@they-juanreina/compost-cli 0.1.2 → 0.1.3

package/dist/lib/agreement.js

@@ -0,0 +1,261 @@
+import { existsSync } from 'node:fs';
+import Database from 'better-sqlite3';
+import { CompostError } from '../errors.js';
+// ---------------------------------------------------------------- κ (binary)
+/** Cohen's κ for a single binary variable across paired ratings. */
+export function cohensKappaBinary(a, b) {
+    if (a.length !== b.length)
+        throw new Error('cohensKappaBinary: rating arrays differ in length');
+    const n = a.length;
+    if (n === 0)
+        return { kappa: null, po: 0, pe: 0, n: 0 };
+    let n11 = 0;
+    let n00 = 0;
+    let aTrue = 0;
+    let bTrue = 0;
+    for (let i = 0; i < n; i++) {
+        if (a[i])
+            aTrue++;
+        if (b[i])
+            bTrue++;
+        if (a[i] && b[i])
+            n11++;
+        if (!a[i] && !b[i])
+            n00++;
+    }
+    const po = (n11 + n00) / n;
+    const pYesA = aTrue / n;
+    const pYesB = bTrue / n;
+    const pe = pYesA * pYesB + (1 - pYesA) * (1 - pYesB);
+    if (1 - pe === 0) {
+        // Degenerate: both marginals saturated. κ is conventionally 1 iff perfect.
+        return { kappa: po === 1 ? 1 : 0, po, pe, n };
+    }
+    return { kappa: (po - pe) / (1 - pe), po, pe, n };
+}
+// ------------------------------------------------- Krippendorff α (nominal)
+/**
+ * Krippendorff's α (nominal metric) over a units × coders matrix. Cells may be
+ * null (a coder didn't code that unit). Units with fewer than two values are
+ * dropped (not pairable). General coincidence-matrix algorithm.
+ */
+export function krippendorffAlphaNominal(units) {
+    // Coincidence matrix o[c][k] and value marginals.
+    const o = new Map();
+    const bump = (c, k, by) => {
+        if (!o.has(c))
+            o.set(c, new Map());
+        const row = o.get(c);
+        row.set(k, (row.get(k) ?? 0) + by);
+    };
+    for (const unit of units) {
+        const vals = unit.filter((v) => v !== null);
+        const m = vals.length;
+        if (m < 2)
+            continue;
+        for (let i = 0; i < m; i++) {
+            for (let j = 0; j < m; j++) {
+                if (i === j)
+                    continue;
+                bump(vals[i], vals[j], 1 / (m - 1));
+            }
+        }
+    }
+    const values = [...o.keys()];
+    let n = 0;
+    const marginal = new Map();
+    for (const c of values) {
+        let rowSum = 0;
+        for (const k of values)
+            rowSum += o.get(c)?.get(k) ?? 0;
+        marginal.set(c, rowSum);
+        n += rowSum;
+    }
+    if (n < 2)
+        return null;
+    // Observed disagreement (nominal δ = 1 when c≠k).
+    let Do = 0;
+    for (const c of values) {
+        for (const k of values) {
+            if (c === k)
+                continue;
+            Do += o.get(c)?.get(k) ?? 0;
+        }
+    }
+    Do /= n;
+    // Expected disagreement.
+    let De = 0;
+    for (const c of values) {
+        for (const k of values) {
+            if (c === k)
+                continue;
+            De += marginal.get(c) * marginal.get(k);
+        }
+    }
+    De /= n * (n - 1);
+    if (De === 0)
+        return Do === 0 ? 1 : 0;
+    return 1 - Do / De;
+}
+// ------------------------------------------------------- agreement over codings
+function landisKoch(k) {
+    if (k === null)
+        return 'undefined';
+    if (k < 0)
+        return 'poor (worse than chance)';
+    if (k <= 0.2)
+        return 'slight';
+    if (k <= 0.4)
+        return 'fair';
+    if (k <= 0.6)
+        return 'moderate';
+    if (k <= 0.8)
+        return 'substantial';
+    return 'almost perfect';
+}
+/**
+ * Compute agreement from a flat list of (coder, unit, code) codings. Only units
+ * coded by BOTH coders count (the doubly-coded set); the codebook is the union of
+ * codes either coder used on those units.
+ */
+export function computeAgreement(codings, opts = {}) {
+    const minUnits = opts.minUnits ?? 10;
+    const excluded = opts.excludedUnnamedMachineCodes ?? 0;
+    const byCoderUnit = {
+        human: new Map(),
+        machine: new Map(),
+    };
+    const allCodes = new Set();
+    for (const { coder, unit, code } of codings) {
+        if (!byCoderUnit[coder].has(unit))
+            byCoderUnit[coder].set(unit, new Set());
+        byCoderUnit[coder].get(unit)?.add(code);
+        allCodes.add(code);
+    }
+    const doublyCoded = [...byCoderUnit.human.keys()].filter((u) => byCoderUnit.machine.has(u)).sort();
+    const codes = [...allCodes].sort();
+    const base = {
+        doubly_coded_units: doublyCoded.length,
+        codes: codes.length,
+        excluded_unnamed_machine_codes: excluded,
