npm - @monoes/monograph - Versions diffs - 1.6.15 → 2.24.1 - Mend

@monoes/monograph 1.6.15 → 2.24.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (18) hide show

package/dist/src/pipeline/orchestrator.d.ts.map +1 -1
package/dist/src/pipeline/orchestrator.js +3 -33
package/dist/src/pipeline/orchestrator.js.map +1 -1
package/dist/src/pipeline/phases/communities.d.ts.map +1 -1
package/dist/src/pipeline/phases/communities.js +21 -16
package/dist/src/pipeline/phases/communities.js.map +1 -1
package/dist/src/pipeline/phases/processes.d.ts.map +1 -1
package/dist/src/pipeline/phases/processes.js +7 -0
package/dist/src/pipeline/phases/processes.js.map +1 -1
package/dist/src/pipeline/phases/stale-sweep.d.ts +21 -0
package/dist/src/pipeline/phases/stale-sweep.d.ts.map +1 -0
package/dist/src/pipeline/phases/stale-sweep.js +49 -0
package/dist/src/pipeline/phases/stale-sweep.js.map +1 -0
package/dist/src/storage/node-store.d.ts.map +1 -1
package/dist/src/storage/node-store.js +23 -9
package/dist/src/storage/node-store.js.map +1 -1
package/dist/tsconfig.tsbuildinfo +1 -1
package/package.json +1 -1

package/dist/src/pipeline/orchestrator.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AACvE,OAAO,EAAoB,KAAK,eAAe,EAA2B,MAAM,iBAAiB,CAAC;AA4BlG,OAAO,KAAK,EAAmB,eAAe,EAAE,MAAM,YAAY,CAAC;AAgBnE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;GAKG;AACH,MAAM,MAAM,WAAW,GACnB;IACE,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IACzC,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAC1C,GACD;IACE,MAAM,EAAE,SAAS,CAAC;IAClB,MAAM,EAAE,QAAQ,GAAG,OAAO,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,wEAAwE;IACxE,MAAM,CAAC,EAAE,eAAe,CAAC;CAC1B,CAAC;AAQN,wBAAsB,UAAU,CAC9B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,CAAC,CAiBtB;AAkOD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EAAE,EACzB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,GAAG,IAAI,CAAC,CAa7B"}

package/dist/src/pipeline/orchestrator.js CHANGED Viewed

@@ -6,7 +6,7 @@ import { ExtractionCache } from '../cache/extraction-cache.js';
 import { generateGraphReport } from '../reporting/graph-report.js';
 import { closeDb, openDb } from '../storage/db.js';
 import { acquireBuildLock, describeBuildLockHolder } from './build-lock.js';
-import { isWithinScope, readIndexScope, scopeForOptions, writeIndexScope } from './index-scope.js';
+import { readIndexScope, scopeForOptions, writeIndexScope } from './index-scope.js';
 import { bridgeResolverPhase } from './phases/bridge-resolver.js';
 import { communitiesPhase } from './phases/communities.js';
 import { contextualProximityPhase } from './phases/contextual-proximity.js';
@@ -25,6 +25,7 @@ import { processesPhase } from './phases/processes.js';
 import { routesPhase } from './phases/routes.js';
 import { scanPhase } from './phases/scan.js';
 import { clearWorkspacePackageMapCache, scopeResolutionPhase } from './phases/scope-resolution.js';
+import { staleSweepPhase } from './phases/stale-sweep.js';
 import { structurePhase } from './phases/structure.js';
 import { suggestPhase } from './phases/suggest.js';
 import { surprisesPhase } from './phases/surprises.js';
@@ -168,6 +169,7 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
             scopeResolutionPhase,
             bridgeResolverPhase,
             mroPhase,
+            staleSweepPhase,
             communitiesPhase,
             processesPhase,
             godNodesPhase,
@@ -192,38 +194,6 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
                 process.stderr.write(`[monograph] ${summary}\n`);
             }
         }
-        // Sweep orphaned rows for files that were renamed/deleted since the last build.
-        // This MUST run unconditionally — even when every remaining file cache-hit
-        // (ctx.allFilesCached === true), a file may have been deleted from disk between
-        // builds, which produces zero cache misses but still leaves ghost rows in the DB
-        // unless we compare the DB's known file set against the current on-disk set.
-        //
-        // The sweep is confined to the current build's source domain (`activeScope`).
-        // A narrowed build never looked at files outside its domain, so their absence
-        // from `filePaths` says nothing about whether they still exist on disk —
-        // deleting those rows is how a code-only refresh used to erase every Document
-        // node in the graph.
-        const scanOut = outputs.get('scan');
-        if (scanOut) {
-            const liveFiles = new Set(scanOut.filePaths.map((f) => resolve(f)));
-            const staleFiles = db.prepare('SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL').all()
-                .map((r) => r.file_path)
-                .filter((f) => isWithinScope(f, activeScope) && !liveFiles.has(resolve(ctx.repoPath, f)));
-            if (staleFiles.length > 0) {
-                const deleteStale = db.transaction((files) => {
-                    const deleteEdges = db.prepare(`
-            DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file_path = ?)
-               OR target_id IN (SELECT id FROM nodes WHERE file_path = ?)
-          `);
-                    const deleteNodesStmt = db.prepare('DELETE FROM nodes WHERE file_path = ?');
-                    for (const f of files) {
-                        deleteEdges.run(f, f);
-                        deleteNodesStmt.run(f);
-                    }
-                });
-                deleteStale(staleFiles);
-            }
-        }
         // Populate churnScore on File nodes from git history (6-month window)
         try {
             const churnResult = await analyzeChurn(ctx.repoPath, '6m');

