Run each migration inside a transaction

Migrations.apply() now wraps each migration function and its
_sqlite_migrations tracking row in db.atomic(), so they commit
together: a failing migration rolls back cleanly, is not recorded,
and stays pending, eliminating the double-apply hazard where a
partially-failed migration left committed side effects behind.

Migrations that cannot run inside a transaction (VACUUM, journal
mode changes, manual transaction management) can opt out by
registering with @migrations(transactional=False).

Also fixed the test fixtures which used db.query() for INSERT
statements - query() is a lazy generator, so those inserts never
actually executed.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UnLnhsH25Nnv7LHhekUfPd

tests/test_migrations.py

@@ -14,7 +14,7 @@ def migrations():
     @migrations()
     def m002(db):
         db["cats"].create({"name": str})
-        db.query("insert into dogs (name) values ('Pancakes')")
+        db.execute("insert into dogs (name) values ('Pancakes')")
 
     return migrations
 
@@ -32,7 +32,7 @@ def migrations_not_ordered_alphabetically():
     @migrations()
     def m001(db):
         db["cats"].create({"name": str})
-        db.query("insert into dogs (name) values ('Pancakes')")
+        db.execute("insert into dogs (name) values ('Pancakes')")
 
     return migrations
 
@@ -80,6 +80,76 @@ def test_order_does_not_matter(migrations, migrations_not_ordered_alphabetically
     assert db1.schema == db2.schema
 
 
+def test_failing_migration_rolls_back(migrations):
+    @migrations()
+    def m003(db):
+        db["birds"].create({"name": str})
+        db.execute("insert into dogs (name) values ('Dozer')")
+        raise ValueError("boom")
+
+    db = sqlite_utils.Database(memory=True)
+    with pytest.raises(ValueError):
+        migrations.apply(db)
+    # m001 and m002 committed before the failure and stay applied
+    assert set(db.table_names()) == {"_sqlite_migrations", "dogs", "cats"}
+    assert [r["name"] for r in db["dogs"].rows] == ["Cleo", "Pancakes"]
+    assert [m.name for m in migrations.applied(db)] == ["m001", "m002"]
+    # Everything m003 did was rolled back and it is still pending
+    assert [m.name for m in migrations.pending(db)] == ["m003"]
+
+
+def test_rerun_after_failure_applies_each_migration_once():
+    state = {"fail": True}
+    migrations = Migrations("test")
+
+    @migrations()
+    def m001(db):
+        db["dogs"].insert({"name": "Cleo"})
+
+    @migrations()
+    def m002(db):
+        db["dogs"].insert({"name": "Pancakes"})
+        if state["fail"]:
+            raise ValueError("boom")
+
+    db = sqlite_utils.Database(memory=True)
+    with pytest.raises(ValueError):
+        migrations.apply(db)
+    state["fail"] = False
+    migrations.apply(db)
+    # m001 must not have been re-applied, m002 applied exactly once
+    assert [r["name"] for r in db["dogs"].rows] == ["Cleo", "Pancakes"]
+    assert [m.name for m in migrations.applied(db)] == ["m001", "m002"]
+
+
+def test_non_transactional_migration_allows_vacuum(tmpdir):
+    path = str(tmpdir / "test.db")
+    db = sqlite_utils.Database(path)
+    migrations = Migrations("test")
+
+    @migrations()
+    def m001(db):
+        db["dogs"].insert({"name": "Cleo"})
+
+    @migrations(transactional=False)
+    def m002(db):
+        db.execute("VACUUM")
+
+    migrations.apply(db)
+    assert [m.name for m in migrations.applied(db)] == ["m001", "m002"]
+    db.close()
+
+
+def test_apply_composes_inside_outer_transaction(migrations):
+    db = sqlite_utils.Database(memory=True)
+    with pytest.raises(ZeroDivisionError):
+        with db.atomic():
+            migrations.apply(db)
+            raise ZeroDivisionError
+    # The outer transaction rolled back, taking the migrations with it
+    assert db.table_names() == []
+
+
 @pytest.mark.parametrize(
     "create_table,pk",
     (