murmurent 2026.9.3__tar.gz

murmurent-2026.9.3/.gitignore

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+.claude/settings.local.json
+.DS_Store
+
+## Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.venv/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+
+## LaTeX build artefacts (in case of ad-hoc compiles in this repo)
+*.aux
+*.bbl
+*.blg
+*.log
+*.out
+*.fdb_latexmk
+*.fls
+*.synctex.gz
+texput.log
+node_modules/
+package-lock.json
+package.json
+site/
+
+# Local-only agents (not part of the commons)
+agents/pm.md
+
+## Local doc render artefacts (R Markdown / pandoc)
+.Rhistory
+docs/*.html

murmurent-2026.9.3/CHANGELOG.md

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+# Changelog
+
+All notable, release-worthy changes to murmurent are recorded here. The format
+follows [Keep a Changelog](https://keepachangelog.com/); the version scheme is
+**CalVer `YYYY.M.MICRO`** (see [`docs/versioning.md`](docs/versioning.md)).
+
+**When to add an entry:** bump the version and add a section only for a
+*structural* release — a new commons agent, a marker/schema change, or anything
+that should make existing murmurent-ready repos want `murmurent repo upgrade`.
+Agent-content edits (prompt tweaks, rule wording, docs) propagate automatically
+via the `.claude/agents` symlinks and need **no** version bump — don't add a
+changelog entry or a tag for those. Developers append to `[Unreleased]` as
+structural changes land; it's cut to a dated version at release time.
+
+The version lives in exactly one place: `src/murmurent/__init__.py`
+(`__version__`). `pyproject.toml` reads it from there.
+
+## [Unreleased]
+
+## [2026.9.3] — 2026-09-01
+
+### Added
+- **`uv tool install murmurent` is now a complete install.** The wheel
+  force-includes the commons (`agents/`, `rules/`, `skills/`, `templates/`,
+  `CLAUDE.md`) under `murmurent/commons/`; `core/commons.py` resolves them, and
+  a new `murmurent setup` wires them into `~/.claude/`. No clone and no
+  `curl | bash` required. A clone still wins over the packaged copy, decided by
+  content rather than by name, so editing an agent in a clone takes effect at
+  once and an empty directory from a failed clone cannot win.
+
+### Changed
+- **`murmurent install` with no flags now performs the whole install** (wire
+  the commons, then register hooks) instead of printing "not yet implemented in
+  v1". `--hooks` still means hooks only, so `scripts/bootstrap.sh` and existing
+  callers are unaffected.
+- Licence metadata is Apache-2.0 throughout, with a matching PyPI classifier.
+
+## [2026.9.2] — 2026-09-01
+
+### Added
+- **PyPI publishing** via `.github/workflows/publish.yml`, using trusted
+  publishing (no stored token). The build job runs on every release; the
+  upload job is gated on the `PYPI_ENABLED` repository variable so it is
+  visibly skipped rather than silently absent until PyPI is configured.
+- **`DEVELOPING.md`** (development repository only): the dev setup, what
+  `rules/local/` is for, the pre-push checks, and how a release is cut.
+
+### Changed
+- `README.md` now says plainly that this repository carries released versions
+  only, and points bug reports at the development repository's issues.
+
+## [2026.9.1] — 2026-09-01
+
+### Fixed
+- **Author email in the package metadata was wrong** (`hallett.mike.t@gmail.com`);
+  it is `michael.hallett@uwo.ca`. This shipped in 2026.9.0 and would have been
+  the contact address on PyPI.
+- **Licence metadata contradicted the licence.** `pyproject.toml` declared MIT
+  while `LICENSE` is, and has always been, Apache-2.0. The metadata now matches
+  the file. No licence has changed; the declaration was wrong.
+
+## [2026.9.0] — 2026-09-01
+
+**First public release.** Development moves to `murmurent_dev`; this repo now
+carries released versions only, one commit per release.
