CLAUDE.md). ## Schema The schema is defined once in -[`wiki/CLAUDE.md`](wiki/CLAUDE.md) and inherited by -all sub-wikis. Each sub-wiki has its own `CLAUDE.md` that diverges +[`wiki/AGENTS.md`](wiki/AGENTS.md) and inherited by +all sub-wikis. Each sub-wiki has its own `AGENTS.md` that diverges only on the `## Scope` section. Per-page frontmatter, naming conventions, `[[wiki-links]]`, status flags (`stub | drafted | reviewed`), and source-page layout are uniform across sub-wikis. diff --git a/reading-queue.md b/reading-queue.md index 678bbb8..9c9a8c8 100644 --- a/reading-queue.md +++ b/reading-queue.md @@ -28,7 +28,7 @@ Papers waiting to be read and filed. Format: - A line that is *only* an arXiv link is still a paper — the title was just never written, so the board labels it `arXiv:`. - Filing a read paper: add its canonical entry to `bibliography/`, stub it in - the matching `wiki//sources/*.md` page per `wiki/CLAUDE.md`, then + the matching `wiki//sources/*.md` page per `wiki/AGENTS.md`, then mark the line DONE and run `make validate`. (Moved from `admin_jammy/papers.md` on 2026-05-22, when this repo — then diff --git a/scripts/board.py b/scripts/board.py index fe35e86..40aa154 100644 --- a/scripts/board.py +++ b/scripts/board.py @@ -5,7 +5,7 @@ how mature each sub-wiki is — each work queue carrying a one-tap 📋 copy block holding a paste-ready Claude Code prompt that executes this repo's own documented workflow (``bibliography/README.md`` "Adding a paper", -``wiki/CLAUDE.md``'s schema) — plus contents cards with ``/memory `` +``wiki/AGENTS.md``'s schema) — plus contents cards with ``/memory `` recall chips. Reading-queue sections expand to the individual papers: each title links out to the arXiv abstract page (or, when the line carries no ref, a title search — see ``scripts/arxiv_refs.py``), carries a 📄 button onto the @@ -508,7 +508,7 @@ def _queue_issue_url(snapshot: dict, section: str, paper: dict, f"{where}\n\n" f"{notes}\n\n" "Workflow (bibliography/README.md \"Adding a paper\", " - "wiki/CLAUDE.md): verify the paper against an authoritative " + "wiki/AGENTS.md): verify the paper against an authoritative " "record, add its canonical entry to the bibliography/ BibTeX " "file, add a minimal section to the matching " "wiki//sources/ page — canonical key plus the notes " @@ -522,7 +522,7 @@ def _queue_issue_url(snapshot: dict, section: str, paper: dict, f"{where}\n\n" f"{notes}\n\n" "Workflow (bibliography/README.md \"Adding a paper\", " - "wiki/CLAUDE.md): verify the paper against an authoritative " + "wiki/AGENTS.md): verify the paper against an authoritative " "record, add its canonical entry to the bibliography/ BibTeX " "file, stub it in the matching wiki//sources/ page — " "incorporating the notes above — mark its queue line " @@ -661,7 +661,7 @@ def _read_prompt(snapshot: dict, section: str) -> str: f"{repo}/reading-queue.md: verify it against an authoritative " f"record, add its canonical entry to the bibliography/ BibTeX " f"file, stub it in the matching wiki//sources/ page per " - f"wiki/CLAUDE.md, mark its queue line 'DONE — ', " + f"wiki/AGENTS.md, mark its queue line 'DONE <date> — <title>', " f"and run make validate.") @@ -678,7 +678,7 @@ def _stub_prompt(snapshot: dict, wiki: str) -> str: repo = snapshot.get("repo") or "the memory repo" return (f"Upgrade one stub page in {repo}/wiki/{wiki}/ to drafted: verify " f"its claims against the cited sources, expand it per the schema " - f"in wiki/CLAUDE.md, set status: drafted, and run make validate.") + f"in wiki/AGENTS.md, set status: drafted, and run make validate.") def _inbox_freshness(snapshot: dict, key: str = "inbox_last_digest") -> dict: diff --git a/scripts/validate_wikilinks.py b/scripts/validate_wikilinks.py index 2526eb1..cd147de 100644 --- a/scripts/validate_wikilinks.py +++ b/scripts/validate_wikilinks.py @@ -1,8 +1,8 @@ """Resolve every ``[[wikilink]]`` in the wiki against the pages that exist. -``[[slug]]`` is the wiki's cross-reference mechanism (``wiki/CLAUDE.md``, +``[[slug]]`` is the wiki's cross-reference mechanism (``wiki/AGENTS.md``, "Cross-references"): a slug is a page's filename without ``.md``, slugs are -unique across sub-wikis so a link needs no path (``wiki/smbh/CLAUDE.md``), and +unique across sub-wikis so a link needs no path (``wiki/smbh/AGENTS.md``), and a link with no target yet is *legal* — it marks a page somebody meant to write. That last rule is why this lint is a **ratchet, not a gate**. The wiki carries @@ -64,7 +64,7 @@ #: The schema page itself is documentation *of* the syntax, not a page of #: references: every example slug in it is illustrative. -SKIP_FILES = ("wiki/CLAUDE.md",) +SKIP_FILES = ("wiki/AGENTS.md", "wiki/CLAUDE.md") def strip_code(text: str) -> str: diff --git a/tests/test_board.py b/tests/test_board.py index 18a0951..026cde0 100644 --- a/tests/test_board.py +++ b/tests/test_board.py @@ -175,7 +175,7 @@ def test_work_queue_prompts_reference_the_documented_workflow(tmp_path): assert "reading-queue.md" in html # file-the-next-paper prompt assert "make validate" in html # every prompt ends at the gate assert "/memory demo" in html # the recall chip - assert "wiki/CLAUDE.md" in html # the schema anchor + assert "wiki/AGENTS.md" in html # the schema anchor def test_paper_links_and_issue_actions(tmp_path): diff --git a/wiki/AGENTS.md b/wiki/AGENTS.md new file mode 100644 index 0000000..5c20a04 --- /dev/null +++ b/wiki/AGENTS.md @@ -0,0 +1,167 @@ +# PyAutoMemory wikis — shared schema + usage rules + +Every sub-wiki under `wiki/` gives an AI assistant broad scientific context +for one domain. They follow Karpathy's "LLM Wiki" pattern: concise, +cross-linked pages are read at query time, while canonical citation metadata +lives