+    };
+    if (doublyCoded.length < minUnits) {
+        return {
+            status: 'insufficient',
+            ...base,
+            per_code: [],
+            pooled_kappa: null,
+            krippendorff_alpha: null,
+            interpretation: 'undefined',
+            note: `Only ${doublyCoded.length} doubly-coded unit(s); need ≥ ${minUnits} for a meaningful κ. Code more highlights with \`compost recode --blind\`.`,
+        };
+    }
+    const has = (coder, unit, code) => byCoderUnit[coder].get(unit)?.has(code) ?? false;
+    // Per-code binary κ.
+    const perCode = [];
+    for (const code of codes) {
+        const a = [];
+        const b = [];
+        let support = 0;
+        for (const u of doublyCoded) {
+            const h = has('human', u, code);
+            const m = has('machine', u, code);
+            a.push(h);
+            b.push(m);
+            if (h || m)
+                support++;
+        }
+        perCode.push({ code, kappa: cohensKappaBinary(a, b).kappa, support });
+    }
+    // Pooled κ over every (unit, code) cell, and α as a cross-check on the same cells.
+    const pooledA = [];
+    const pooledB = [];
+    const alphaUnits = [];
+    for (const u of doublyCoded) {
+        for (const code of codes) {
+            const h = has('human', u, code);
+            const m = has('machine', u, code);
+            pooledA.push(h);
+            pooledB.push(m);
+            alphaUnits.push([h ? 'present' : 'absent', m ? 'present' : 'absent']);
+        }
+    }
+    const pooled = cohensKappaBinary(pooledA, pooledB).kappa;
+    return {
+        status: 'ok',
+        ...base,
+        per_code: perCode,
+        pooled_kappa: pooled,
+        krippendorff_alpha: krippendorffAlphaNominal(alphaUnits),
+        interpretation: landisKoch(pooled),
+    };
+}
+/**
+ * Extract codings from a seed's event log. Machine codings come from named `code`
+ * create events (actor ai/agent) via their `evidence` highlight ids; unnamed
+ * cluster codes (similarity-scanner `members`) have no shared label and are
+ * excluded (counted, never silently dropped). Human codings come from blind
+ * `coding` link events (actor researcher, payload.blind === true). Artifacts with
+ * a reject/unlink event are excluded.
+ */
+export function readCodings(eventsDbPath) {
+    if (!existsSync(eventsDbPath)) {
+        throw new CompostError('FILE_NOT_FOUND', `No events.sqlite at ${eventsDbPath}`);
+    }
+    const db = new Database(eventsDbPath, { readonly: true, fileMustExist: true });
+    try {
+        const archived = new Set(db
+            .prepare("SELECT DISTINCT artifact_id FROM events WHERE action IN ('reject','unlink')")
+            .all().map((r) => r.artifact_id));
+        const codings = [];
+        let excludedUnnamed = 0;
+        const machineRows = db
+            .prepare("SELECT artifact_id, actor_type, payload FROM events WHERE action='create' AND artifact_kind='code' AND actor_type IN ('ai','agent')")
+            .all();
+        for (const row of machineRows) {
+            if (archived.has(row.artifact_id))
+                continue;
+            const p = safeParse(row.payload);
+            const code = typeof p.name === 'string' ? p.name : undefined;
+            const units = (p.evidence ?? p.members);
+            if (code === undefined) {
+                if (Array.isArray(units) && units.length > 0)
+                    excludedUnnamed++;
+                continue;
+            }
+            if (!Array.isArray(units))
+                continue;
+            for (const u of units) {
+                if (typeof u === 'string')
+                    codings.push({ coder: 'machine', unit: u, code });
+            }
+        }
+        const humanRows = db
+            .prepare("SELECT artifact_id, actor_type, payload FROM events WHERE action='link' AND artifact_kind='coding' AND actor_type='researcher'")
+            .all();
+        for (const row of humanRows) {
+            if (archived.has(row.artifact_id))
+                continue;
+            const p = safeParse(row.payload);
+            if (p.blind !== true)
+                continue;
+            if (typeof p.code === 'string' && typeof p.highlight === 'string') {
+                codings.push({ coder: 'human', unit: p.highlight, code: p.code });
+            }
+        }
+        return { codings, excludedUnnamedMachineCodes: excludedUnnamed };
+    }
+    finally {
+        db.close();
+    }
+}
+function safeParse(s) {
+    try {
+        const v = JSON.parse(s);
+        return v !== null && typeof v === 'object' ? v : {};
+    }
+    catch {
+        return {};
+    }
+}
+//# sourceMappingURL=agreement.js.map

