specthis 0.0.12

A notary for a research pipeline DAG: specs promise, code delivers, artifacts are receipts — one git-versioned ledger says which claims still hold and whether repair needs a mind, a machine, or patience.

specthis

A notary for a DAG it also knows how to build. You describe what the pipeline should be in a clean set of specs; specthis keeps one ledger, versioned in git, of claims about the project — and answers, cheaply and at any moment: which claims are still true, and what kind of repair does each broken one need — a mind (re-judge), a machine (re-run), or patience (upstream will heal it).

Status: implemented and tested — the ledger verbs (check / status / run / vouch / migrate), the scaffolding (install / init), the live dashboard (export / serve) with spec browsing and host-doc routing, the journal view, and the remote cache. See Roadmap for the deliberately-deferred extensions.

The model

The claim unit is the entry: one script(-set), one output, one deliverable. A spec file is a bundle of entries plus the prose contract they are judged against. The exception is kind: library — entries whose chain stops at code (package modules with no artifact): they carry only the attested claim, are ready once vouched at the current digests, and contribute their code manifest as the upstream digest to whatever consumes them — so editing a library spec or module flags exactly that entry for re-judgment and exactly its consumers for re-run, instead of detonating every vouch through the package blob.

Two species of claim, verified in opposite directions:

• Attested (spec ↔ code, in specs/vouches.toml): someone who did not author the change judged that the code satisfies the contract, at exact digests. Verified backward — are the blobs unchanged since the vouch?
• Derived (code → artifact, in specs/runs.toml): this artifact came from this code on these exact inputs, captured as a composed signature over scripts + package blob + upstream artifact digests
  • workflow config. Verified forward — recompute, compare.

Judgment cannot be computed; computation need not be judged.

Claims are shallow; trust propagates. A vouch covers only the entry's own blobs. When something upstream moves, downstream vouches don't expire — they get flagged. specthis check walks the DAG and reports the frontier: entries broken for local reasons itemized, everything merely downstream summarized. Per entry the diagnosis is one of:

status	meaning	repair
unimplemented	no code on disk	author it
audit needed	your spec or code moved since the vouch (or was never judged)	a mind
rejected	a judge said no at exactly these digests	a mind
stale	inputs moved (or it never ran); the vouch stands	a machine
upstream-unverified	your claim stands on ground that moved	patience
ready	every claim checks out	—

Two kinds of edge, only one carries trust. consumes: edges are artifact flows — they enter signatures and propagate status. references: edges are vocabulary — visible to readers and agents, invisible to the ledger. A definitions hub can be edited without detonating the certificate graph.

The pen is guarded. Attested claims are written only by specthis vouch, which requires a named attester (--as, no git-config default — friction is the feature) and must never be run by the author of the change, human or agent. A rejection binds at its exact digest pair: vouch refuses an ok over a standing rejection until something changes.

Executors are ingredients, never authorities. Intensive entries dispatch to a configured runner (e.g. scripthut — its cache key is its own business); quick entries run locally. git holds claims, caches hold bytes, digests join them. No mtime appears anywhere in ledger logic: a fresh clone on another machine gives identical answers.

Division of labor

Three roles, three pens — and only one of them is free-form:

role	writes	via
author (you, or an implementer agent)	spec edits, code, and the binding in specs/bindings.toml (where the code lives, how to run it)	any editor
critic (a non-author: a colleague, you-next-week, a designated critic session)	attested claims in specs/vouches.toml	specthis vouch --as — only
machine	derived claims in specs/runs.toml	specthis run — only

The author's pen is unguarded because nothing it writes becomes trusted on its own: a binding edit changes which files the code manifest covers, which expires the standing vouch — it can revoke trust, never mint it. And when the critic vouches, the binding is swept up in the judgment anyway: the code_sha they attest is computed over exactly the files the binding names, and run executes exactly the command it gives. Author proposes, critic attests, machine executes — and check believes none of them without re-deriving the digests.

The five verbs

specthis check                 # the frontier; exit non-zero on any local break
specthis status [entry]        # table / detail, incl. WHICH input moved
specthis run <entry>           # resolve+record upstream digests -> dispatch -> runs.toml
specthis run --stale           # rebuild every machine-repairable entry in dependency order
specthis vouch <entry> --as NAME [--reject] [--note TEXT]

Boundaries are load-bearing: check/status never write, run never touches vouches.toml, vouch never touches runs.toml.

Two more verbs render views — regenerated, never read back by the ledger:

specthis lint      # grammar check: EVERY problem across all files at once
specthis export    # write specs/specs.html + _index.json + _routing.json
specthis serve     # live dashboard at localhost:8765; re-renders on any
                   # spec / ledger / code / output / host-doc change (writes nothing)

Readers are lenient, writers are strict: check, lint, and the dashboard load whatever parses and surface the grammar problems (in the page, in a red "does not parse" sidebar group with the broken file's markdown still rendered best-effort, and in check's output — which exits non-zero on problems). run, vouch, and migrate refuse to write ledgers against a tree that doesn't parse. The /specthis-lint slash command explains each problem and fixes the mechanical ones.

