experiments: fix git stash mtime race condition (#4727)

dvc/repo/experiments/__init__.py

@@ -263,9 +263,6 @@ class Experiments:
                 if os.path.getsize(tmp):
                     logger.debug("Patching experiment workspace")
                     self.scm.repo.git.apply(tmp)
-                elif not params and not allow_unchanged:
-                    # experiment matches original baseline
-                    raise UnchangedExperimentError(rev)
             finally:
                 remove(tmp)
 
@@ -273,6 +270,10 @@ class Experiments:
         if params:
             self._update_params(params)
 
+        if not self.scm.is_dirty(untracked_files=True) and not allow_unchanged:
+            # experiment matches original baseline
+            raise UnchangedExperimentError(rev)
+
         # save additional repro command line arguments
         self._pack_args(*args, **kwargs)
 
@@ -317,6 +318,12 @@ class Experiments:
             with modify_data(path, tree=self.exp_dvc.tree) as data:
                 _update(data, params[params_fname])
 
+        # Force params file changes to be staged in git
+        # Otherwise in certain situations the changes to params file may be
+        # ignored when we `git stash` them since mtime is used to determine
+        # whether the file is dirty
+        self.scm.add(list(params.keys()))
+
     def _commit(
         self, exp_hash, check_exists=True, create_branch=True, checkpoint=False
     ):

tests/func/experiments/test_experiments.py

@@ -1,7 +1,6 @@
 from textwrap import dedent
 
 import pytest
-from flaky.flaky_decorator import flaky
 from funcy import first
 
 from dvc.utils.serialize import PythonFileCorruptedError
@@ -206,8 +205,6 @@ def test_update_py_params(tmp_dir, scm, dvc):
         dvc.experiments.run(stage.addressing, params=["params.py:INT=2a"])
 
 
-# See: https://github.com/iterative/dvc/issues/4717
-@flaky(max_runs=3, min_passes=1)
 def test_extend_branch(tmp_dir, scm, dvc):
     tmp_dir.gen("copy.py", COPY_SCRIPT)
     tmp_dir.gen("params.yaml", "foo: 1")
@@ -232,6 +229,7 @@ def test_extend_branch(tmp_dir, scm, dvc):
     )
     exp_b = first(results)
 
+    assert exp_a != exp_b
     assert dvc.experiments._get_branch_containing(exp_b) == exp_branch
 
     dvc.experiments.checkout(exp_a)