exp run: do not autostage on dvc repro (#9344)

dvc/repo/experiments/executor/base.py

@@ -13,6 +13,7 @@ from typing import (
     Callable,
     Dict,
     Iterable,
+    Iterator,
     List,
     NamedTuple,
     Optional,
@@ -259,6 +260,12 @@ class BaseExecutor(ABC):
             **kwargs,
         )
 
+    @classmethod
+    def _get_top_level_paths(cls, repo: "Repo") -> Iterable["str"]:
+        yield from _collect_top_level_metrics(repo)
+        yield from _collect_top_level_params(repo)
+        yield from repo.index._plot_sources  # pylint: disable=protected-access
+
     @classmethod
     def save(
         cls,
@@ -280,11 +287,7 @@ class BaseExecutor(ABC):
             os.chdir(dvc.root_dir)
 
         include_untracked = include_untracked or []
-        include_untracked.extend(_collect_top_level_metrics(dvc))
-        include_untracked.extend(_collect_top_level_params(dvc))
-        include_untracked.extend(
-            dvc.index._plot_sources  # pylint: disable=protected-access
-        )
+        include_untracked.extend(cls._get_top_level_paths(dvc))
         # dvc repro automatically stages dvc.lock. Running redundant `git add`
         # on it causes an error when exiting the detached head context.
         if LOCK_FILE in dvc.scm.untracked_files():
@@ -540,11 +543,19 @@ class BaseExecutor(ABC):
                 info.name,
                 repro_force or checkpoint_reset,
             )
+
+            def after_repro():
+                paths = list(cls._get_top_level_paths(dvc))
+                if paths:
+                    logger.debug("Staging top-level files: %s", paths)
+                    dvc.scm_context.add(paths)
+
             stages = dvc_reproduce(
                 dvc,
                 *args,
                 on_unchanged=filter_pipeline,
                 checkpoint_func=checkpoint_func,
+                after_repro_callback=after_repro,
                 **kwargs,
             )
 
@@ -614,7 +625,7 @@ class BaseExecutor(ABC):
         log_errors: bool = True,
         copy_paths: Optional[List[str]] = None,
         **kwargs,
-    ):
+    ) -> Iterator["Repo"]:
         from dvc_studio_client.post_live_metrics import post_live_metrics
 
         from dvc.repo import Repo

dvc/repo/reproduce.py

@@ -3,8 +3,6 @@ from functools import partial
 from typing import TYPE_CHECKING, Iterator, List
 
 from dvc.exceptions import DvcException, ReproductionError
-from dvc.repo.metrics.show import _collect_top_level_metrics
-from dvc.repo.params.show import _collect_top_level_params
 from dvc.repo.scm_context import scm_context
 from dvc.stage.exceptions import CheckpointKilledError
 
@@ -76,25 +74,15 @@ def _track_stage(stage: "Stage") -> None:
     return context.track_changed_files()
 
 
-def _track_top_level(repo: "Repo") -> None:
-    context = repo.scm_context
-    for metric_file in _collect_top_level_metrics(repo):
-        context.track_file(metric_file)
-    for param_file in _collect_top_level_params(repo):
-        context.track_file(param_file)
-    for plot_file in repo.index._plot_sources:  # pylint: disable=protected-access
-        context.track_file(plot_file)
-    context.track_changed_files()
-
-
 @locked
 @scm_context
-def reproduce(  # noqa: C901
+def reproduce(  # noqa: C901, PLR0912
     self: "Repo",
     targets=None,
     recursive=False,
     pipeline=False,
     all_pipelines=False,
+    after_repro_callback=None,
     **kwargs,
 ):
     from .graph import get_pipeline, get_pipelines
@@ -139,12 +127,18 @@ def reproduce(  # noqa: C901
             )
 
     result = _reproduce_stages(self.index.graph, list(stages), **kwargs)
-    _track_top_level(self)
+    if callable(after_repro_callback):
+        after_repro_callback()
     return result
 
 
 def _reproduce_stages(  # noqa: C901
-    graph, stages, downstream=False, single_item=False, on_unchanged=None, **kwargs
+    graph,
+    stages,
+    downstream=False,
+    single_item=False,
+    on_unchanged=None,
+    **kwargs,
 ):
     r"""Derive the evaluation of the given node for the given graph.