separately in [`../bibliography/`](../bibliography/README.md). This +file defines the schema once; each sub-wiki's own `AGENTS.md` diverges only +on scope. + +## Layout + +``` +PyAutoMemory/ # repo root +├── wiki/ # all sub-wikis (in git) +│ ├── AGENTS.md # this file — schema + usage rules +│ └── <domain>/ # one domain per sub-wiki, e.g. lensing/ +│ ├── AGENTS.md # the sub-wiki's scope notes +│ ├── index.md # the sub-wiki's own navigation +│ ├── log.md # append-only compilation log +│ ├── concepts/ # one topic per page — the science +│ ├── entities/ # named things: surveys, instruments, software +│ ├── sources/ # compact claim support (one paper = one section) +│ └── seed/ # unverified 2026-05 import, not citeable yet +└── bibliography/ # canonical BibTeX and citation tooling +``` + +Papers are the ground truth; wiki pages are syntheses. If they disagree, update +the wiki and note the change in the sub-wiki's `log.md`. + +## References and citation metadata + +- `sources/*.md` records compact guidance about what claims a paper supports. +- `seed/*.md` is the same shape, unverified: the 2026-05 import's stubs, held + apart so nothing cites them by accident. +- `../bibliography/pyautomemory.bib` records canonical metadata and keys. + +Never record local PDF paths or fabricate metadata — source PDFs live +off-repo. One declared exception: a page's frontmatter may carry an +`archive:` list — the **read-only archival filenames** of the off-repo PDFs +the 2026-05 import seeded it from (e.g. `Strong_Lens/Suyu2016Holicow.pdf`). +These are provenance history, never live paths; nothing may resolve or grow +them — new papers cite the bibliography, not an archive path. A canonical +key is local to PyAutoMemory: resolve it against a target project's `.bib` +before patching LaTeX. See +[`../bibliography/README.md`](../bibliography/README.md) for the workflow. + +## Page types + +| Type | Folder | Scope | +|-------------|--------------|-------------------------------------------------------| +| Concept | `concepts/` | One scientific concept (e.g. mass-sheet degeneracy) | +| Entity | `entities/` | One named thing (survey, lens, code, collaboration) | +| Sources | `sources/` | Claim support for one topic, one section per paper | +| Seed | `seed/` | Source pages from the 2026-05 import whose every entry is still a filename-inferred stub (`Canonical BibTeX key: TODO`) — never cite one until the paper is verified and the entry promoted into `sources/` | +| Index/log | root | Navigation and provenance | + +## Naming + +- File names are lowercase kebab-case: `mass-sheet-degeneracy.md`, + `h0licow.md`, `time-delay-cosmography.md`. +- One concept per concept page. If a page tries to cover two ideas, split it. +- Source-collection pages are named by topic: `sources/dark-matter-substructure.md`. + +## Cross-references + +Use `[[page-slug]]` for wiki-internal links — for example +`[[mass-sheet-degeneracy]]` or `[[h0licow]]`. Slugs match the filename without +`.md`; a `sources/` page also answers to `[[sources-<topic>]]` and a `seed/` +page to `[[seed-<topic>]]`. A `[[link]]` that has no target file yet is fine — +it marks a future page to write, and `scripts/validate_wikilinks.py` ratchets +that backlog (it fails only on a *new* unresolved target, against +`scripts/wikilink_baseline.txt`). + +External references use verified DOI, arXiv, journal, or author/year/title +metadata, never a local path. + +## Frontmatter + +Every wiki file starts with YAML frontmatter: + +```yaml +--- +title: Mass-sheet degeneracy +type: concept # concept | entity | sources | meta +topics: [degeneracies, cosmography] +sources: # optional — papers most relevant to this page + - Suyu et al. 2017 — H0LiCOW overview + - Birrer et al. 2020 — TDCOSMO IV +status: stub # stub | drafted | reviewed +--- +``` + +Sources may be `[]` for pages that synthesize general field knowledge. + +## Concept page structure + +``` +# Title + +## TL;DR +One paragraph an assistant can quote back to a user. + +## What it is +The physics / definition. + +## Why it matters +How this concept shows up in the decisions the domain's software users make. + +## Key results from the literature +Bullet list. Each bullet ends with `([[author-year-stub]])` so the LLM can +follow the link to the per-paper section. + +## See also +- [[related-concept-1]] +- [[related-concept-2]] +``` + +## Entity page structure + +Same idea but the headings are "What it is / Key facts / Papers / See also". +Use entity pages for: surveys (BELLS, H0liCOW), specific objects +(Abell 1201, the Cosmic Horseshoe), software (PyAutoLens, lenstronomy), +collaborations (TDCOSMO, Space Warps). + +## Source-collection page structure + +``` +# Sources: <topic> + +Papers covering this topic. Each paper has its own H2 section; cross-link with +`[[sources-<topic>#author-year-slug]]`. + +## Author Year — short tag + +**Canonical BibTeX key:** `KeyYYYY` +**Reference:** DOI/arXiv/journal reference if known +**Concepts:** [[concept-1]], [[concept-2]] + +**Supports:** +- Claim this paper directly supports. +- Another claim this paper directly supports. + +**Use when:** +- Situation where the citation is appropriate. + +**Do not use for:** +- Similar but unsupported claim. +``` + +Keep entries short: normally 2–5 support bullets and no long prose. Do not copy +abstracts or infer claims from filenames. Add a TODO when support is unverified. + +## How the assistant should use a wiki + +1. On a user question, first open the sub-wiki's `index.md`. +2. Follow the relevant `concepts/` or `entities/` page. +3. Follow the source entry for claim scope and its canonical key for metadata. +4. Resolve that key against downstream `.bib` files before changing LaTeX. +5. If support