The views include host-doc routing: for each report spec declaring host_doc: + section_label:, is every exported .tex actually \input into that labelled section? Orphaned exports and missing labels show on the dashboard and as warnings in check — warnings only, never the exit code, because routing is a view concern, not a claim.

And the remote cache moves bytes without ever touching claims:

specthis cache push <entry>     # upload certified outputs, keyed by signature
specthis cache fetch <entry>    # download + verify against the recorded claim
specthis run --stale --fetch    # try the cache before recomputing
specthis run <entry> --push     # push after a successful run

Configure with [cache] url = "s3://bucket/prefix" (needs specthis[s3]) or file:///shared/drive (no extras) in specs/bindings.toml, or SPECTHIS_CACHE_URL. push refuses bytes that don't match the recorded run; fetch verifies digests before anything lands on disk; neither writes a ledger row — git carries the claim, the cache carries the bytes.

Use cases

Change a spec, implement, vouch, run. The authoring loop. You tighten the contract in specs/compute-alpha.md; every entry in that file immediately reads audit needed — the old vouch bound different bytes. You (or the spec-implementer agent) update the script to match. Then the two claims are recorded, in order and by different hands:

vim specs/compute-alpha.md          # contract edit -> entries flagged: audit needed
vim scripts/fit_alpha.py            # bring the code back in line
specthis vouch fit-alpha --as ana   # a NON-author judges code vs contract
specthis run fit-alpha              # execute, record the derived claim
specthis check                      # ready — and downstream entries now
                                    # show stale, ready for `run --stale`

Did anything change? The daily question — after a git pull, after an editing session, or when you come back to the project after a month. One read-only command answers it and names the repair:

$ specthis check
frontier (broken for local reasons):
  audit needed    fit-beta        spec or code moved since vouch
  stale           fig-gamma       moved: upstream:fit-gamma
waiting on the frontier: 3 upstream-unverified
ready: 11/16

Re-judge fit-beta, machine-rebuild fig-gamma, and the three downstream entries heal on their own. To see exactly what moved on one entry — which script, which workflow file, which upstream artifact — ask specthis status fit-beta.

Rebuild everything a machine can fix. After an upstream fit re-ran, or after a migration, every downstream entry with a standing vouch is just compute:

specthis run --stale     # topo order; skips audit-needed entries
                         # ("needs a mind, not a machine")

Reject bad work. A critic reads an implementation and disagrees with it. The rejection is a claim too — recorded, attributed, and binding at exactly those digests:

specthis vouch fit-beta --as ben --reject --note "loss ignores weights"

The entry reads rejected until the spec or the code actually changes; vouch refuses an ok over the standing rejection at the same pair, so nobody can quietly re-stamp the same bytes.

Onboard a machine (or a collaborator). Clone the repo anywhere and run specthis check: same claims, same digests, same answer — no mtimes to confuse a fresh checkout. Vouches travel with git; artifacts don't have to. Whatever reads stale is one specthis run --stale --fetch away: entries whose recorded claim matches today's inputs are pulled from the cache (digest-verified, zero recompute, zero ledger writes); only genuinely new work executes.

Let agents work, keep the pen. The spec-auditor runs the checks and judges contract-in-spirit but only ever proposes verdicts; the spec-implementer authors code, smoke-tests it, and stops at the vouch. Sessions end, the ledger remembers: what was judged, by whom, at which digests — and what still needs a mind, a machine, or patience.

Route the audit queue: humans judge intent, agents read drift. A vouch binds an exact (spec_sha, code_sha) pair, so audit needed on a previously-vouched entry splits into two lanes. If the spec moved, the contract itself changed — re-judging the code against new intent is human work. If only the code moved, the contract is stable and the question is drift against a fixed target — exactly what the spec-auditor is built to read; its proposal gets stamped cheaply with vouch --as, attention reserved for the contract lane. Never-vouched entries (a fresh migration, say) have no pair to diff, so the first pass through the queue is all human-grade judgment — and it's that baseline that makes later drift legible and delegable.

State: three human-readable files, all in git

• specs/vouches.toml — attested claims: (spec_sha, code_sha, verdict, attester, when, note) per entry.
• specs/runs.toml — derived claims: the composed signature, the output digest, the executor, and the full [inputs] table (each script, workflow file, the package blob, and one upstream:<entry> digest per consumed artifact — so an upstream re-run is never invisible).
• specs/bindings.toml — hand-edited vocabulary, not a claim: entry → scripts, run command, workflow files, executor; plus [package] globs for the shared library that every code manifest covers. Unbound entries follow the scripts/<entry>.py convention.

