From cc4192fb21e0ccc953cfc715b520c7efe2a245d5 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Fri, 5 Jun 2026 23:19:04 +0100
Subject: [PATCH] Fix Pyodide sqlite bootstrap

---
 build.sh                        | 20 ++++++++++++++---
 content-hash.txt                |  2 +-
 tests/test_notebooks_pyodide.py | 39 +++++++++++++++++++++++++++++++++
 3 files changed, 57 insertions(+), 4 deletions(-)

diff --git a/build.sh b/build.sh
index add8a83..c0a9468 100755
--- a/build.sh
+++ b/build.sh
@@ -37,22 +37,36 @@ kernel_extension_dir = Path(
 load_pyodide_pattern = re.compile(
     r"\(await ([A-Za-z_$][\w$]*|__webpack_require__)\(476\)\(([A-Za-z_$][\w$]*)\)\)\.loadPyodide"
 )
+dynamic_import_patched_files = []
 patched_files = []
 worker_type_patched_files = []
+sqlite_bootstrap_patched_files = []
 for path in kernel_extension_dir.glob("*.js"):
     source = path.read_text()
     patched = load_pyodide_pattern.sub(r"(await import(\2)).loadPyodide", source)
+    if patched != source:
+        dynamic_import_patched_files.append(path.name)
+    before_worker_patch = patched
     patched = patched.replace("{type:void 0}", '{type:"module"}')
+    if "{type:void 0}" in before_worker_patch and '{type:"module"}' in patched:
+        worker_type_patched_files.append(path.name)
+    before_sqlite_patch = patched
+    patched = patched.replace(
+        '["sqlite3","ipykernel","comm","pyodide_kernel","jedi","ipython"]',
+        '["ipykernel","comm","pyodide_kernel","jedi","ipython"]',
+    )
+    if '"sqlite3","ipykernel"' in before_sqlite_patch and '"sqlite3","ipykernel"' not in patched:
+        sqlite_bootstrap_patched_files.append(path.name)
     if patched != source:
         path.write_text(patched)
         patched_files.append(path.name)
-    if "{type:void 0}" in source and '{type:"module"}' in patched:
-        worker_type_patched_files.append(path.name)
 
-if not patched_files:
+if not dynamic_import_patched_files:
     raise SystemExit("No Pyodide dynamic import bundle entry was patched")
 if not worker_type_patched_files:
     raise SystemExit("No Pyodide worker type entry was patched")
+if not sqlite_bootstrap_patched_files:
+    raise SystemExit("No Pyodide sqlite bootstrap entry was patched")
 PY
 python3 - <<'PY'
 import hashlib
diff --git a/content-hash.txt b/content-hash.txt
index 6eeffa0..542d8e5 100644
--- a/content-hash.txt
+++ b/content-hash.txt
@@ -1 +1 @@
-757a3beb0900ec3b676d915aaed054bbca25bcd7d7cb6146435ed617adf3d765
+ef4b18000bb5a070fd3ae51e556e4844a7dbaab494e555c5dfaca2b780ade7d5
diff --git a/tests/test_notebooks_pyodide.py b/tests/test_notebooks_pyodide.py
index 2c4a1c0..5025201 100644
--- a/tests/test_notebooks_pyodide.py
+++ b/tests/test_notebooks_pyodide.py
@@ -1,8 +1,12 @@
 import json
 import os
+import shutil
+import subprocess
+import textwrap
 from pathlib import Path
 
 import nbformat
+import pytest
 from nbclient import NotebookClient
 
 
@@ -71,6 +75,41 @@ def test_pyodide_kernel_uses_module_workers():
   assert "{type:void 0}" not in bundle_source
 
 
+def test_pyodide_kernel_does_not_piplite_install_sqlite3():
+  extension_dir = DIST / "extensions" / "@jupyterlite" / "pyodide-kernel-extension" / "static"
+  js_files = list(extension_dir.glob("*.js"))
+  assert js_files
+  bundle_source = "\n".join(path.read_text(encoding="utf8") for path in js_files)
+  assert '"sqlite3","ipykernel"' not in bundle_source
+  assert '["ipykernel","comm","pyodide_kernel","jedi","ipython"]' in bundle_source
+
+
+def test_pyodide_runtime_imports_sqlite3():
+  if shutil.which("node") is None:
+    pytest.skip("node is required to smoke-test the local Pyodide runtime")
+
+  script = textwrap.dedent(
+    """
+    import { loadPyodide } from './dist/static/pyodide/pyodide.mjs';
+    const pyodide = await loadPyodide({ indexURL: './dist/static/pyodide/' });
+    await pyodide.runPythonAsync(`
+    import sqlite3, _sqlite3
+    assert sqlite3.sqlite_version
+    assert _sqlite3.sqlite_version
+    `);
+    """
+  )
+  result = subprocess.run(
+    ["node", "--input-type=module", "-e", script],
+    cwd=ROOT,
+    capture_output=True,
+    text=True,
+    timeout=60,
+    check=False,
+  )
+  assert result.returncode == 0, result.stdout + result.stderr
+
+
 def _execute_notebook(notebook_path: Path, *, cells: int | None = None, timeout: int = 600) -> None:
   """Execute a notebook using the local CPython kernel.