or metadata is unclear, read the public paper and add a TODO + rather than guessing. Log verified upgrades. + +## Adding a sub-wiki + +Create `wiki/<domain>/` with its own `AGENTS.md` (scope notes only — this +schema is inherited, not copied), `index.md`, `log.md`, and the page folders it +needs (`seed/` only if it is taking an unverified import). Give it a row in the +repo-root `index.md` and `README.md` tables. diff --git a/wiki/CLAUDE.md b/wiki/CLAUDE.md index 7982c74..d1905df 100644 --- a/wiki/CLAUDE.md +++ b/wiki/CLAUDE.md @@ -1,167 +1,5 @@ -# PyAutoMemory wikis — shared schema + usage rules +# Claude Code adapter -Every sub-wiki under `wiki/` gives an AI assistant broad scientific context -for one domain. They follow Karpathy's "LLM Wiki" pattern: concise, -cross-linked pages are read at query time, while canonical citation metadata -lives separately in [`../bibliography/`](../bibliography/README.md). This -file defines the schema once; each sub-wiki's own `CLAUDE.md` diverges only -on scope. +Shared instructions live in [AGENTS.md](AGENTS.md). -## Layout - -``` -PyAutoMemory/ # repo root -├── wiki/ # all sub-wikis (in git) -│ ├── CLAUDE.md # this file — schema + usage rules -│ └── <domain>/ # one domain per sub-wiki, e.g. lensing/ -│ ├── CLAUDE.md # the sub-wiki's scope notes -│ ├── index.md # the sub-wiki's own navigation -│ ├── log.md # append-only compilation log -│ ├── concepts/ # one topic per page — the science -│ ├── entities/ # named things: surveys, instruments, software -│ ├── sources/ # compact claim support (one paper = one section) -│ └── seed/ # unverified 2026-05 import, not citeable yet -└── bibliography/ # canonical BibTeX and citation tooling -``` - -Papers are the ground truth; wiki pages are syntheses. If they disagree, update -the wiki and note the change in the sub-wiki's `log.md`. - -## References and citation metadata - -- `sources/*.md` records compact guidance about what claims a paper supports. -- `seed/*.md` is the same shape, unverified: the 2026-05 import's stubs, held - apart so nothing cites them by accident. -- `../bibliography/pyautomemory.bib` records canonical metadata and keys. - -Never record local PDF paths or fabricate metadata — source PDFs live -off-repo. One declared exception: a page's frontmatter may carry an -`archive:` list — the **read-only archival filenames** of the off-repo PDFs -the 2026-05 import seeded it from (e.g. `Strong_Lens/Suyu2016Holicow.pdf`). -These are provenance history, never live paths; nothing may resolve or grow -them — new papers cite the bibliography, not an archive path. A canonical -key is local to PyAutoMemory: resolve it against a target project's `.bib` -before patching LaTeX. See -[`../bibliography/README.md`](../bibliography/README.md) for the workflow. - -## Page types - -| Type | Folder | Scope | -|-------------|--------------|-------------------------------------------------------| -| Concept | `concepts/` | One scientific concept (e.g. mass-sheet degeneracy) | -| Entity | `entities/` | One named thing (survey, lens, code, collaboration) | -| Sources | `sources/` | Claim support for one topic, one section per paper | -| Seed | `seed/` | Source pages from the 2026-05 import whose every entry is still a filename-inferred stub (`Canonical BibTeX key: TODO`) — never cite one until the paper is verified and the entry promoted into `sources/` | -| Index/log | root | Navigation and provenance | - -## Naming - -- File names are lowercase kebab-case: `mass-sheet-degeneracy.md`, - `h0licow.md`, `time-delay-cosmography.md`. -- One concept per concept page. If a page tries to cover two ideas, split it. -- Source-collection pages are named by topic: `sources/dark-matter-substructure.md`. - -## Cross-references - -Use `[[page-slug]]` for wiki-internal links — for example -`[[mass-sheet-degeneracy]]` or `[[h0licow]]`. Slugs match the filename without -`.md`; a `sources/` page also answers to `[[sources-<topic>]]` and a `seed/` -page to `[[seed-<topic>]]`. A `[[link]]` that has no target file yet is fine — -it marks a future page to write, and `scripts/validate_wikilinks.py` ratchets -that backlog (it fails only on a *new* unresolved target, against -`scripts/wikilink_baseline.txt`). - -External references use verified DOI, arXiv, journal, or author/year/title -metadata, never a local path. - -## Frontmatter - -Every wiki file starts with YAML frontmatter: - -```yaml ---- -title: Mass-sheet degeneracy -type: concept # concept | entity | sources | meta -topics: [degeneracies, cosmography] -sources: # optional — papers most relevant to this page - - Suyu et al. 2017 — H0LiCOW overview - - Birrer et al. 2020 — TDCOSMO IV -status: stub # stub | drafted | reviewed ---- -``` - -Sources may be `[]` for pages that synthesize general field knowledge. - -## Concept page structure - -``` -# Title - -## TL;DR -One paragraph an assistant can quote back to a user. - -## What it is -The physics / definition. - -## Why it matters -How this concept shows up in the decisions the domain's software users make. - -## Key results from the literature -Bullet list. Each bullet ends with `([[author-year-stub]])` so the LLM can -follow the link to the per-paper section. - -## See also -- [[related-concept-1]] -- [[related-concept-2]] -``` - -## Entity page structure - -Same idea but the headings are "What it is / Key facts / Papers / See also". -Use entity pages for: surveys (BELLS, H0liCOW), specific objects -(Abell 1201, the Cosmic Horseshoe), software (PyAutoLens, lenstronomy), -collaborations (TDCOSMO, Space Warps). - -## Source-collection page structure - -``` -# Sources: <topic> - -Papers covering this topic. Each paper has its own H2 section; cross-link with -`[[sources-<topic>#author-year-slug]]`. - -## Author Year — short tag - -**Canonical BibTeX key:** `KeyYYYY` -**Reference:** DOI/arXiv/journal reference if known -**Concepts:** [[concept-1]], [[concept-2]] - -**Supports:** -- Claim this paper directly supports. -- Another claim this paper directly supports. - -**Use when:** -- Situation where the citation is appropriate. - -**Do not use for:** -- Similar but unsupported claim. -``` - -Keep entries short: normally 2–5 support bullets and no long prose. Do not copy -abstracts or infer claims from filenames. Add a TODO when support is unverified. - -## How the assistant should use a wiki - -1. On a user question, first open the sub-wiki's `index.md`. -2. Follow the relevant `concepts/` or `entities/` page. -3. Follow the source entry for claim scope and its canonical key for metadata. -4. Resolve that key against downstream `.bib` files before changing LaTeX. -5. If support or metadata is unclear, read the public paper and add a TODO - rather than guessing. Log verified upgrades. - -## Adding a sub-wiki - -Create `wiki/<domain>/` with its own `CLAUDE.md` (scope notes only — this -schema is inherited, not copied), `index.md`, `log.md`, and the page folders it -needs (`seed/` only if it is taking an unverified import). Give it a row in the -repo-root `index.md` and `README.md` tables. +@AGENTS.md diff --git a/wiki/cti/AGENTS.md b/wiki/cti/AGENTS.md index 7140970..931778d 100644 --- a/wiki/cti/AGENTS.md +++ b/wiki/cti/AGENTS.md @@ -1,4 +1,48 @@ -# Agent Instructions +# CTI AI Assistant — Charge Transfer Inefficiency Wiki -Read `CLAUDE.md` in this directory. It is the shared source of truth for local -agent instructions; adapt Claude-specific wording to the current agent. +This sub-wiki gives an AI assistant the scientific context of Charge +Transfer Inefficiency (CTI) in CCDs — the physics of charge trapping +and release in silicon, its impact on astronomical imaging, the +forward-model correction algorithms (`arctic`), and the Euclid VIS +detector calibration programme. Sibling of `../lensing/` under +`PyAutoMemory/`, same Karpathy "LLM Wiki" pattern. + +## Layout + +``` +cti/ +├── AGENTS.md # this file — schema + scope +├── index.md # top-level navigation +├── log.md # append-only compilation log +├── concepts/ # CTI physics + algorithmic topics +├── entities/ # Euclid VIS, Hubble ACS, arctic, etc. +└── sources/ # per-topic claim support +``` + +## Schema + +Inherits verbatim from [`../AGENTS.md`](../AGENTS.md) +— page types, naming, `[[wiki-links]]`, frontmatter, concept-page +structure, source-collection structure, `status: stub|drafted|reviewed`. +This file only diverges on scope. + +## Scope + +CTI physics, correction algorithms, trap-pumping calibration, charge +injection, the Euclid VIS detector and calibration pipeline, and the +Hall-Shockley-Read trap-emission theory underlying CTI. Source PDFs live +off-repo (the wiki was compiled from an off-repo CTI/Euclid paper corpus); +what's here is the durable knowledge plus canonical citation metadata in +`../../bibliography/`. + +Adjacent topics that link out: +- Sampling / Bayesian inference of trap-density posteriors — + `../methods/`. +- Cosmological weak-lensing shape biases from residual CTI — + `../lensing/` ([[weak-lensing]] when written). + +## How the assistant should use this wiki + +Same protocol as `../AGENTS.md`: follow concepts/entities to +compact source claims, use canonical metadata from `../../bibliography/`, resolve +downstream keys before editing LaTeX, and never fabricate. diff --git a/wiki/cti/CLAUDE.md b/wiki/cti/CLAUDE.md index bcc5fab..d1905df 100644 --- a/wiki/cti/CLAUDE.md +++ b/wiki/cti/CLAUDE.md @@ -1,48 +1,5 @@ -# CTI AI Assistant — Charge Transfer Inefficiency Wiki +# Claude Code adapter -This sub-wiki gives an AI assistant the scientific context of Charge -Transfer Inefficiency (CTI) in CCDs — the physics of charge trapping -and release in silicon, its impact on astronomical imaging, the -forward-model correction algorithms (`arctic`), and the Euclid VIS -detector calibration programme. Sibling of `../lensing/` under -`PyAutoMemory/`, same Karpathy "LLM Wiki" pattern. +Shared instructions live in [AGENTS.md](AGENTS.md). -## Layout - -``` -cti/ -├── CLAUDE.md # this file — schema + scope -├── index.md # top-level navigation -├── log.md # append-only compilation log -├── concepts/ # CTI physics + algorithmic topics -├── entities/ # Euclid VIS, Hubble ACS, arctic, etc. -└── sources/ # per-topic claim support -``` - -## Schema - -Inherits verbatim from [`../CLAUDE.md`](../CLAUDE.md) -— page types, naming, `[[wiki-links]]`, frontmatter, concept-page -structure, source-collection structure, `status: stub|drafted|reviewed`. -This file only diverges on scope. - -## Scope - -CTI physics, correction algorithms, trap-pumping calibration, charge -injection, the Euclid VIS detector and calibration pipeline, and the -Hall-Shockley-Read trap-emission theory underlying CTI. Source PDFs live -off-repo (the wiki was compiled from an off-repo CTI/Euclid paper corpus); -what's here is the durable knowledge plus canonical citation metadata in -`../../bibliography/`. - -Adjacent topics that link out: -- Sampling / Bayesian inference of trap-density posteriors — - `../methods/`. -- Cosmological weak-lensing shape biases from residual CTI — - `../lensing/` ([[weak-lensing]] when written). - -## How the assistant should use this wiki - -Same protocol as `../CLAUDE.md`: follow concepts/entities to -compact source claims, use canonical metadata from `../../bibliography/`, resolve -downstream keys before editing LaTeX, and never fabricate. +@AGENTS.md diff --git a/wiki/cti/index.md b/wiki/cti/index.md index 997b043..f63283d 100644 --- a/wiki/cti/index.md +++ b/wiki/cti/index.md @@ -1,6 +1,6 @@ # CTI Wiki — Index -Top-level navigation. See `CLAUDE.md` for the schema and how the assistant +Top-level navigation. See [AGENTS.md](AGENTS.md) for the schema and how the assistant should use this wiki. ## Start here @@ -54,5 +54,5 @@ live in [`../../bibliography/`](../../bibliography/README.md). ## Meta -- [[CLAUDE]] — schema and usage rules. +- [AGENTS.md](AGENTS.md) — schema and usage rules. - [[log]] — compilation history. diff --git a/wiki/galaxies/AGENTS.md b/wiki/galaxies/AGENTS.md index 7140970..8e13c08 100644 --- a/wiki/galaxies/AGENTS.md +++ b/wiki/galaxies/AGENTS.md @@ -1,4 +1,62 @@ -# Agent Instructions +# Galaxies AI Assistant — Galaxy Formation & Evolution Wiki -Read `CLAUDE.md` in this directory. It is the shared source of truth for local -agent instructions; adapt Claude-specific wording to the current agent. +This sub-wiki gives an AI assistant the scientific context of galaxy +formation and evolution as it bears on PyAutoLens / PyAutoGalaxy work: +elliptical-galaxy structure, bulge/disk/halo decompositions, light- +profile fitting, stellar halos, IFU kinematics, high-redshift galaxies, +COSMOS / COSMOS-Web morphology, dark-matter halo geometry from +galaxy-scale dynamics, and halo-galaxy connection statistics. Sibling +of `../lensing/` under `PyAutoMemory/`, same Karpathy "LLM Wiki" +pattern. + +## Layout + +``` +galaxies/ +├── AGENTS.md # this file — schema + scope +├── index.md # top-level navigation +├── log.md # append-only compilation log +├── concepts/ # galaxy-formation & morphology topics +├── entities/ # surveys (MaNGA, SAMI, COSMOS-Web), notable galaxies +├── sources/ # per-topic claim support +└── seed/ # unverified 2026-05 import — never cite from here +``` + +## Schema + +Inherits verbatim from [`../AGENTS.md`](../AGENTS.md). + +## Scope + +In-scope folders: + +- `MassiveEllPaper/` — massive elliptical galaxy paper drafts and refs. +- `Ellipticals/` — elliptical-galaxy structure and kinematics. +- `Bulge_Disk_Decomp/` — bulge+disk image decomposition methodology. +- `LightProFFits/` — light-profile fitting (Sérsic, MGE, free-form). +- `IFUs/` — integral-field unit spectroscopy methodology and results. +- `Manga/` — MaNGA survey-specific results. +- `COSMOS/` — COSMOS / COSMOS-Web survey papers. +- `StellarHalos/` — stellar-halo science, halo-mass proxies. +- `High_Redshift_galaxies/` — z > 4 galaxy structure, JWST results. +- `Dark_Matter_Geometry/` — galaxy-scale dark-matter halo shapes, + rotation-curve inference, dwarf-galaxy dynamics (this is *not* the + cluster/lensing dark-matter geometry — those live in + `../lensing/`). +- Several root-level singletons: `ETGKine1.pdf`, `ETGKine2.pdf`, + `Tinker2017*.pdf`, `Tinker2018*.pdf`, `Charlton2017*.pdf`, + `Leathuad2018LensingisLow.pdf`, `Saito2018*.pdf`, `Oh2016*.pdf`, + `Cohen2018DragonflyV.pdf`, `Greco2017*.pdf`, `Ferraras2019*.pdf`, + `COSMOSWeb.pdf`, `Hubble1926.321H`, `RimondiniGaia2018.pdf`, + `DuttonDarkMatterCore2018.pdf`. + +Adjacent topics that link out: +- Stellar mass / lensing constraints — + `../lensing/concepts/bulge-halo-decomposition.md`. +- Dark-matter substructure as seen in *lensed* systems — + `../lensing/concepts/dark-matter-substructure.md`. +- SMBH-host galaxy scaling relations — `../smbh/`. + +## How the assistant should use this wiki + +Same protocol as `../AGENTS.md`. diff --git a/wiki/galaxies/CLAUDE.md b/wiki/galaxies/CLAUDE.md index 8318434..d1905df 100644 --- a/wiki/galaxies/CLAUDE.md +++ b/wiki/galaxies/CLAUDE.md @@ -1,62 +1,5 @@ -# Galaxies AI Assistant — Galaxy Formation & Evolution Wiki +# Claude Code adapter -This sub-wiki gives an AI assistant the scientific context of galaxy -formation and evolution as it bears on PyAutoLens / PyAutoGalaxy work: -elliptical-galaxy structure, bulge/disk/halo decompositions, light- -profile fitting, stellar halos, IFU kinematics, high-redshift galaxies, -COSMOS / COSMOS-Web morphology, dark-matter halo geometry from -galaxy-scale dynamics, and halo-galaxy connection statistics. Sibling -of `../lensing/` under `PyAutoMemory/`, same Karpathy "LLM Wiki" -pattern. +Shared instructions live in [AGENTS.md](AGENTS.md). -## Layout - -``` -galaxies/ -├── CLAUDE.md # this file — schema + scope -├── index.md # top-level navigation -├── log.md # append-only compilation log -├── concepts/ # galaxy-formation & morphology topics -├── entities/ # surveys (MaNGA, SAMI, COSMOS-Web), notable galaxies -├── sources/ # per-topic claim support -└── seed/ # unverified 2026-05 import — never cite from here -``` - -## Schema - -Inherits verbatim from [`../CLAUDE.md`](../CLAUDE.md). - -## Scope - -In-scope folders: - -- `MassiveEllPaper/` — massive elliptical galaxy paper drafts and refs. -- `Ellipticals/` — elliptical-galaxy structure and kinematics. -- `Bulge_Disk_Decomp/` — bulge+disk image decomposition methodology. -- `LightProFFits/` — light-profile fitting (Sérsic, MGE, free-form). -- `IFUs/` — integral-field unit spectroscopy methodology and results. -- `Manga/` — MaNGA survey-specific results. -- `COSMOS/` — COSMOS / COSMOS-Web survey papers. -- `StellarHalos/` — stellar-halo science, halo-mass proxies. -- `High_Redshift_galaxies/` — z > 4 galaxy structure, JWST results. -- `Dark_Matter_Geometry/` — galaxy-scale dark-matter halo shapes, - rotation-curve inference, dwarf-galaxy dynamics (this is *not* the - cluster/lensing dark-matter geometry — those live in - `../lensing/`). -- Several root-level singletons: `ETGKine1.pdf`, `ETGKine2.pdf`, - `Tinker2017*.pdf`, `Tinker2018*.pdf`, `Charlton2017*.pdf`, - `Leathuad2018LensingisLow.pdf`, `Saito2018*.pdf`, `Oh2016*.pdf`, - `Cohen2018DragonflyV.pdf`, `Greco2017*.pdf`, `Ferraras2019*.pdf`, - `COSMOSWeb.pdf`, `Hubble1926.321H`, `RimondiniGaia2018.pdf`, - `DuttonDarkMatterCore2018.pdf`. - -Adjacent