The spec files themselves carry YAML frontmatter (name, kind, tier, consumes, references) and ### entry blocks declaring each entry's Output: / Export outputs:. The whole file, frontmatter included, is the contract — any edit returns its entries to audit needed. No Script:, no Status:: bindings live in bindings.toml, status is derived. See src/specthis/templates/specs/README.md for the full convention (the bundled templates ship a research/paper instantiation — compute entries producing JSON, report entries exporting .tex into a host document — but the ledger model is domain-general).

Install

pip install specthis          # core: CLI + agent templates
pip install "specthis[s3]"    # adds the remote (S3) cache backend (stub)

Or with uv — no install needed, works from any directory:

uvx specthis serve            # run straight from PyPI
uv tool install specthis      # or install a persistent `specthis` command

From a clone of this repo, uv run specthis <command> (at the repo root) builds the local source and runs it.

The dashboard serves on 127.0.0.1:8765 by default; pass --port/--host to specthis serve if that port is taken.

Journal

Alongside the claims lives the narrative: journal/ at the project root holds dated entries, one markdown file per story —

journal/2026-06-30-smc-ffbs-resampling-fix.md
journal/2026-06-10-abb-calibration-and-lom-fits.md

A journal entry is prose, not a claim: the ledger neither reads nor hashes it, no status depends on it, and there is nothing to vouch. It records what the ledger cannot — why a result looks the way it does, which alternatives died and how, the numbers behind a decision. Small shareable artefacts (a JSON bundle, a figure) can be committed next to their entry so they stay downloadable even when the results directory is gitignored.

The dashboard picks the directory up automatically: a journal group in the sidebar, a filterable card index (date + title), and one page per entry with the narrative rendered. Markdown links cross the two worlds in both directions — a spec linking journal/2026-06-30-….md and an entry linking ../specs/compute-alpha.md both become hash-routed links in the page. The date comes from the filename prefix, the title from the first # heading (or frontmatter title:).

The /specthis-journal [topic] slash command (installed by specthis install) writes an entry from the current Claude Code session: what was attempted, what was decided and why, the dead ends worth remembering, with links to the specs involved.

Scaffold a project

specthis install    # writes the Claude Code subagents into .claude/agents/
specthis init       # creates specs/ with README.md + AGENTS.md templates

Four Claude Code subagents and the slash commands cover the daily operations:

• spec-auditor — runs specthis check/status for the mechanical layer, judges contract-in-spirit for entries on the frontier, and proposes verdicts. It never vouches.
• spec-implementer — authors code for an unimplemented entry, binds it, smoke-tests it, then stops and proposes the vouch. It authored the change, so the pen is not its.
• experiment-runner — launches a long run in the background (preferring specthis run <entry> so the claim is recorded), watches the log, reports completion.
• spec-critic + /specthis-vouch [entries…] — the one sanctioned agent pen. The slash command is your explicit commission (your name comes from git config user.name): it spawns the critic as a fresh session that authored nothing, which re-reads spec and code from disk, vouches clear passes as spec-critic (for <name>) (so the ledger shows the judgment was agent-made and who asked for it), rejects clear violations, and leaves every doubt unvouched for you. Independence here is contextual, not personal — the ledger records exactly that.
• /specthis-run [entries…] — the machine half: rebuilds the stale queue in dependency order (run --stale, with --fetch when a cache is configured), backgrounds and monitors intensive entries instead of blocking, and reports what was rebuilt, fetched, and skipped as needing a mind. Together the two commands split the frontier by repair kind: /specthis-vouch for minds, /specthis-run for machines.
• /specthis-journal [topic] — the narrative pen: writes a dated entry into journal/ from the current session (see Journal). No ledger is touched — the journal records the why, the ledgers record the what.

Migrating from the old _lock.json

specthis migrate            # dry-run report
specthis migrate --write    # import run rows

Old certified inputs import as derived claims only — no vouches migrate, by design: judgment does not transfer from a hash file. Post-migration everything reads audit needed or stale, and the humans work the queue with specthis vouch / specthis run --stale.

Roadmap

Done: spec/bindings parsing, content hashing + composed signatures, both ledgers, status derivation + frontier, the five verbs, migration, scaffolding, agent templates, the dashboard (export + serve with live reload, stdlib only), host-doc routing (_routing.json + orphaned-export checks), the remote cache (file:// and s3:// backends, digest-verified fetch keyed by the composed signature), and the journal (journal/ narratives rendered into the dashboard, plus /specthis-journal).

Also done: skip: true in frontmatter — comment a spec out while developing. Skipped entries leave the frontier and every count; run/vouch refuse them; their ledger rows stay dormant; the body is not grammar-checked; consuming a skipped entry is a lint problem; the dashboard renders the spec greyed and marked skipped. Honesty is content-addressed: a spec edited while skipped comes back as audit needed (its bytes moved), while a pure skip/un-skip round-trip restores the exact vouched bytes and trust returns with them.

Known future extensions — each additive, none precluded by the core:

• Output-schema-into-signature.
• Quick-tier caching as an executor concern.
• Section-scoped spec hashing if whole-file contract hashing ever causes too much re-judgment churn.

License

MIT — see LICENSE.