+
+### Added
+- **`murmurent keyring`** — distribute a centre's shared secrets (the Slack token,
+  and later the onboarding age key) across a principal's machines via per-machine
+  `age` identities and multi-recipient `age` boxes committed to the `lab_info`
+  repo, locked **per role** so a `server` machine cannot open a `mayor`-only box
+  (e.g. the root CA). Commands: `init`, `authorize`, `set-secret`,
+  `rotate-secret`, `revoke`, `sync`, `status`, `check`, `verify`. Self-heals via
+  `murmurent reconcile`. Introduces a `.keyring/` store under `lab_info`. Design
+  and runbooks in [`docs/keyring.md`](docs/keyring.md) /
+  [`docs/keyring_deploy.md`](docs/keyring_deploy.md).
+- **`rules/local/`** — a deployment layer for facts true of one centre only
+  (its own private repos, Slack IDs, local conventions). `scripts/setup.sh`
+  symlinks these alongside the shared rules when the directory exists; a clone
+  without one simply skips it.
+
+### Changed
+- `CLAUDE.md` is institution-agnostic: no hardcoded university, GitHub owner
+  written as `<owner>`, and no reference to any one centre's private repos.
+- `rules/slack.md` carries the posting protocol only. The channel, workspace
+  and bot are deployment facts and belong in `rules/local/`.
+
+### Fixed
+- **Slack notifications no longer default to one lab's channel.**
+  `dashboard/slack_notify.py` and `commands/reconcile_cmd.py` each hardcoded a
+  channel ID as the last-resort destination for every notification, so any
+  installation would have posted there. Both now resolve from
+  `MURMURENT_SLACK_DEFAULT_CHANNEL` / `MURMURENT_SLACK_INFRA_CHANNEL` or
+  `~/.config/murmurent/`, and decline to post when unset.
+
+## [2026.7.0] — 2026-07-16
+
+First numbered release. Establishes version tracking itself (issue #24):
+
+### Changed
+- **Single source of truth for the version.** `pyproject.toml` now reads
+  `__version__` from `src/murmurent/__init__.py` via Hatchling's
+  `[tool.hatch.version]`, so the package metadata, `murmurent --version`, and
+  the `bootstrap_version` stamped into every repo's `.murmurent.yaml` can no
+  longer disagree. Previously `pyproject.toml` said `1.0.0` while the runtime
+  reported `0.1.0`.
+- **Adopted CalVer** (`YYYY.M.MICRO`), bumped only on structural releases and
+  tied to the `murmurent repo upgrade` mechanism: if the version changed, run
+  `murmurent repo upgrade --all`; if it didn't, you're current.
+
+### Notes
+- Because `Readiness.needs_upgrade` compares the stamped `bootstrap_version`
+  against the current version by string inequality, existing murmurent-ready
+  repos (stamped `0.1.0`) will show `needs_upgrade = True` once. That's the
+  intended "a new release shipped" signal — run `murmurent repo upgrade --all`
+  to re-stamp them. Harmless if you don't; agent content is already current via
+  the symlinks.
+- The on-disk/on-wire schema versions (`MARKER_SCHEMA`, `CARD_VERSION`,
+  `SIGNED_CARD_VERSION`) are versioned independently of this release number and
+  bump only when their own format changes.

murmurent-2026.9.3/CLAUDE.md

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+# Murmurent — an agentic AI village for a research centre
+
+Murmurent is shared agentic-AI infrastructure that lets research groups
+work independently, pool agents and data when collaboration benefits
+them, and accumulate institutional knowledge across every project.
+
+An overview is in [`docs/index.md`](docs/index.md) and
+[`docs/overview.md`](docs/overview.md). In short:
+
+- **Choreography, not orchestration.** Each group runs its own
+  documented workflow using the shared agents and rules, and retains
+  authority over its own members and data. Distributing control this
+  way limits the scope of any single failure and preserves each
+  group's autonomy. ("Choreography" is the term used throughout the
+  code for a recurring multi-actor workflow recipe.)
+- **Four social units**: individual members; groups (each a lab or a
+  core, led by a PI); projects (units of work that bring members
+  together, potentially across groups); and the administration
+  (centre-level governance and registry).