topics that link out: -- Stellar mass / lensing constraints — - `../lensing/concepts/bulge-halo-decomposition.md`. -- Dark-matter substructure as seen in *lensed* systems — - `../lensing/concepts/dark-matter-substructure.md`. -- SMBH-host galaxy scaling relations — `../smbh/`. - -## How the assistant should use this wiki - -Same protocol as `../CLAUDE.md`. +@AGENTS.md diff --git a/wiki/galaxies/index.md b/wiki/galaxies/index.md index 64dc6de..bad67a7 100644 --- a/wiki/galaxies/index.md +++ b/wiki/galaxies/index.md @@ -1,6 +1,6 @@ # Galaxies Wiki — Index -Top-level navigation. See `CLAUDE.md` for the schema and how the assistant +Top-level navigation. See [AGENTS.md](AGENTS.md) for the schema and how the assistant should use this wiki. ## Start here @@ -97,5 +97,5 @@ live in [`../../bibliography/`](../../bibliography/README.md). ## Meta -- [[CLAUDE]] — schema and usage rules. +- [AGENTS.md](AGENTS.md) — schema and usage rules. - [[log]] — compilation history. diff --git a/wiki/lensing/AGENTS.md b/wiki/lensing/AGENTS.md index 7140970..459d42c 100644 --- a/wiki/lensing/AGENTS.md +++ b/wiki/lensing/AGENTS.md @@ -1,4 +1,39 @@ -# Agent Instructions +# PyAutoLens AI Assistant — Strong Lensing Wiki -Read `CLAUDE.md` in this directory. It is the shared source of truth for local -agent instructions; adapt Claude-specific wording to the current agent. +This sub-wiki gives a PyAutoLens AI assistant broad scientific context for +strong gravitational lensing: the lens equation, mass models, source +reconstruction, degeneracies, time-delay cosmography, dark-matter +substructure, the major surveys and the software landscape. It is the +primary sub-wiki; the shared schema is defined in +[`../AGENTS.md`](../AGENTS.md). + +## Schema + +Inherits verbatim from [`../AGENTS.md`](../AGENTS.md) — page types, naming, +`[[wiki-links]]`, frontmatter, concept-page structure, source-collection +structure, `status: stub|drafted|reviewed`. This file only diverges on +scope. In concept pages, "Why it matters" is written for PyAutoLens users +("Why it matters for PyAutoLens"). + +## Scope + +Strong gravitational lensing end to end: galaxy- and cluster-scale lenses, +substructure and dark-matter detection, lens searches and samples, source +reconstruction, cosmography. Source PDFs live off-repo (the wiki was +compiled from an off-repo corpus: Strong_Lens, Substructure, +StrongLensCluster, Dark_Matter_Detection, DarkMatterModels); what's here is +the durable knowledge plus canonical citation metadata in +`../../bibliography/`. + +Adjacent topics that link out: +- Weak lensing, LSS, clusters as cosmology probes — out of scope until + explicitly added; see `log.md` for the decision. +- Bayesian inference and samplers — `../methods/`. +- Galaxy structure and evolution of the deflector population — + `../galaxies/`. + +## How the assistant should use this wiki + +Same protocol as [`../AGENTS.md`](../AGENTS.md): follow concepts/entities to +compact source claims, use canonical metadata from `../../bibliography/`, +resolve downstream keys before editing LaTeX, and never fabricate. diff --git a/wiki/lensing/CLAUDE.md b/wiki/lensing/CLAUDE.md index 380dfd0..d1905df 100755 --- a/wiki/lensing/CLAUDE.md +++ b/wiki/lensing/CLAUDE.md @@ -1,39 +1,5 @@ -# PyAutoLens AI Assistant — Strong Lensing Wiki +# Claude Code adapter -This sub-wiki gives a PyAutoLens AI assistant broad scientific context for -strong gravitational lensing: the lens equation, mass models, source -reconstruction, degeneracies, time-delay cosmography, dark-matter -substructure, the major surveys and the software landscape. It is the -primary sub-wiki; the shared schema is defined in -[`../CLAUDE.md`](../CLAUDE.md). +Shared instructions live in [AGENTS.md](AGENTS.md). -## Schema - -Inherits verbatim from [`../CLAUDE.md`](../CLAUDE.md) — page types, naming, -`[[wiki-links]]`, frontmatter, concept-page structure, source-collection -structure, `status: stub|drafted|reviewed`. This file only diverges on -scope. In concept pages, "Why it matters" is written for PyAutoLens users -("Why it matters for PyAutoLens"). - -## Scope - -Strong gravitational lensing end to end: galaxy- and cluster-scale lenses, -substructure and dark-matter detection, lens searches and samples, source -reconstruction, cosmography. Source PDFs live off-repo (the wiki was -compiled from an off-repo corpus: Strong_Lens, Substructure, -StrongLensCluster, Dark_Matter_Detection, DarkMatterModels); what's here is -the durable knowledge plus canonical citation metadata in -`../../bibliography/`. - -Adjacent topics that link out: -- Weak lensing, LSS, clusters as cosmology probes — out of scope until - explicitly added; see `log.md` for the decision. -- Bayesian inference and samplers — `../methods/`. -- Galaxy structure and evolution of the deflector population — - `../galaxies/`. - -## How the assistant should use this wiki - -Same protocol as [`../CLAUDE.md`](../CLAUDE.md): follow concepts/entities to -compact source claims, use canonical metadata from `../../bibliography/`, -resolve downstream keys before editing LaTeX, and never fabricate. +@AGENTS.md diff --git a/wiki/lensing/index.md b/wiki/lensing/index.md index 0b1352b..447f134 100755 --- a/wiki/lensing/index.md +++ b/wiki/lensing/index.md @@ -1,6 +1,6 @@ # PyAutoLens Strong Lensing Wiki — Index -Top-level navigation. See `CLAUDE.md` for the schema and how the assistant +Top-level navigation. See [AGENTS.md](AGENTS.md) for the schema and how the assistant should use this wiki. ## Start here @@ -117,5 +117,5 @@ live in [`../../bibliography/`](../../bibliography/README.md). ## Meta -- [[CLAUDE]] — schema and usage