experiments: handle exp run from within subdirs/subrepos (#5093)

* experiments: add test cases for stage in subdir & subrepo

* git: fix relpath handling in dulwich add()

* repro: move exp file git staging from stage.run into repro

* experiments: support running experiments from outside DVC root

* experiments: setup logger inside multiprocessing (executor) context

* git: fix dulwich add in submodules

dvc/repo/experiments/__init__.py

@@ -269,7 +269,7 @@ class Experiments:
         logger.debug("Using experiment params '%s'", params)
 
         for params_fname in params:
-            path = PathInfo(self.repo.root_dir) / params_fname
+            path = PathInfo(params_fname)
             suffix = path.suffix.lower()
             modify_data = MODIFIERS[suffix]
             with modify_data(path, tree=self.repo.tree) as data:
@@ -496,6 +496,8 @@ class Experiments:
 
         manager = Manager()
         pid_q = manager.Queue()
+
+        rel_cwd = relpath(os.getcwd(), self.repo.root_dir)
         with ProcessPoolExecutor(max_workers=jobs) as workers:
             futures = {}
             for rev, executor in executors.items():
@@ -505,6 +507,8 @@ class Experiments:
                     pid_q,
                     rev,
                     name=executor.name,
+                    rel_cwd=rel_cwd,
+                    log_level=logger.getEffectiveLevel(),
                 )
                 futures[future] = (rev, executor)
 

dvc/repo/experiments/executor.py

@@ -196,8 +196,9 @@ class BaseExecutor:
         dvc_dir: str,
         queue: "Queue",
         rev: str,
-        cwd: Optional[str] = None,
+        rel_cwd: Optional[str] = None,
         name: Optional[str] = None,
+        log_level: Optional[int] = None,
     ) -> Tuple[Optional[str], bool]:
         """Run dvc repro and return the result.
 
@@ -211,6 +212,7 @@ class BaseExecutor:
         unchanged = []
 
         queue.put((rev, os.getpid()))
+        cls._set_log_level(log_level)
 
         def filter_pipeline(stages):
             unchanged.extend(
@@ -223,9 +225,11 @@ class BaseExecutor:
         try:
             dvc = Repo(dvc_dir)
             old_cwd = os.getcwd()
-            new_cwd = cwd if cwd else dvc.root_dir
-            os.chdir(new_cwd)
-            logger.debug("Running repro in '%s'", cwd)
+            if rel_cwd:
+                os.chdir(os.path.join(dvc.root_dir, rel_cwd))
+            else:
+                os.chdir(dvc.root_dir)
+            logger.debug("Running repro in '%s'", os.getcwd())
 
             args_path = os.path.join(
                 dvc.tmp_dir, BaseExecutor.PACKED_ARGS_FILE
@@ -321,6 +325,18 @@ class BaseExecutor:
         scm.set_ref(EXEC_BRANCH, branch, symbolic=True)
         return new_rev
 
+    @staticmethod
+    def _set_log_level(level):
+        from dvc.logger import disable_other_loggers
+
+        # When executor.reproduce is run in a multiprocessing child process,
+        # dvc.main will not be called for that child process so we need to
+        # setup logging ourselves
+        dvc_logger = logging.getLogger("dvc")
+        disable_other_loggers()
+        if level is not None:
+            dvc_logger.setLevel(level)
+
 
 class LocalExecutor(BaseExecutor):
     """Local machine experiment executor."""

dvc/repo/reproduce.py

@@ -1,4 +1,5 @@
 import logging
+import os
 import typing
 from functools import partial
 
@@ -18,6 +19,7 @@ logger = logging.getLogger(__name__)
 def _reproduce_stage(stage, **kwargs):
     def _run_callback(repro_callback):
         _dump_stage(stage)
+        _track_stage(stage)
         repro_callback([stage])
 
     checkpoint_func = kwargs.pop("checkpoint_func", None)
@@ -42,7 +44,10 @@ def _reproduce_stage(stage, **kwargs):
         return []
 
     if not kwargs.get("dry", False):
+        track = checkpoint_func is not None
         _dump_stage(stage)
+        if track:
+            _track_stage(stage)
 
     return [stage]
 
@@ -54,6 +59,13 @@ def _dump_stage(stage):
     dvcfile.dump(stage, update_pipeline=False)
 
 
+def _track_stage(stage):
+    for out in stage.outs:
+        if not out.use_scm_ignore and out.is_in_repo:
+            stage.repo.scm.track_file(os.fspath(out.path_info))
+    stage.repo.scm.track_changed_files()
+
+
 def _get_active_graph(G):
     import networkx as nx
 

dvc/scm/git/backend/dulwich.py

@@ -4,8 +4,9 @@ import logging
 import os
 import stat
 from io import BytesIO, StringIO
-from typing import Callable, Iterable, Optional, Tuple
+from typing import Callable, Dict, Iterable, Optional, Tuple
 
+from dvc.path_info import PathInfo
 from dvc.scm.base import SCMError
 from dvc.utils import relpath
 
@@ -67,8 +68,24 @@ class DulwichBackend(BaseGitBackend):  # pylint:disable=abstract-method
         except NotGitRepository as exc:
             raise SCMError(f"{root_dir} is not a git repository") from exc
 
+        self._submodules: Dict[str, "PathInfo"] = self._find_submodules()
         self._stashes: dict = {}
 