+- **The commons** = centre-wide AI infrastructure every member draws
+  on (reference agents + data-governance rules + baseline workflows).
+  Group/core toolkits are built on top.
+
+## Reference agents (the commons)
+
+Defined in [`agents/`](agents/), symlinked into `~/.claude/agents/`
+by [`scripts/setup.sh`](scripts/setup.sh). Each MUST begin its final
+reply with a ≤200-char verdict line (see
+[`rules/headline_first.md`](rules/headline_first.md)).
+
+| Agent | Role |
+|---|---|
+| [`oracle`](agents/oracle.md) | Personal research memory (per-user Obsidian vault) |
+| [`lab_oracle`](agents/lab_oracle.md) | Lab-shared institutional memory (read-only; promoted via `murmurent oracle publish`) |
+| [`bookworm`](agents/bookworm.md) | Literature + database integration |
+| [`blacksmith`](agents/blacksmith.md) | Computation, statistics, feature engineering |
+| [`adversary`](agents/adversary.md) | Methodological audit + peer review; auto-refers IP-bearing work to the [`lawyer`](agents/lawyer.md) and folds their verdict into its own |
+| [`artist`](agents/artist.md) | Visualization, communication, education |
+| [`teacher`](agents/teacher.md) | Three modes, one entry point — `teacher debrief` \| `explain` \| `course` (see below). Debrief is "wait, what?" — fired at the sentence CC just wrote that was jargon, overcomplicated, or handed you an unexplained decision; it re-pitches that in plain words in chat, under 60s, from the tail of the real session transcript. Explain covers any method or paper; course recognises a subject and hands it to the course skill. Only explain renders a self-contained HTML page, on request, annotated in `lavish-axi` — where "wait, what?" gets that same re-pitch. Bullet-led and jargon-light, and it makes things **visual — reusing before drawing**: first a real image it found and may reuse (inlined with its licence, captioned with what to notice), then a video it actually loaded, and only then something hand-drawn (inline SVG, mermaid, a slider) when nothing suitable exists or the reader needs a knob to drag. Figures needing real data still go to the [`artist`](agents/artist.md). It has `WebSearch`/`WebFetch` for exactly this, **scoped: `debrief` is offline entirely**, since a search query is outbound text and session transcripts are not public. It never emits a URL, title, or attribution it did not load; citations it cannot verify escalate to the [`bookworm`](agents/bookworm.md). (persona: Richard Feynman — answers to "Feynman") |
+| [`conscience`](agents/conscience.md) | EDID + bias review. **Reviewing is the default and is not a mode** — located, line-by-line findings, every one with a citation, and its rules bind whatever else the agent is doing. One entry point, no mode to select: it is pointed at something and infers from it whether one of two other things is wanted instead, each inferred rather than named: **explain** fires on a flag the author disputed or missed, and re-pitches that one flag — in chat, or on request as an HTML page annotated in `lavish-axi`; it either teaches the concept or names an existing training module. and **design** fires when nothing has been built yet, returning the equitable blueprint — the design itself, not objections to one already built. Never speaks for — or as — a marginalized community; doesn't browse — the [`bookworm`](agents/bookworm.md) curates its resources. **No persona:** it works in a tradition (bell hooks, Freire, Lorde, Baldwin) and cites it rather than impersonating it. |
+| [`lawyer`](agents/lawyer.md) | Patent counsel + freedom-to-operate (formerly `saul_goodman`); reached on request **or** by automatic referral from the [`adversary`](agents/adversary.md) mid-audit — triages first, so a referral with no IP surface costs one step, not six database searches |
+| [`cable_guy`](agents/cable_guy.md) | Infrastructure provisioner |
+| [`centre_cable_guy`](agents/centre_cable_guy.md) | Centre-wide infrastructure reconciler (cross-lab ACLs, drift loop) |
+| [`judge`](agents/judge.md) | Combines and presents member contributions in a compositional choreography |
+| [`registrar`](agents/registrar.md) | Centre-wide registry of labs/cores/collaborations |
+| [`security_guard`](agents/security_guard.md) | Secrets, PHI, world-accessible files audit |
+
+Group/core toolkits build on top of the commons — discipline-specific
+agents (medchem, segmenter, cohort, …) live in the owning group's
+own repo and compose against this reference set.