package/dist/src/pipeline/orchestrator.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/src/pipeline/phases/communities.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/src/pipeline/phases/communities.js CHANGED Viewed

@@ -205,6 +205,7 @@ export const communitiesPhase = {
     name: 'communities',
     deps: [
         'parse',
+        'stale-sweep',
         'cross-file',
         'mro',
         'routes',
@@ -249,23 +250,27 @@ export const communitiesPhase = {
         }
         // Compute all cohesion scores in one O(N+E) pass instead of O(K*(N+E))
         const cohesionScores = computeAllCohesionScores(memberships, allUsedEdges);
-        // Persist community assignments to the DB
-        if (memberships.size > 0) {
-            const commSizes = new Map();
-            for (const commId of memberships.values()) {
-                commSizes.set(commId, (commSizes.get(commId) ?? 0) + 1);
-            }
-            const updateNode = ctx.db.prepare('UPDATE nodes SET community_id = ? WHERE id = ?');
-            const upsertComm = ctx.db.prepare('INSERT OR REPLACE INTO communities (id, label, size, cohesion_score) VALUES (?, ?, ?, ?)');
-            ctx.db.transaction(() => {
-                for (const [nodeId, commId] of memberships) {
-                    updateNode.run(commId, nodeId);
-                }
-                for (const [commId, label] of communityLabels) {
-                    upsertComm.run(commId, label, commSizes.get(commId) ?? 0, cohesionScores.get(commId) ?? 0);
-                }
-            })();
+        // Persist community assignments to the DB. The previous run's assignments are
+        // cleared first so a node that is no longer clustered, or a community that no
+        // longer exists, does not keep serving a stale id.
+        const commSizes = new Map();
+        for (const commId of memberships.values()) {
+            commSizes.set(commId, (commSizes.get(commId) ?? 0) + 1);
         }
+        const clearNodes = ctx.db.prepare('UPDATE nodes SET community_id = NULL WHERE community_id IS NOT NULL');
+        const clearComms = ctx.db.prepare('DELETE FROM communities');
+        const updateNode = ctx.db.prepare('UPDATE nodes SET community_id = ? WHERE id = ?');
+        const upsertComm = ctx.db.prepare('INSERT OR REPLACE INTO communities (id, label, size, cohesion_score) VALUES (?, ?, ?, ?)');
+        ctx.db.transaction(() => {
+            clearNodes.run();
+            clearComms.run();
+            for (const [nodeId, commId] of memberships) {
+                updateNode.run(commId, nodeId);
+            }
+            for (const [commId, label] of communityLabels) {
+                upsertComm.run(commId, label, commSizes.get(commId) ?? 0, cohesionScores.get(commId) ?? 0);
+            }
+        })();
         return { memberships, communityLabels, cohesionScores };
     },
 };