+    def _find_submodules(self) -> Dict[str, "PathInfo"]:
+        """Return dict mapping submodule names to submodule paths.
+
+        Submodule paths will be relative to Git repo root.
+        """
+        from dulwich.config import ConfigFile, parse_submodules
+
+        submodules: Dict[str, "PathInfo"] = {}
+        config_path = os.path.join(self.root_dir, ".gitmodules")
+        if os.path.isfile(config_path):
+            config = ConfigFile.from_path(config_path)
+            for path, _url, section in parse_submodules(config):
+                submodules[os.fsdecode(section)] = PathInfo(os.fsdecode(path))
+        return submodules
+
     def close(self):
         self.repo.close()
 
@@ -101,8 +118,19 @@ class DulwichBackend(BaseGitBackend):  # pylint:disable=abstract-method
 
         files = []
         for path in paths:
-            if not os.path.isabs(path):
-                path = os.path.join(self.root_dir, path)
+            if not os.path.isabs(path) and self._submodules:
+                # NOTE: If path is inside a submodule, Dulwich expects the
+                # staged paths to be relative to the submodule root (not the
+                # parent git repo root). We append path to root_dir here so
+                # that the result of relpath(path, root_dir) is actually the
+                # path relative to the submodule root.
+                path_info = PathInfo(path).relative_to(self.root_dir)
+                for sm_path in self._submodules.values():
+                    if path_info.isin(sm_path):
+                        path = os.path.join(
+                            self.root_dir, path_info.relative_to(sm_path)
+                        )
+                        break
             if os.path.isdir(path):
                 files.extend(walk_files(path))
             else:
@@ -138,8 +166,6 @@ class DulwichBackend(BaseGitBackend):  # pylint:disable=abstract-method
         raise NotImplementedError
 
     def is_tracked(self, path: str) -> bool:
-        from dvc.path_info import PathInfo
-
         rel = PathInfo(path).relative_to(self.root_dir).as_posix().encode()
         rel_dir = rel + b"/"
         for path in self.repo.open_index():

dvc/stage/run.py

@@ -211,9 +211,5 @@ def _kill_nt(proc):
 def _run_callback(stage, callback_func):
     stage.save(allow_missing=True)
     stage.commit(allow_missing=True)
-    for out in stage.outs:
-        if not out.use_scm_ignore and out.is_in_repo:
-            stage.repo.scm.track_file(os.fspath(out.path_info))
-    stage.repo.scm.track_changed_files()
     logger.debug("Running checkpoint callback for stage '%s'", stage)
     callback_func()

tests/func/experiments/test_experiments.py

@@ -5,6 +5,7 @@ import stat
 import pytest
 from funcy import first
 
+from dvc.dvcfile import PIPELINE_FILE
 from dvc.repo.experiments.utils import exp_refs_by_rev
 from dvc.utils.serialize import PythonFileCorruptedError
 from tests.func.test_repro_multistage import COPY_SCRIPT
@@ -436,3 +437,79 @@ def test_list(tmp_dir, scm, dvc, exp_stage):
         baseline_a: {ref_info_a.name, ref_info_b.name},
         baseline_c: {ref_info_c.name},
     }
+
+
+def test_subdir(tmp_dir, scm, dvc):
+    subdir = tmp_dir / "dir"
+    subdir.gen("copy.py", COPY_SCRIPT)
+    subdir.gen("params.yaml", "foo: 1")
+
+    with subdir.chdir():
+        dvc.run(
+            cmd="python copy.py params.yaml metrics.yaml",
+            metrics_no_cache=["metrics.yaml"],
+            params=["foo"],
+            name="copy-file",
+            no_exec=True,
+        )
+        scm.add(
+            [subdir / "dvc.yaml", subdir / "copy.py", subdir / "params.yaml"]
+        )
+        scm.commit("init")
+
+        results = dvc.experiments.run(PIPELINE_FILE, params=["foo=2"])
+        assert results
+
+    exp = first(results)
+    ref_info = first(exp_refs_by_rev(scm, exp))
+
+    tree = scm.get_tree(exp)
+    for fname in ["metrics.yaml", "dvc.lock"]:
+        assert tree.exists(subdir / fname)
+    with tree.open(subdir / "metrics.yaml") as fobj:
+        assert fobj.read().strip() == "foo: 2"
+
+    assert dvc.experiments.get_exact_name(exp) == ref_info.name
+    assert scm.resolve_rev(ref_info.name) == exp
+
+
+def test_subrepo(tmp_dir, scm):
+    from tests.unit.tree.test_repo import make_subrepo
+
+    subrepo = tmp_dir / "dir" / "repo"
+    make_subrepo(subrepo, scm)
+
+    subrepo.gen("copy.py", COPY_SCRIPT)
+    subrepo.gen("params.yaml", "foo: 1")
+
+    with subrepo.chdir():
+        subrepo.dvc.run(
+            cmd="python copy.py params.yaml metrics.yaml",
+            metrics_no_cache=["metrics.yaml"],
+            params=["foo"],
+            name="copy-file",
+            no_exec=True,
+        )
+        scm.add(
+            [
+                subrepo / "dvc.yaml",
+                subrepo / "copy.py",
+                subrepo / "params.yaml",
+            ]
+        )
+        scm.commit("init")
+
+        results = subrepo.dvc.experiments.run(PIPELINE_FILE, params=["foo=2"])
+        assert results
+
+    exp = first(results)
+    ref_info = first(exp_refs_by_rev(scm, exp))
+
+    tree = scm.get_tree(exp)
+    for fname in ["metrics.yaml", "dvc.lock"]:
+        assert tree.exists(subrepo / fname)
+    with tree.open(subrepo / "metrics.yaml") as fobj:
+        assert fobj.read().strip() == "foo: 2"
+
+    assert subrepo.dvc.experiments.get_exact_name(exp) == ref_info.name
+    assert scm.resolve_rev(ref_info.name) == exp