exp run: fix failure when dependencies are from inside submodules (#10831)

tests/func/experiments/test_experiments.py

@@ -793,3 +793,18 @@ def test_custom_commit_message(tmp_dir, scm, dvc, tmp):
         )
     )
     assert scm.resolve_commit(exp).message == "custom commit message"
+
+
+@pytest.mark.parametrize("dep", ["submodule", "submodule/file"])
+def test_experiments_run_with_submodule_dependencies(dvc, scm, make_tmp_dir, dep):
+    external_repo = make_tmp_dir("external_repo", scm=True)
+    external_repo.scm_gen("file", "content", commit="add file")
+
+    submodules = scm.pygit2.repo.submodules
+    submodules.add(os.fspath(external_repo), "submodule")
+    submodules.update(init=True)
+    scm.add_commit([".gitmodules"], message="add submodule")
+
+    dvc.stage.add(cmd="echo foo", deps=[dep], name="foo")
+
+    assert dvc.experiments.run()

tests/unit/repo/test_scm_context.py

@@ -39,7 +39,7 @@ def test_scm_track_changed_files(scm_context):
 
     scm_context.track_file("foo")
     scm_context.track_changed_files()
-    scm_context.scm.add.assert_called_once_with({"foo"})
+    scm_context.scm.add.assert_called_once_with(["foo"])
 
 
 def test_ignore(scm_context):
@@ -73,7 +73,7 @@ def test_scm_context_autostage_changed_files(scm_context):
 
     assert not scm_context.files_to_track
     assert not scm_context.ignored_paths
-    scm_context.scm.add.assert_called_once_with({"foo"})
+    scm_context.scm.add.assert_called_once_with(["foo"])
 
 
 def test_scm_context_clears_ignores_on_error(scm_context):
@@ -141,4 +141,4 @@ def test_scm_context_decorator(scm_context, mocker):
     method = mocker.MagicMock(wraps=test_method)
     decorator(method, autostage=True)(repo, "arg", kw=1)
     method.assert_called_once_with(repo, "arg", kw=1)
-    scm_context.scm.add.assert_called_once_with({"foo"})
+    scm_context.scm.add.assert_called_once_with(["foo"])