rules. +- [AGENTS.md](AGENTS.md) — schema and usage rules. - [[log]] — compilation history. diff --git a/wiki/methods/AGENTS.md b/wiki/methods/AGENTS.md index 7140970..678325c 100644 --- a/wiki/methods/AGENTS.md +++ b/wiki/methods/AGENTS.md @@ -1,4 +1,57 @@ -# Agent Instructions +# Methods AI Assistant — Statistical & Computational Methods Wiki -Read `CLAUDE.md` in this directory. It is the shared source of truth for local -agent instructions; adapt Claude-specific wording to the current agent. +This sub-wiki gives an AI assistant the scientific context of the +**methodological** tooling that underpins PyAutoLens, PyAutoFit, and +related codes: Bayesian inference, nested and Hamiltonian sampling, +deep learning for astrophysics, probabilistic programming languages, +linear-algebra primitives (NUFFT, message passing), and the wider +scientific-software ecosystem. Sibling of `../lensing/` under +`PyAutoMemory/`, same Karpathy "LLM Wiki" pattern. + +## Layout + +``` +methods/ +├── AGENTS.md # this file — schema + scope +├── index.md # top-level navigation +├── log.md # append-only compilation log +├── concepts/ # Bayes basics, samplers, deep learning, etc. +├── entities/ # PyAutoFit, PolyChord, BlackJAX, jax-finufft, … +├── sources/ # per-topic claim support +└── seed/ # unverified 2026-05 import — never cite from here +``` + +## Schema + +Inherits verbatim from [`../AGENTS.md`](../AGENTS.md). + +## Scope + +In-scope folders: + +- `Stats/` — Bayesian methods, likelihood-free inference, MCMC, + sampler comparisons. +- `GaussianLinearModels/` — Gaussian linear models, conjugate priors, + closed-form posteriors used in linear inversion. +- `PPLs/` — probabilistic programming languages (Stan, PyMC, NumPyro, + Pyro, etc.). +- `Deep Learning/` — CNNs, BNNs, simulation-based inference applied + to astrophysics (cross-references `../lensing/sources-deep-learning-lensing.md`). +- `Software/` — general-purpose scientific software references (samplers, + optimisers, JAX ecosystem). +- `Simulation/` — Monte Carlo simulation methodology, hierarchical + forward modelling. +- Root-level `PolyChord.pdf`, `linearalgebra.pdf`, `NUFFTPAper.pdf`, + `PYNUFFT.pdf`, `MessagePassingIsAWayOfLife.pdf`, `BigData.pdf`, + `PyLops` (folder), `imfit.pdf`, `Profit2019.pdf`. + +Adjacent topics that link out: +- Lens-modelling-specific Bayesian / regularisation methods — + `../lensing/concepts/bayesian-inference-lensing.md` and + `../lensing/concepts/regularization.md`. +- Mass-model / source-reconstruction software entities — + `../lensing/entities/{pyautolens,pyautofit,lenstronomy}.md`. + +## How the assistant should use this wiki + +Same protocol as `../AGENTS.md`. diff --git a/wiki/methods/CLAUDE.md b/wiki/methods/CLAUDE.md index b76cde9..d1905df 100644 --- a/wiki/methods/CLAUDE.md +++ b/wiki/methods/CLAUDE.md @@ -1,57 +1,5 @@ -# Methods AI Assistant — Statistical & Computational Methods Wiki +# Claude Code adapter -This sub-wiki gives an AI assistant the scientific context of the -**methodological** tooling that underpins PyAutoLens, PyAutoFit, and -related codes: Bayesian inference, nested and Hamiltonian sampling, -deep learning for astrophysics, probabilistic programming languages, -linear-algebra primitives (NUFFT, message passing), and the wider -scientific-software ecosystem. Sibling of `../lensing/` under -`PyAutoMemory/`, same Karpathy "LLM Wiki" pattern. +Shared instructions live in [AGENTS.md](AGENTS.md). -## Layout - -``` -methods/ -├── CLAUDE.md # this file — schema + scope -├── index.md # top-level navigation -├── log.md # append-only compilation log -├── concepts/ # Bayes basics, samplers, deep learning, etc. -├── entities/ # PyAutoFit, PolyChord, BlackJAX, jax-finufft, … -├── sources/ # per-topic claim support -└── seed/ # unverified 2026-05 import — never cite from here -``` - -## Schema - -Inherits verbatim from [`../CLAUDE.md`](../CLAUDE.md). - -## Scope - -In-scope folders: - -- `Stats/` — Bayesian methods, likelihood-free inference, MCMC, - sampler comparisons. -- `GaussianLinearModels/` — Gaussian linear models, conjugate priors, - closed-form posteriors used in linear inversion. -- `PPLs/` — probabilistic programming languages (Stan, PyMC, NumPyro, - Pyro, etc.). -- `Deep Learning/` — CNNs, BNNs, simulation-based inference applied - to astrophysics (cross-references `../lensing/sources-deep-learning-lensing.md`). -- `Software/` — general-purpose scientific software references (samplers, - optimisers, JAX ecosystem). -- `Simulation/` — Monte Carlo simulation methodology, hierarchical - forward modelling. -- Root-level `PolyChord.pdf`, `linearalgebra.pdf`, `NUFFTPAper.pdf`, - `PYNUFFT.pdf`, `MessagePassingIsAWayOfLife.pdf`, `BigData.pdf`, - `PyLops` (folder), `imfit.pdf`, `Profit2019.pdf`. - -Adjacent topics that link out: -- Lens-modelling-specific Bayesian / regularisation methods — - `../lensing/concepts/bayesian-inference-lensing.md` and - `../lensing/concepts/regularization.md`. -- Mass-model / source-reconstruction software entities — - `../lensing/entities/{pyautolens,pyautofit,lenstronomy}.md`. - -## How the assistant should use this wiki - -Same protocol as `../CLAUDE.md`. +@AGENTS.md diff --git a/wiki/methods/index.md b/wiki/methods/index.md index 0c8a8d3..1c275a9 100644 --- a/wiki/methods/index.md +++ b/wiki/methods/index.md @@ -1,6 +1,6 @@ # Methods Wiki — Index -Top-level navigation. See `CLAUDE.md` for the schema and how the assistant +Top-level navigation. See [AGENTS.md](AGENTS.md) for the schema and how the assistant should use this wiki. ## Start here @@ -100,5 +100,5 @@ live in [`../../bibliography/`](../../bibliography/README.md). ## Meta -- [[CLAUDE]] — schema and usage rules. +- [AGENTS.md](AGENTS.md) — schema and usage rules. - [[log]] — compilation