package/dist/lib/agreement.js.map

@@ -0,0 +1 @@
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package/dist/lib/artifacts.d.ts

@@ -1,5 +1,5 @@
 import Database from 'better-sqlite3';
-import { type Author } from './events.js';
+import { type AiInputBundle, type Author } from './events.js';
 export interface CreatedArtifact {
     id: string;
     artifact_id: string;
@@ -12,6 +12,7 @@ export interface CreateHighlightInput {
     span: [number, number];
     text: string;
     author: Author;
+    inputs?: AiInputBundle;
 }
 export declare function createHighlight(seedPath: string, input: CreateHighlightInput): CreatedArtifact;
 export interface CreateCodeInput {
@@ -19,6 +20,7 @@ export interface CreateCodeInput {
     definition: string;
     evidence?: string[];
     author: Author;
+    inputs?: AiInputBundle;
 }
 export declare function createCode(seedPath: string, input: CreateCodeInput): CreatedArtifact;
 export interface CreateThemeInput {
@@ -26,6 +28,7 @@ export interface CreateThemeInput {
     summary: string;
     codes?: string[];
     author: Author;
+    inputs?: AiInputBundle;
 }
 export declare function createTheme(seedPath: string, input: CreateThemeInput): CreatedArtifact;
 interface CreateEventRow {
@@ -58,6 +61,34 @@ export declare function endorseArtifact(seedPath: string, artifactRef: string, r
     parent_event_id: string;
     already_endorsed?: true;
 };
+/**
+ * Resolve an artifact ref to its create event, then emit a researcher reject
+ * chaining the artifact's latest event. Reject archives (current_state is
+ * preserved for audit) — the three-actor model's "delete", where nothing is
+ * ever truly removed. Idempotent: a second reject by the same researcher is a
+ * no-op returning the existing reject.
+ */
+export declare function rejectArtifact(seedPath: string, artifactRef: string, researcherId: string, note?: string): {
+    artifact_id: string;
+    reject_event_id: string;
+    parent_event_id: string;
+    already_rejected?: true;
+};
+/**
+ * Resolve an artifact ref, then emit a field-level update chaining the latest
+ * event. The event log records `{ field, before, after }` so blame shows what
+ * changed. `before` is best-effort context for the audit trail; the reducer
+ * applies only `after`.
+ */
+export declare function updateArtifact(seedPath: string, artifactRef: string, patch: {
+    field: string;
+    before?: unknown;
+    after: unknown;
+}, author: Author): {
+    artifact_id: string;
+    update_event_id: string;
+    parent_event_id: string;
+};
 /** Read the configured researcher identity: COMPOST_USER env, else fallback. */
 export declare function defaultResearcherId(): string;
 export {};

