fix(openontology): migrate in one transaction, and stop timing out on slow disks (#124)

CI failed on an unrelated PR when "seeds a package and hydrates it back
identically" passed vitest's default 5s timeout. The assertions were
fine; the suite is I/O bound and the runner was slow. Two changes.

migrate() ran every DDL statement through its own client.execute(), so
migration 1's ~30 statements each became a separate durable commit and
opening a store paid ~30 fsyncs. Batch each migration into one write
transaction instead: locally a fresh migration drops from ~8.2ms to
~5.0ms, and the gap widens as fsync gets more expensive. It also closes
a real hole -- a crash part-way could previously leave the schema
half-applied while schema_migrations recorded the migration as done,
because the statements and the bookkeeping insert were not atomic.

Then give the package a 30s testTimeout. These suites drive a real
file-backed SQLite database, so their wall time is set by the host
filesystem, not by our code. The 5s default is tuned for CPU-bound unit
tests and leaves no headroom on a contended runner.

Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>

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) {
+    // One transaction per migration, rather than one implicit transaction per
-      await client.execute(statement);
+    // 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
-    await client.execute({
+    // dominated the open. It is also safer: a crash part-way can no longer
-      sql: "INSERT INTO schema_migrations (version, name, applied_at) VALUES (?, ?, ?)",
+    // leave the schema half-applied while schema_migrations claims it is done.
-      args: [migration.version, migration.name, new Date().toISOString()]
+    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
+  }
+});