fix: perform proper provision in an annex remote

datalad_remake/annexremotes/tests/test_hierarchies.py

@@ -130,3 +130,41 @@ def test_end_to_end(tmp_path, cfgman, monkeypatch, output_pattern):
         monkeypatch.chdir(root_dataset.pathobj)
         datalad_Get()('d2_subds0/d2_subds1/a1.txt')
         _check_content(root_dataset, test_file_content)
+
+
+@skip_if_on_windows
+def test_input_subdatasets(tmp_path, cfgman):
+    simple_test_method = """
+    parameters = ['first', 'second', 'third']
+    command = ["bash", "-c", "echo content: {first} > 'a0.txt'"]
+    """
+
+    root_dataset = create_simple_computation_dataset(
+        tmp_path, 'd3', 1, simple_test_method
+    )
+
+    # run `make` command
+    root_dataset.make(
+        template='test_method',
+        parameter=[
+            'first=first',
+            'second=second',
+            'third=third',
+        ],
+        input=['d3_subds0/a.txt'],
+        output=['a0.txt'],
+        result_renderer='disabled',
+        allow_untrusted_execution=True,
+    )
+
+    _drop_files(root_dataset, ['a0.txt'])
+
+    with cfgman.overrides(
+        {
+            # Allow the special remote to execute untrusted operations on the
+            # dataset `root_dataset`
+            allow_untrusted_execution_key
+            + Dataset(root_dataset.pathobj).id: ConfigItem('true'),
+        }
+    ):
+        root_dataset.get('a0.txt', result_renderer='disabled')

datalad_remake/commands/provision_cmd.py

@@ -41,6 +41,7 @@
 from datalad_remake.commands.make_cmd import read_list
 from datalad_remake.utils.chdir import chdir
 from datalad_remake.utils.glob import glob
+from datalad_remake.utils.patched_env import patched_env
 
 if TYPE_CHECKING:
     from collections.abc import Generator, Iterable
@@ -390,7 +391,8 @@ def install_subdataset(
             absolute_path.as_uri(),
         ]
         call_git_lines(args)
-    worktree.get(str(subdataset_path), get_data=False, result_renderer='disabled')
+    with patched_env(remove=['GIT_DIR', 'GIT_WORK_TREE']):
+        worktree.get(str(subdataset_path), get_data=False, result_renderer='disabled')
     uninstalled_subdatasets.remove(subdataset_path)
     uninstalled_subdatasets.update(get_uninstalled_subdatasets(worktree))
 

datalad_remake/utils/patched_env.py

@@ -0,0 +1,41 @@
+from __future__ import annotations
+
+from contextlib import contextmanager
+
+
+@contextmanager
+def patched_env(
+    add: dict | None = None,
+    remove: list[str] | None = None,
+):
+    """
+    Patch the environment for the duration of the context manager.
+
+    Parameters
+    ----------
+    add : dict
+        The environment variables to add.
+    remove : list[str]
+        The environment variables to remove.
+
+    Yields
+    -------
+    None
+    """
+    import os
+
+    # Store the original environment
+    original_env = dict(os.environ)
+
+    # Update the environment
+    os.environ.update(add or {})
+    for var in remove or []:
+        if var in os.environ:
+            del os.environ[var]
+
+    try:
+        yield
+    finally:
+        # Restore the original environment
+        os.environ.clear()
+        os.environ.update(original_env)