package/dist/lib/artifacts.d.ts.map

@@ -1 +1 @@
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package/dist/lib/artifacts.js

@@ -2,7 +2,7 @@ import { existsSync, mkdirSync, readdirSync, rmSync, writeFileSync } from 'node:
 import { join } from 'node:path';
 import Database from 'better-sqlite3';
 import { CompostError } from '../errors.js';
-import { artifactId, emitCreate, emitEndorse, openSeedEvents } from './events.js';
+import { artifactId, emitCreate, emitEndorse, emitReject, emitUpdate, openSeedEvents, } from './events.js';
 // ---------------------------------------------------------------- helpers
 /** Next sequential H-NNN in highlights/, scanning existing files. */
 function nextHighlightId(dir) {
@@ -96,6 +96,7 @@ export function createHighlight(seedPath, input) {
         artifactKind: 'highlight',
         initialState,
         author: input.author,
+        ...(input.inputs !== undefined ? { inputs: input.inputs } : {}),
     });
     return { id, artifact_id: sha, path, event_id };
 }
@@ -122,6 +123,7 @@ export function createCode(seedPath, input) {
         artifactKind: 'code',
         initialState,
         author: input.author,
+        ...(input.inputs !== undefined ? { inputs: input.inputs } : {}),
     });
     return { id, artifact_id: sha, path, event_id };
 }
@@ -149,6 +151,7 @@ export function createTheme(seedPath, input) {
         artifactKind: 'theme',
         initialState,
         author: input.author,
+        ...(input.inputs !== undefined ? { inputs: input.inputs } : {}),
     });
     return { id, artifact_id: sha, path, event_id };
 }
@@ -171,6 +174,46 @@ export function tryResolveHumanRef(db, ref) {
         .prepare("SELECT id, artifact_kind, artifact_id FROM events WHERE action = 'create' AND json_extract(payload, '$.id') = ? ORDER BY ts, rowid LIMIT 1")
         .get(ref);
 }
+/**
+ * Resolve an artifact ref (human id, full/prefix SHA, or `latest:<kind>=<seed>`)
+ * to its create event row. Shared by endorse/reject/update so every mutation
+ * path accepts the same refs `compost create`/blame print (#168). Throws
+ * INVALID_INPUT only when the ref is neither human-, SHA-, nor latest-shaped;
+ * returns undefined when it's well-shaped but matches no create event (callers
+ * raise a clearer FILE_NOT_FOUND).
+ */
+function findCreateEvent(db, artifactRef) {
+    const human = tryResolveHumanRef(db, artifactRef);
+    if (human !== undefined)
+        return human;
+    const latest = /^latest:(\w+)=(.+)$/.exec(artifactRef);
+    if (latest) {
+        const kind = latest[1];
+        return db
+            .prepare("SELECT id, artifact_kind, artifact_id FROM events WHERE artifact_kind = ? AND action = 'create' ORDER BY ts DESC, rowid DESC LIMIT 1")
+            .get(kind);
+    }
+    if (/^[a-f0-9]{8,64}$/i.test(artifactRef)) {
+        return db
+            .prepare("SELECT id, artifact_kind, artifact_id FROM events WHERE artifact_id LIKE ? AND action = 'create' ORDER BY ts, rowid LIMIT 1")
+            .get(`${artifactRef.toLowerCase()}%`);
+    }
+    if (!HUMAN_REF_RE.test(artifactRef)) {
+        // Not human-shaped, not SHA-shaped, not latest: → user typed something
+        // unparseable. (Human-shaped refs that didn't resolve return undefined so
+        // callers raise FILE_NOT_FOUND with a clearer message.)
+        throw new CompostError('INVALID_INPUT', `Invalid artifact ref "${artifactRef}". Use the id from \`compost create\` (e.g. C-slug, H-001), a SHA256 prefix, or latest:<kind>=<seed>.`);
+    }
+    return undefined;
+}
+/** Latest event id on an artifact's timeline — the parent a new reject/update