+
+## Hard rules (always loaded)
+
+Auto-loaded into every CC session via `~/.claude/rules/`:
+
+- [`rules/data-storage.md`](rules/data-storage.md) — the `immutable/`
+  directory is read-only and `append_only/` is append-only (data lives under
+  `$MURMURENT_DATA_ROOT`; legacy `raw/`/`refined/` and `MURMURENT_LAB_VM_ROOT`
+  stay recognized during the transition). Upheld for agents by the
+  [`raw_guard`](src/murmurent/hooks/raw_guard.py) +
+  [`protected_paths`](src/murmurent/hooks/protected_paths.py) hooks, which
+  refuse deletes and overwrites under immutable/append_only **from inside a
+  Claude Code session**. This is a guardrail, not a security perimeter: the
+  hooks are per-user and inert in a plain shell, in a script run outside a
+  session, and for any member who has not installed them. The trees themselves
+  are group-writable on disk.
+- [`rules/project-structure.md`](rules/project-structure.md) —
+  `~/repos/<project>/{exp,src,obsolete,data}`, snake_case, integer-versioned files.
+- [`rules/oracle_schema.md`](rules/oracle_schema.md) — every Oracle
+  entry needs `title`, `date`, `project`, `sensitivity`, `tags`, `sources`.
+- [`rules/headline_first.md`](rules/headline_first.md) — every agent's
+  final reply leads with a ≤200-char verdict.
+- [`rules/slack.md`](rules/slack.md) — Slack-posting protocol (after
+  every `git push`, post to the group's own channel). Which channel,
+  workspace and bot is a deployment fact and lives in `rules/local/`.
+
+**Deployment-specific rules.** A centre may add its own rules under
+`rules/local/`, which `scripts/setup.sh` symlinks alongside the shared
+ones when the directory exists. That is where private repos, Slack IDs
+and local conventions belong, so that nothing tied to one centre reaches
+another. A fresh clone has no `rules/local/` and simply skips it.
+
+## User-invocable skills (the commons)
+
+Defined in [`skills/`](skills/), symlinked into `~/.claude/skills/` by
+[`scripts/setup.sh`](scripts/setup.sh). Each is a single-purpose slash
+command available in any murmurent-bootstrapped CC session.
+
+| Skill | Role |
+|---|---|
+| [`/murmurent-push`](skills/murmurent-push/SKILL.md) | Murmurent-aware stage/commit/push: skips per-machine + secret-shaped files, refuses large files that belong in `append_only/`, never touches the data root's `immutable/`\|`append_only/` (or legacy `raw/`\|`refined/`), posts a Slack release note. Use instead of generic `/commit-push` for any **murmurent-ready** repo (`.murmurent.yaml`, or a legacy `CHARTER.md` bootstrap). |
+| [`/murmurent-project-push`](skills/murmurent-project-push/SKILL.md) | Project-WIDE commit/push: backs up **every** repo a project owns (via `murmurent project push`), running the `/murmurent-push` pre-flight per repo (secret scan, secret-shaped names, governed-data + large-file guards). A repo that fails is blocked, the rest proceed; one plain-language summary + one Slack note to the project channel. Use to "back up my whole project". |
+| [`/murmurent-admin`](skills/murmurent-admin/SKILL.md) | Prime context before admin-level (centre / mayor / registrar / join / provisioning) work: reloads murmurent's purpose from the code and docs, and pins Obsidian maps-legends and CC guidance to the top. A centre with its own reference documents adds them via `rules/local/`. |
+| [`/murmurent-reset`](skills/murmurent-reset/SKILL.md) | Back up, then reset this machine's murmurent state to a fresh start (so `centre-init` is first-run again). Tiered `centre`/`install`/`full`; always tarballs `~/.murmurent` first; credentials + other-project installs are protected behind explicit `--nuke` flags; `--dry-run` previews. Use for a clean slate / fresh copy from the repo. |
+| [`/murmurent-onboard`](skills/murmurent-onboard/SKILL.md) | Mayor/registrar helper: process an incoming **encrypted** join-request email end to end — decrypt + file it, show who's asking, then (on explicit OK) approve + provision (lab/core Slack channel, GitHub repo, FS ACLs) or decline. Approval reads the Slack token from env **or** the `~/.config` file so the channel is created without exporting anything. |