history. diff --git a/wiki/smbh/AGENTS.md b/wiki/smbh/AGENTS.md index 7140970..606a522 100644 --- a/wiki/smbh/AGENTS.md +++ b/wiki/smbh/AGENTS.md @@ -1,4 +1,55 @@ -# Agent Instructions +# SMBH AI Assistant — Supermassive Black Holes Wiki -Read `CLAUDE.md` in this directory. It is the shared source of truth for local -agent instructions; adapt Claude-specific wording to the current agent. +This sub-wiki gives an AI assistant the scientific context of supermassive +black holes (SMBHs): their binaries, recoil, scouring of galactic nuclei, +mass functions, and the nanohertz gravitational-wave background. It is a +sibling of `../lensing/` under the same `PyAutoMemory/` repo and follows +the same Karpathy "LLM Wiki" pattern: source PDFs live off-repo, and this +folder is the compiled, cross-linked knowledge layer that lives in git. + +## Layout + +``` +smbh/ +├── AGENTS.md # this file — schema + scope +├── index.md # top-level navigation +├── log.md # append-only compilation log +├── concepts/ # one topic per page — the physics +├── entities/ # named surveys, collaborations, codes +└── sources/ # per-topic claim support (one paper = one section) +``` + +## Schema + +All schema rules — page types, naming, `[[wiki-links]]`, frontmatter, +concept page structure, source-collection structure, status flags +(`stub | drafted | reviewed`) — are inherited verbatim from +[`../AGENTS.md`](../AGENTS.md). Read that file +first; this one only diverges on scope. + +Cross-wiki links use the same slug form as everything else: +`[[smbh-from-lensing]]` — slugs are unique across sub-wikis, so no path +prefix is ever needed (the slug-only rule in `../AGENTS.md`). + +## Scope + +In-scope folders (PDFs live alongside this wiki, gitignored): + +- `SMBHs/` — primary; ~44 PDFs on SMBH formation, binaries, recoil, + scouring, dual AGN, mass functions. +- `GWB/` — gravitational-wave background (pulsar-timing array + detections, theoretical predictions). +- Selected root-level PDFs assigned by topic (e.g. `Krist2011TinyTim.pdf` + for HST/JWST PSF modelling of AGN host decompositions). + +Adjacent topics that link out: +- Galaxy-scale dynamics, host-galaxy properties — `../galaxies/`. +- Bayesian inference on hierarchical population models — `../methods/`. +- SMBHs detected/constrained via strong lensing — `../lensing/` + ([[smbh-from-lensing]]). + +## How the assistant should use this wiki + +Follow the protocol in `../AGENTS.md`: trace claims through compact +source entries, use canonical metadata from `../../bibliography/`, resolve keys +against downstream projects before changing LaTeX, and never fabricate. diff --git a/wiki/smbh/CLAUDE.md b/wiki/smbh/CLAUDE.md index e44df54..d1905df 100644 --- a/wiki/smbh/CLAUDE.md +++ b/wiki/smbh/CLAUDE.md @@ -1,55 +1,5 @@ -# SMBH AI Assistant — Supermassive Black Holes Wiki +# Claude Code adapter -This sub-wiki gives an AI assistant the scientific context of supermassive -black holes (SMBHs): their binaries, recoil, scouring of galactic nuclei, -mass functions, and the nanohertz gravitational-wave background. It is a -sibling of `../lensing/` under the same `PyAutoMemory/` repo and follows -the same Karpathy "LLM Wiki" pattern: source PDFs live off-repo, and this -folder is the compiled, cross-linked knowledge layer that lives in git. +Shared instructions live in [AGENTS.md](AGENTS.md). -## Layout - -``` -smbh/ -├── CLAUDE.md # this file — schema + scope -├── index.md # top-level navigation -├── log.md # append-only compilation log -├── concepts/ # one topic per page — the physics -├── entities/ # named surveys, collaborations, codes -└── sources/ # per-topic claim support (one paper = one section) -``` - -## Schema - -All schema rules — page types, naming, `[[wiki-links]]`, frontmatter, -concept page structure, source-collection structure, status flags -(`stub | drafted | reviewed`) — are inherited verbatim from -[`../CLAUDE.md`](../CLAUDE.md). Read that file -first; this one only diverges on scope. - -Cross-wiki links use the same slug form as everything else: -`[[smbh-from-lensing]]` — slugs are unique across sub-wikis, so no path -prefix is ever needed (the slug-only rule in `../CLAUDE.md`). - -## Scope - -In-scope folders (PDFs live alongside this wiki, gitignored): - -- `SMBHs/` — primary; ~44 PDFs on SMBH formation, binaries, recoil, - scouring, dual AGN, mass functions. -- `GWB/` — gravitational-wave background (pulsar-timing array - detections, theoretical predictions). -- Selected root-level PDFs assigned by topic (e.g. `Krist2011TinyTim.pdf` - for HST/JWST PSF modelling of AGN host decompositions). - -Adjacent topics that link out: -- Galaxy-scale dynamics, host-galaxy properties — `../galaxies/`. -- Bayesian inference on hierarchical population models — `../methods/`. -- SMBHs detected/constrained via strong lensing — `../lensing/` - ([[smbh-from-lensing]]). - -## How the assistant should use this wiki - -Follow the protocol in `../CLAUDE.md`: trace claims through compact -source entries, use canonical metadata from `../../bibliography/`, resolve keys -against downstream projects before changing LaTeX, and never fabricate. +@AGENTS.md diff --git a/wiki/smbh/index.md b/wiki/smbh/index.md index 691cb52..956289c 100644 --- a/wiki/smbh/index.md +++ b/wiki/smbh/index.md @@ -1,6 +1,6 @@ # SMBH Wiki — Index -Top-level navigation. See `CLAUDE.md` for the schema and how the assistant +Top-level navigation. See [AGENTS.md](AGENTS.md) for the schema and how the assistant should use this wiki. ## Start here @@ -74,5 +74,5 @@ live in [`../../bibliography/`](../../bibliography/README.md). ## Meta -- [[CLAUDE]] — schema and usage rules. +- [AGENTS.md](AGENTS.md) — schema and usage rules. - [[log]] — compilation history.