+ * event chains to (vs endorse, which chains to create for #168 round-tripping). */
+function latestEventId(db, artifactId) {
+    const row = db
+        .prepare('SELECT id FROM events WHERE artifact_id = ? ORDER BY ts DESC, rowid DESC LIMIT 1')
+        .get(artifactId);
+    return row?.id;
+}
 /**
  * Resolve an artifact ref (human id, full/prefix SHA, or `latest:<kind>=<seed>`)
  * to its create event, then emit a researcher endorse chaining it. Mirrors
@@ -188,27 +231,7 @@ export function endorseArtifact(seedPath, artifactRef, researcherId) {
     // connection once and avoid a stat/open dance.
     let existingEndorse;
     try {
-        createRow = tryResolveHumanRef(db, artifactRef);
-        if (createRow === undefined) {
-            const latest = /^latest:(\w+)=(.+)$/.exec(artifactRef);
-            if (latest) {
-                const kind = latest[1];
-                createRow = db
-                    .prepare("SELECT id, artifact_kind, artifact_id FROM events WHERE artifact_kind = ? AND action = 'create' ORDER BY ts DESC, rowid DESC LIMIT 1")
-                    .get(kind);
-            }
-            else if (/^[a-f0-9]{8,64}$/i.test(artifactRef)) {
-                createRow = db
-                    .prepare("SELECT id, artifact_kind, artifact_id FROM events WHERE artifact_id LIKE ? AND action = 'create' ORDER BY ts, rowid LIMIT 1")
-                    .get(`${artifactRef.toLowerCase()}%`);
-            }
-            else if (!HUMAN_REF_RE.test(artifactRef)) {
-                // Not human-shaped, not SHA-shaped, not latest: → user typed something
-                // unparseable. (Human-shaped refs that didn't resolve fall through to
-                // the FILE_NOT_FOUND below with a clearer message.)
-                throw new CompostError('INVALID_INPUT', `Invalid artifact ref "${artifactRef}". Use the id from \`compost create\` (e.g. C-slug, H-001), a SHA256 prefix, or latest:<kind>=<seed>.`);
-            }
-        }
+        createRow = findCreateEvent(db, artifactRef);
         if (createRow !== undefined) {
             existingEndorse = db
                 .prepare("SELECT id, parent_event FROM events WHERE artifact_id = ? AND action = 'endorse' AND actor_id = ? ORDER BY ts, rowid LIMIT 1")
@@ -247,6 +270,117 @@ export function endorseArtifact(seedPath, artifactRef, researcherId) {
         events.close();
     }
 }
+/**
+ * Resolve an artifact ref to its create event, then emit a researcher reject
+ * chaining the artifact's latest event. Reject archives (current_state is
+ * preserved for audit) — the three-actor model's "delete", where nothing is
+ * ever truly removed. Idempotent: a second reject by the same researcher is a
+ * no-op returning the existing reject.
+ */
+export function rejectArtifact(seedPath, artifactRef, researcherId, note) {
+    const eventsDb = join(seedPath, '.compost', 'events.sqlite');
+    if (!existsSync(eventsDb)) {
+        throw new CompostError('FILE_NOT_FOUND', `No events.sqlite in seed; nothing to reject.`);
+    }
+    const db = new Database(eventsDb, { readonly: true, fileMustExist: true });
+    let resolved;
+    let existingReject;
+    try {
+        const createRow = findCreateEvent(db, artifactRef);
+        if (createRow !== undefined) {
+            existingReject = db
+                .prepare("SELECT id, parent_event FROM events WHERE artifact_id = ? AND action = 'reject' AND actor_id = ? ORDER BY ts, rowid LIMIT 1")
+                .get(createRow.artifact_id, researcherId);
+            resolved = {
+                createRow,
+                parentEventId: latestEventId(db, createRow.artifact_id) ?? createRow.id,