+| [`/murmurent-course`](skills/murmurent-course/SKILL.md) | **COURSE mode of the [`teacher`](agents/teacher.md)** — reached by typing `teacher course <subject>`, not by the slash command. Teaches a subject across **multiple sessions** using a course directory as stateful memory: interviews for the mission, sources it through the [`bookworm`](agents/bookworm.md), writes self-contained HTML lessons the learner annotates in `lavish-axi`, and keeps learning records so it never re-teaches what they've demonstrated. Sources **watching as well as reading** — every lesson carries a drawn figure, and where a public explainer beats the page, it assigns the video and writes the bridge instead of competing. Runs in the main session — a subagent can neither interview nor persist. |
+
+## The `teacher <mode>` convention
+
+The [`teacher`](agents/teacher.md) has **three modes**, and one entry point. Type the verb;
+never the slash command:
+
+| You type | What runs | Why |
+|---|---|---|
+| `teacher debrief` (at the sentence that lost you) | the **subagent**, DEBRIEF mode | isolated context is the point — it reads the transcript under rails the main session doesn't have |
+| `teacher explain <thing>` | the **subagent**, EXPLAIN mode | one artifact, one sitting; keeps the reading out of your context |
+| `teacher course <subject>` | the **[`murmurent-course`](skills/murmurent-course/SKILL.md) skill**, in the main session | a course must interview you and persist; a subagent can do neither |
+
+If the main session mis-routes a course request to the subagent, **mode 3 catches it** — teacher
+returns `Gap — this is a course, not an explanation` and names the skill, and the session
+invokes it on the rebound. Primary and fallback, not redundancy.
+
+**A debrief is "wait, what?", not a catch-up.** Fire it at the sentence CC just wrote that
+was jargon, that made a small mechanism it just built sound intricate, or that asked you to
+decide something it never explained. It re-pitches *that* in plain words and says what
+follows. It is not for narrating a session you looked away from.
+
+**It answers in chat, in under 60 seconds, and stops.** No file, one dispatch, reading the
+tail of the transcript rather than its history — it is read mid-task by someone who wants to
+keep working, and a debrief that arrives after you've moved on has failed however good it is.
+Want an annotatable artifact? That's `teacher explain <the thing>`, which is allowed to cost
+minutes and tens of thousands of tokens. A debrief isn't.
+
+**A debrief does not ask you planning questions.** Deciding what to do next is a back-and-forth,
+and a subagent replies once and never hears your answer. Use the **`grilling`** skill for that —
+not part of the commons; install it with `npx skills add mattpocock/skills`. It runs in your
+session, so it can actually follow up.
+
+**Nothing now forces that step, and that is a real trade.** The design it replaced made the
+challenge unskippable. If a plan being explained and then executed without ever being
+questioned turns out to matter, the fix belongs in how you dispatch — not inside teacher, which
+replies once and cannot hold a back-and-forth.
+
+## Linked references (loaded on-demand)
+
+- [`docs/edid_resources.md`](docs/edid_resources.md) — the EDID resource pool the
+  [`conscience`](agents/conscience.md) cites from: five domains, each with its own
+  *flag this / suggest that* directive, plus an ingestion backlog the bookworm owns.
+- [`docs/oracle-workflow.md`](docs/oracle-workflow.md) — personal vs lab Oracle, publish flow, MCP search.
+- [`docs/obsidian-layout.md`](docs/obsidian-layout.md) — vault-side conventions + cross-reference to vault's own `CLAUDE.md` and `maps-legends/`.
+- [`docs/vscode-workflow.md`](docs/vscode-workflow.md) — launcher, 4-quadrant layout, agent reporter, tmux copy-paste.
