Fix sqlite store in 2.x (#2880)

* Fix sqlite store

* Ignore unclosed dataset warning

* Add release note

Author: dstansby

docs/release.rst

@@ -20,6 +20,11 @@ Release notes
 Unreleased
 ----------
 
+Fixes
+~~~~~
+* Fixed ``SQLiteStore`` with the latest version of ``sqlite3``.
+  By :user:`David Stansby <dstansby>`
+
 Deprecations
 ~~~~~~~~~~~~
 

pyproject.toml

@@ -130,6 +130,7 @@ filterwarnings = [
     "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
     "ignore:The .* is deprecated and will be removed in a Zarr-Python version 3*:FutureWarning",
     "ignore:The experimental Zarr V3 implementation in this version .*:FutureWarning",
+    "ignore:unclosed database in <sqlite3.Connection.*:ResourceWarning",
 ]
 doctest_subpackage_requires = [
     "zarr/core.py = numpy>=2",

zarr/_storage/v3.py

@@ -490,7 +490,7 @@ def rmdir(self, path=None):
         if path:
             for base in [meta_root, data_root]:
                 with self.lock:
-                    self.cursor.execute('DELETE FROM zarr WHERE k LIKE (? || "/%")', (base + path,))
+                    self.cursor.execute("DELETE FROM zarr WHERE k LIKE (? || '/%')", (base + path,))
             # remove any associated metadata files
             sfx = _get_metadata_suffix(self)
             meta_dir = (meta_root + path).rstrip("/")

zarr/storage.py

@@ -2779,9 +2779,9 @@ def listdir(self, path=None):
         sep = "_" if path == "" else "/"
         keys = self.cursor.execute(
             f"""
-            SELECT DISTINCT SUBSTR(m, 0, INSTR(m, "/")) AS l FROM (
-                SELECT LTRIM(SUBSTR(k, LENGTH(?) + 1), "/") || "/" AS m
-                FROM zarr WHERE k LIKE (? || "{sep}%")
+            SELECT DISTINCT SUBSTR(m, 0, INSTR(m, '/')) AS l FROM (
+                SELECT LTRIM(SUBSTR(k, LENGTH(?) + 1), '/') || '/' AS m
+                FROM zarr WHERE k LIKE (? || '{sep}%')
             ) ORDER BY l ASC
             """,
             (path, path),
@@ -2794,8 +2794,8 @@ def getsize(self, path=None):
         size = self.cursor.execute(
             """
             SELECT COALESCE(SUM(LENGTH(v)), 0) FROM zarr
-            WHERE k LIKE (? || "%") AND
-                  0 == INSTR(LTRIM(SUBSTR(k, LENGTH(?) + 1), "/"), "/")
+            WHERE k LIKE (? || '%') AND
+                  0 == INSTR(LTRIM(SUBSTR(k, LENGTH(?) + 1), '/'), '/')
             """,
             (path, path),
         )
@@ -2806,7 +2806,7 @@ def rmdir(self, path=None):
         path = normalize_storage_path(path)
         if path:
             with self.lock:
-                self.cursor.execute('DELETE FROM zarr WHERE k LIKE (? || "/%")', (path,))
+                self.cursor.execute("DELETE FROM zarr WHERE k LIKE (? || '/%')", (path,))
         else:
             self.clear()