exp run: dvc commit DVC-tracked data deps when stashing an experiment

dvc/repo/commit.py

@@ -37,20 +37,32 @@ def prompt_to_commit(stage, changes, force=False):
 
 @locked
 def commit(
-    self, target, with_deps=False, recursive=False, force=False,
+    self,
+    target,
+    with_deps=False,
+    recursive=False,
+    force=False,
+    allow_missing=False,
+    data_only=False,
 ):
     from dvc.dvcfile import Dvcfile
 
-    stages_info = self.stage.collect_granular(
-        target, with_deps=with_deps, recursive=recursive
-    )
+    stages_info = [
+        info
+        for info in self.stage.collect_granular(
+            target, with_deps=with_deps, recursive=recursive
+        )
+        if not data_only or info.stage.is_data_source
+    ]
     for stage_info in stages_info:
         stage = stage_info.stage
         changes = stage.changed_entries()
         if any(changes):
             prompt_to_commit(stage, changes, force=force)
-            stage.save()
-        stage.commit(filter_info=stage_info.filter_info)
+            stage.save(allow_missing=allow_missing)
+        stage.commit(
+            filter_info=stage_info.filter_info, allow_missing=allow_missing
+        )
 
         Dvcfile(self, stage.path).dump(stage, update_pipeline=False)
     return [s.stage for s in stages_info]

dvc/repo/experiments/__init__.py

@@ -186,6 +186,10 @@ def _stash_exp(
                     if params:
                         self._update_params(params)
 
+                    # DVC commit data deps to preserve state across workspace
+                    # & tempdir runs
+                    self._stash_commit_deps(*args, **kwargs)
+
                     if resume_rev:
                         if branch:
                             branch_name = ExpRefInfo.from_ref(branch).name
@@ -242,6 +246,25 @@ def _stash_exp(
 
         return stash_rev
 
+    def _stash_commit_deps(self, *args, **kwargs):
+        if len(args):
+            targets = args[0]
+        else:
+            targets = kwargs.get("targets")
+        if isinstance(targets, str):
+            targets = [targets]
+        elif not targets:
+            targets = [None]
+        for target in targets:
+            self.repo.commit(
+                target,
+                with_deps=True,
+                recursive=kwargs.get("recursive", False),
+                force=True,
+                allow_missing=True,
+                data_only=True,
+            )
+
     def _stash_msg(
         self,
         rev: str,

dvc/stage/__init__.py

@@ -433,15 +433,21 @@ def compute_md5(self):
         return m
 
     def save(self, allow_missing=False):
-        self.save_deps()
+        self.save_deps(allow_missing=allow_missing)
         self.save_outs(allow_missing=allow_missing)
         self.md5 = self.compute_md5()
 
         self.repo.stage_cache.save(self)
 
-    def save_deps(self):
+    def save_deps(self, allow_missing=False):
+        from dvc.dependency.base import DependencyDoesNotExistError
+
         for dep in self.deps:
-            dep.save()
+            try:
+                dep.save()
+            except DependencyDoesNotExistError:
+                if not allow_missing:
+                    raise
 
     def save_outs(self, allow_missing=False):
         from dvc.output.base import OutputDoesNotExistError

tests/func/experiments/test_experiments.py

@@ -1,3 +1,4 @@
+import itertools
 import logging
 import os
 import stat
@@ -624,3 +625,52 @@ def test_fix_exp_head(tmp_dir, scm, tail):
     scm.set_ref(EXEC_BASELINE, "refs/heads/master")
     assert EXEC_BASELINE + tail == fix_exp_head(scm, head)
     assert "foo" + tail == fix_exp_head(scm, "foo" + tail)
+
+
+@pytest.mark.parametrize(
+    "workspace, params, target",
+    itertools.product((True, False), ("foo: 1", "foo: 2"), (True, False)),
+)
+def test_modified_data_dep(tmp_dir, scm, dvc, workspace, params, target):
+    tmp_dir.dvc_gen("data", "data")
+    tmp_dir.gen("copy.py", COPY_SCRIPT)
+    tmp_dir.gen("params.yaml", "foo: 1")
+    exp_stage = dvc.run(
+        cmd="python copy.py params.yaml metrics.yaml",
+        metrics_no_cache=["metrics.yaml"],
+        params=["foo"],
+        name="copy-file",
+        deps=["copy.py", "data"],
+    )
+    scm.add(
+        [
+            "dvc.yaml",
+            "dvc.lock",
+            "copy.py",
+            "params.yaml",
+            "metrics.yaml",
+            "data.dvc",
+            ".gitignore",
+        ]
+    )
+    scm.commit("init")
+
+    tmp_dir.gen("params.yaml", params)
+    tmp_dir.gen("data", "modified")
+
+    results = dvc.experiments.run(
+        exp_stage.addressing if target else None, tmp_dir=not workspace
+    )
+    exp = first(results)
+
+    for rev in dvc.brancher(revs=[exp]):
+        if rev != exp:
+            continue
+        with dvc.repo_fs.open(tmp_dir / "metrics.yaml") as fobj:
+            assert fobj.read().strip() == params
+        with dvc.repo_fs.open(tmp_dir / "data") as fobj:
+            assert fobj.read().strip() == "modified"
+
+    if workspace:
+        assert (tmp_dir / "metrics.yaml").read_text().strip() == params
+        assert (tmp_dir / "data").read_text().strip() == "modified"