+- [`docs/setup.md`](docs/setup.md) — per-machine + per-project install steps.
+- [`docs/vault-setup.md`](docs/vault-setup.md) — members: create/adopt your
+  personal vault (`murmurent vault init [--adopt]`); the symlinked-folder gotcha.
+- [`docs/ready_vs_projects.md`](docs/ready_vs_projects.md) — "murmurent-ready"
+  (repo-level: `.murmurent.yaml` + commons agents) vs. a project
+  (governance-level: repos + certified members, in `cert_projects/`) — the
+  split that replaced adopt-also-minting-a-project.
+- [`docs/reconcile.md`](docs/reconcile.md) — `murmurent reconcile` drift-detection routine + daily `/routine` schedule.
+- [`docs/versioning.md`](docs/versioning.md) — CalVer scheme (`YYYY.M.MICRO`),
+  single-source version in `__init__.py`, when to bump vs not, releases; schema
+  versions are independent.
+- [`docs/style/code-style.md`](docs/style/code-style.md) — Python/R style
+  preferences (CC follows the same defaults; this is for human reference,
+  not always-loaded).
+- [`docs/style/documentation.md`](docs/style/documentation.md) — script-header + README conventions.
+- [`docs/group_level.md`](docs/group_level.md) — group-level architecture notes.
+- [`docs/cli_manual.md`](docs/cli_manual.md) — CLI command reference.
+- [`docs/keyring.md`](docs/keyring.md) — the `murmurent keyring`: sync a centre's
+  shared secrets across a principal's machines (per-machine `age` identities +
+  multi-recipient boxes in `lab_info`, locked per role); deploy + test runbooks
+  in [`docs/keyring_deploy.md`](docs/keyring_deploy.md).
+- [`docs/project_creation.md`](docs/project_creation.md) — vignettes: creating
+  intra- and inter-group projects (lead-signed certificates, private channel,
+  shared-workspace gate).
+- [`docs/slack_setup.md`](docs/slack_setup.md) — mayor's one-time Slack setup:
+  workspace + bot token + scopes, `centre-slack-smoke` / `centre-slack-setup`,
+  and how lab/core/mayor channels + broadcasts get created.
+
+## Related repos + the public hub
+
+A murmurent deployment spans this repo plus a global onboarding hub, and
+each group adds a governance repo of its own. Name them precisely, and
+keep every deployment institution-agnostic: drive names off a centre's
+`unique_name`, never a hardcoded university or GitHub owner.
+
+`<owner>` below is whoever hosts the deployment. Only the first two rows
+name a fixed location, because they are the repos everyone clones.
+
+| Repo | Purpose |
+|---|---|
+| [`hallettmiket/murmurent`](https://github.com/hallettmiket/murmurent) | **this repo** (public) — agents, rules, hooks, MCP servers, CLI, dashboard. Clone this to install murmurent or bootstrap a centre. |
+| [`hallettmiket/murmurent_public`](https://github.com/hallettmiket/murmurent_public) | global onboarding hub: institution directory + GitHub-issue join intake (no netnames / server paths). Novice-facing README kept trivial; maintainer/mayor setup lives in [`docs/hub_setup.md`](docs/hub_setup.md). |
+| `<owner>/murmurent_lab_mgmt_<lab>` | per-group governance repo (private), one per lab/core — canonical name, see [`docs/lab_mgmt.md`](docs/lab_mgmt.md) |
+| `<owner>/<choreography>` | a choreography: one recurring multi-actor workflow, with its own repo, decision log and data |
+
+A centre with further repos of its own (a manuscript, a grant, internal
+notes) records them in `rules/local/`, not here.
+
+## Quick setup
+
+```bash
+bash scripts/setup.sh              # symlinks agents/ + rules/ + skills/ into ~/.claude/
+murmurent install --hooks            # registers hooks + MCP servers
+```
+
+Full setup notes including remote-host wiring: [`docs/setup.md`](docs/setup.md).

murmurent-2026.9.3/LICENSE

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+                        http://www.apache.org/licenses/
+
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