Fix false cache misses when dependency order changes

mypy/build.py

@@ -3056,7 +3056,10 @@ def is_fresh(self) -> bool:
         # same for suppressed dependencies, even if the first check is OK.
         return (
             self.meta is not None
-            and self.dependencies == self.meta.dependencies
+            # Loading and suppressing dependencies can change their iteration order.
+            and self.dependencies_set == set(self.meta.dependencies)
+            and len(self.dependencies_set) == len(self.dependencies)
+            and len(self.dependencies) == len(self.meta.dependencies)
             and (
                 self.options.fine_grained_incremental
                 or self.meta.suppressed_deps_opts == self.suppressed_deps_opts()

mypy/test/testbuild.py

@@ -0,0 +1,56 @@
+"""Tests for incremental build behavior."""
+
+from __future__ import annotations
+
+import os
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+
+from mypy.test.helpers import Suite
+
+
+class BuildSuite(Suite):
+    def test_reuses_cache_when_dependency_order_changes(self) -> None:
+        with tempfile.TemporaryDirectory() as temporary_directory:
+            tmp_path = Path(temporary_directory)
+            site = tmp_path / "site"
+            typed_subpackage = site / "ns" / "sub"
+            typed_subpackage.mkdir(parents=True)
+            (typed_subpackage / "__init__.py").write_text("", encoding="utf8")
+            (typed_subpackage / "py.typed").touch()
+
+            (tmp_path / "a.py").write_text(
+                "import ns.missing\nimport os\n\ny = os.environ\n", encoding="utf8"
+            )
+            (tmp_path / "b.py").write_text("import ns.sub\n", encoding="utf8")
+            (tmp_path / "e.py").write_text("import b\n", encoding="utf8")
+
+            env = os.environ.copy()
+            env.pop("MYPY_CACHE_DIR", None)
+            env["PYTHONPATH"] = str(site)
+            command = [
+                sys.executable,
+                "-m",
+                "mypy",
+                "-v",
+                f"--cache-dir={tmp_path / 'cache'}",
+                "a.py",
+                "e.py",
+            ]
+
+            def run() -> subprocess.CompletedProcess[str]:
+                return subprocess.run(
+                    command, cwd=tmp_path, env=env, capture_output=True, text=True, check=False
+                )
+
+            first_run = run()
+            second_run = run()
+
+            stale_log = "Scheduling SCC singleton (a) as inherently stale"
+            first_output = first_run.stdout + first_run.stderr
+            second_output = second_run.stdout + second_run.stderr
+            assert first_run.returncode == second_run.returncode == 1
+            assert stale_log in first_output
+            assert stale_log not in second_output