fix(openontology): migrate in one transaction, and stop timing out on slow disks

packages/openontology/src/libsql.ts

@@ -225,13 +225,21 @@ export async function migrate(client: Client): Promise<number> {
   let count = 0;
   for (const migration of MIGRATIONS) {
     if (have.has(migration.version)) continue;
-    for (const statement of migration.statements) {
-      await client.execute(statement);
-    }
-    await client.execute({
-      sql: "INSERT INTO schema_migrations (version, name, applied_at) VALUES (?, ?, ?)",
-      args: [migration.version, migration.name, new Date().toISOString()]
-    });
+    // One transaction per migration, rather than one implicit transaction per
+    // statement. Migration 1 alone is ~30 DDL statements, so opening a store
+    // used to cost ~30 durable commits; on a filesystem with slow fsync that
+    // dominated the open. It is also safer: a crash part-way can no longer
+    // leave the schema half-applied while schema_migrations claims it is done.
+    await client.batch(
+      [
+        ...migration.statements,
+        {
+          sql: "INSERT INTO schema_migrations (version, name, applied_at) VALUES (?, ?, ?)",
+          args: [migration.version, migration.name, new Date().toISOString()] as InArgs
+        }
+      ],
+      "write"
+    );
     count += 1;
   }
   return count;

packages/openontology/vitest.config.ts

@@ -0,0 +1,15 @@
+import { defineConfig } from "vitest/config";
+
+export default defineConfig({
+  test: {
+    // These suites drive a real file-backed SQLite database through
+    // @libsql/client, so their wall time is set by the host filesystem's
+    // durability cost, not by our code. Locally the whole libsql suite runs in
+    // ~250ms; on a contended CI runner a single seed-and-reopen case has been
+    // seen to pass 5s, which is vitest's default and is tuned for CPU-bound
+    // unit tests. Give the I/O-bound cases enough headroom that a slow disk
+    // reports as slow rather than as a spurious failure.
+    testTimeout: 30_000,
+    hookTimeout: 30_000
+  }
+});