+            };
+        }
+    }
+    finally {
+        db.close();
+    }
+    if (resolved === undefined) {
+        throw new CompostError('FILE_NOT_FOUND', `No create event found for ref "${artifactRef}".`);
+    }
+    const { createRow, parentEventId } = resolved;
+    if (existingReject !== undefined) {
+        return {
+            artifact_id: createRow.artifact_id,
+            reject_event_id: existingReject.id,
+            parent_event_id: existingReject.parent_event ?? createRow.id,
+            already_rejected: true,
+        };
+    }
+    const events = openSeedEvents(seedPath);
+    try {
+        const reject = emitReject(events, {
+            artifactKind: createRow.artifact_kind,
+            artifactId: createRow.artifact_id,
+            parentEventId,
+            researcherId,
+            ...(note !== undefined ? { note } : {}),
+        });
+        return {
+            artifact_id: createRow.artifact_id,
+            reject_event_id: reject.id,
+            parent_event_id: parentEventId,
+        };
+    }
+    finally {
+        events.close();
+    }
+}
+/**
+ * Resolve an artifact ref, then emit a field-level update chaining the latest
+ * event. The event log records `{ field, before, after }` so blame shows what
+ * changed. `before` is best-effort context for the audit trail; the reducer
+ * applies only `after`.
+ */
+export function updateArtifact(seedPath, artifactRef, patch, author) {
+    const eventsDb = join(seedPath, '.compost', 'events.sqlite');
+    if (!existsSync(eventsDb)) {
+        throw new CompostError('FILE_NOT_FOUND', `No events.sqlite in seed; nothing to update.`);
+    }
+    const db = new Database(eventsDb, { readonly: true, fileMustExist: true });
+    let resolved;
+    try {
+        const createRow = findCreateEvent(db, artifactRef);
+        if (createRow !== undefined) {
+            resolved = {
+                createRow,
+                parentEventId: latestEventId(db, createRow.artifact_id) ?? createRow.id,
+            };
+        }
+    }
+    finally {
+        db.close();
+    }
+    if (resolved === undefined) {
+        throw new CompostError('FILE_NOT_FOUND', `No create event found for ref "${artifactRef}".`);
+    }
+    const { createRow, parentEventId } = resolved;
+    const events = openSeedEvents(seedPath);
+    try {
+        const update = emitUpdate(events, {
+            artifactKind: createRow.artifact_kind,
+            artifactId: createRow.artifact_id,
+            parentEventId,
+            author,
+            field: patch.field,
+            before: patch.before,
+            after: patch.after,
+        });
+        return {
+            artifact_id: createRow.artifact_id,
+            update_event_id: update.id,
+            parent_event_id: parentEventId,
+        };
+    }
+    finally {
+        events.close();
+    }
+}
 /** Read the configured researcher identity: COMPOST_USER env, else fallback. */
 export function defaultResearcherId() {
     return process.env.COMPOST_USER || process.env.USER || 'researcher';

package/dist/lib/artifacts.js.map

@@ -1 +1 @@
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package/dist/lib/config.d.ts

@@ -1,6 +1,9 @@
 export interface ProviderSettings {
     base_url?: string;
     api_key_env?: string;
+    /** Per-request timeout override (ms). Large local models can need more than
+     * the 120s default just to load into memory. */
+    timeout_ms?: number;
 }
 export interface CompostConfig {
     providers: Record<string, ProviderSettings>;

package/dist/lib/config.d.ts.map

@@ -1 +1 @@
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