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	@@ -1 +1 @@
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1	+ {"version":3,"file":"processes.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/processes.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAIjD,MAAM,WAAW,UAAU;IACzB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,eAAe;IAC9B,aAAa,EAAE;QACb,SAAS,EAAE,UAAU,EAAE,CAAC;QACxB,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACjC,KAAK,EAAE;YAAE,cAAc,EAAE,MAAM,CAAC;YAAC,UAAU,EAAE,MAAM,CAAA;SAAE,CAAC;KACvD,CAAC;CACH;AAyHD,eAAO,MAAM,cAAc,EAAE,aAAa,CAAC,eAAe,CAsHzD,CAAC"}

package/dist/src/pipeline/phases/processes.js CHANGED Viewed

@@ -97,6 +97,13 @@ export const processesPhase = {
             };
         }
         const db = ctx.db;
+        // Process rows are derived from the current call graph; clear the previous run's
+        // so processes whose entry or steps no longer exist stop being served.
+        db.transaction(() => {
+            db.prepare(`DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE label = 'Process')
+            OR target_id IN (SELECT id FROM nodes WHERE label = 'Process')`).run();
+            db.prepare(`DELETE FROM nodes WHERE label = 'Process'`).run();
+        })();
         // Determine how many processes to create based on symbol count
         const symbolCountRow = db
             .prepare(`SELECT COUNT(*) as cnt FROM nodes WHERE label NOT IN ('File', 'Folder', 'Community', 'Process', 'Document')`)

package/dist/src/pipeline/phases/processes.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/src/pipeline/phases/stale-sweep.d.ts ADDED Viewed

@@ -0,0 +1,21 @@
+import type { PipelinePhase } from '../types.js';
+export interface StaleSweepOutput {
+    removedFiles: string[];
+}
+/**
+ * Drop rows for files that were renamed/deleted since the last build.
+ *
+ * This MUST run unconditionally — even when every remaining file cache-hit
+ * (`ctx.allFilesCached`), a file may have been deleted from disk between builds,
+ * which produces zero cache misses but still leaves ghost rows in the DB unless
+ * the DB's known file set is compared against the current on-disk set. It also
+ * MUST run before the derived phases (communities, processes): they re-derive from
+ * the DB, so sweeping afterwards leaves them describing symbols that no longer exist.
+ *
+ * The sweep is confined to the current build's source domain. A narrowed build
+ * never looked at files outside its domain, so their absence from the scan says
+ * nothing about whether they still exist — deleting those rows is how a code-only
+ * refresh used to erase every Document node in the graph.
+ */
+export declare const staleSweepPhase: PipelinePhase<StaleSweepOutput>;
+//# sourceMappingURL=stale-sweep.d.ts.map

package/dist/src/pipeline/phases/stale-sweep.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"stale-sweep.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/stale-sweep.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAGjD,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;CACxB;AAED;;;;;;;;;;;;;;GAcG;AACH,eAAO,MAAM,eAAe,EAAE,aAAa,CAAC,gBAAgB,CAqC3D,CAAC"}

package/dist/src/pipeline/phases/stale-sweep.js ADDED Viewed

@@ -0,0 +1,49 @@
+import { resolve } from 'node:path';
+import { isWithinScope, scopeForOptions } from '../index-scope.js';
+/**
+ * Drop rows for files that were renamed/deleted since the last build.
+ *
+ * This MUST run unconditionally — even when every remaining file cache-hit
+ * (`ctx.allFilesCached`), a file may have been deleted from disk between builds,
+ * which produces zero cache misses but still leaves ghost rows in the DB unless
+ * the DB's known file set is compared against the current on-disk set. It also
+ * MUST run before the derived phases (communities, processes): they re-derive from
+ * the DB, so sweeping afterwards leaves them describing symbols that no longer exist.
+ *
+ * The sweep is confined to the current build's source domain. A narrowed build
+ * never looked at files outside its domain, so their absence from the scan says
+ * nothing about whether they still exist — deleting those rows is how a code-only
+ * refresh used to erase every Document node in the graph.
+ */
+export const staleSweepPhase = {
+    name: 'stale-sweep',
+    deps: ['scan', 'parse'],
+    async execute(ctx, deps) {
+        const { filePaths } = deps.get('scan');
+        const db = ctx.db;
+        const scope = scopeForOptions(ctx.options.codeOnly);
+        const liveFiles = new Set(filePaths.map((f) => resolve(f)));
+        const staleFiles = db.prepare('SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL').all()
+            .map((r) => r.file_path)
+            .filter((f) => isWithinScope(f, scope) && !liveFiles.has(resolve(ctx.repoPath, f)));
+        if (staleFiles.length > 0) {
+            const deleteStale = db.transaction((files) => {
+                const deleteEdges = db.prepare(`
+          DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file_path = ?)
+             OR target_id IN (SELECT id FROM nodes WHERE file_path = ?)
+        `);
+                const deleteNodesStmt = db.prepare('DELETE FROM nodes WHERE file_path = ?');
+                for (const f of files) {
+                    deleteEdges.run(f, f);
+                    deleteNodesStmt.run(f);
+                }
+            });
+            deleteStale(staleFiles);
+            // The graph changed even though no file was re-parsed, so the derived
+            // analyses (communities, processes) must be recomputed.
+            ctx.allFilesCached = false;
+        }
+        return { removedFiles: staleFiles };
+    },
+};
+//# sourceMappingURL=stale-sweep.js.map

package/dist/src/pipeline/phases/stale-sweep.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"stale-sweep.js","sourceRoot":"","sources":["../../../../src/pipeline/phases/stale-sweep.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAQnE;;;;;;;;;;;;;;GAcG;AACH,MAAM,CAAC,MAAM,eAAe,GAAoC;IAC9D,IAAI,EAAE,aAAa;IACnB,IAAI,EAAE,CAAC,MAAM,EAAE,OAAO,CAAC;IACvB,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI;QACrB,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAe,CAAC;QACrD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;QAEpD,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC5D,MAAM,UAAU,GACd,EAAE,CAAC,OAAO,CAAC,kEAAkE,CAAC,CAAC,GAAG,EAGnF;aACE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC;aACvB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAEtF,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC1B,MAAM,WAAW,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,KAAe,EAAE,EAAE;gBACrD,MAAM,WAAW,GAAG,EAAE,CAAC,OAAO,CAAC;;;SAG9B,CAAC,CAAC;gBACH,MAAM,eAAe,GAAG,EAAE,CAAC,OAAO,CAAC,uCAAuC,CAAC,CAAC;gBAC5E,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;oBACtB,WAAW,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;oBACtB,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;gBACzB,CAAC;YACH,CAAC,CAAC,CAAC;YACH,WAAW,CAAC,UAAU,CAAC,CAAC;YACxB,sEAAsE;YACtE,wDAAwD;YACxD,GAAG,CAAC,cAAc,GAAG,KAAK,CAAC;QAC7B,CAAC;QAED,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,CAAC;IACtC,CAAC;CACF,CAAC"}

package/dist/src/storage/node-store.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/src/storage/node-store.js CHANGED Viewed

@@ -1,19 +1,33 @@
 import { MonographError, toNormLabel } from '../types.js';
 import { safeJsonParse } from './utils.js';
-export function insertNode(db, node) {
-    db.prepare(`
-    INSERT OR REPLACE INTO nodes
-      (id, label, name, norm_label, file_path, start_line, end_line,
-       community_id, is_exported, language, properties)
-    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-  `).run(node.id, node.label, node.name, node.normLabel ?? toNormLabel(node.name), node.filePath ?? null, node.startLine ?? null, node.endLine ?? null, node.communityId ?? null, node.isExported ? 1 : 0, node.language ?? null, node.properties ? JSON.stringify(node.properties) : null);
-}
+// An upsert, not INSERT OR REPLACE: replacing the row would reset community_id and
+// properties, wiping community assignments and enrichment (e.g. summaries) from every
+// node a rebuild re-inserts unchanged. Structural columns take the fresh values;
+// community_id and properties written by later phases or tools survive.
 const INSERT_SQL = `
-    INSERT OR REPLACE INTO nodes
+    INSERT INTO nodes
       (id, label, name, norm_label, file_path, start_line, end_line,
        community_id, is_exported, language, properties)
     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    ON CONFLICT(id) DO UPDATE SET
+      label = excluded.label,
+      name = excluded.name,
+      norm_label = excluded.norm_label,
+      file_path = excluded.file_path,
+      start_line = excluded.start_line,
+      end_line = excluded.end_line,
+      community_id = COALESCE(excluded.community_id, nodes.community_id),
+      is_exported = excluded.is_exported,
+      language = excluded.language,
+      properties = CASE
+        WHEN excluded.properties IS NULL THEN nodes.properties
+        WHEN nodes.properties IS NULL THEN excluded.properties
+        ELSE json_patch(nodes.properties, excluded.properties)
+      END
   `;
+export function insertNode(db, node) {
+    db.prepare(INSERT_SQL).run(node.id, node.label, node.name, node.normLabel ?? toNormLabel(node.name), node.filePath ?? null, node.startLine ?? null, node.endLine ?? null, node.communityId ?? null, node.isExported ? 1 : 0, node.language ?? null, node.properties ? JSON.stringify(node.properties) : null);
+}
 export function insertNodes(db, nodes) {
     if (nodes.length === 0)
         return;

package/dist/src/storage/node-store.js.map CHANGED Viewed

	@@ -1 +1 @@
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