fix copy_tree to handle warnings and errors properly

sbillinge · Nov 1, 2025 · Oct 20, 2025 · Oct 20, 2025 · Oct 20, 2025 · Oct 20, 2025
commit d4cddf5797ccf5f24d3b08405e9f566e85d4f3b4
diff --git a/src/diffpy/cmi/packsmanager.py b/src/diffpy/cmi/packsmanager.py
@@ -13,6 +13,7 @@
 #
 ##############################################################################
 import shutil
+import warnings
 from importlib.resources import as_file
 from pathlib import Path
 from typing import List, Union
@@ -150,7 +151,9 @@ def copy_examples(
             Target directory to copy examples into. Defaults to current
             working directory.
         force : bool, optional
-            If ``True``, overwrite existing files. Defaults to ``False``.
+            Defaults to ``False``. If ``True``, existing files are
+            overwritten and directories are merged
+            (extra files in the target are preserved).
         """
         self._target_dir = target_dir.resolve() if target_dir else Path.cwd()
         self._force = force
@@ -207,16 +210,16 @@ def _is_example_name(self, name):
     def _copy_tree_to_target(self, pack_name, example_name, src_path):
         """Helper to handle the actual filesystem copy."""
         dest_dir = self._target_dir / pack_name / example_name
-        if dest_dir.exists():
-            plog.warning(
+        dest_dir.parent.mkdir(parents=True, exist_ok=True)
+        if dest_dir.exists() and not self._force:
+            warn_message = (
                 f"Example directory(ies): '{dest_dir.stem}' already exist. "
-                " Current versions of existing files have "
-                "been left unchanged. To overwrite, please rerun "
-                "and specify --force."
+                "Current versions of existing files have been left unchanged. "
+                "To overwrite, please rerun and specify --force."
             )
+            warnings.warn(warn_message, UserWarning)
             return
-        dest_dir.parent.mkdir(parents=True, exist_ok=True)
-        shutil.copytree(src_path, dest_dir)
+        shutil.copytree(src_path, dest_dir, dirs_exist_ok=self._force)
 
     def _resolve_pack_file(self, identifier: Union[str, Path]) -> Path:
         """Resolve a pack identifier to an absolute .txt path.

diff --git a/tests/test_packsmanager.py b/tests/test_packsmanager.py
@@ -105,13 +105,12 @@ def test_tmp_file_structure(input, expected, example_cases):
     # Test various use cases to copy_examples on case5
     # 1) copy one example (ambiguous)
     # 2) copy list of examples from same pack (ambiguous)
-    # 3) copy list of examples from different pack (ambiguous)
-    # 4) copy one example (unambiguous)
-    # 5) copy list of examples from same pack (unambiguous)
-    # 6) copy list of examples from different pack (unambiguous)
-    # 7) copy all examples from a pack
-    # 8) copy all examples from list of packs
-    # 9) copy all examples from all packs
+    # 3) copy one example (unambiguous)
+    # 4) copy list of examples from same pack (unambiguous)
+    # 5) copy list of examples from different packs (unambiguous)
+    # 6) copy all examples from a pack
+    # 7) copy all examples from list of packs
+    # 8) copy all examples from all packs
     (  # 1) copy one example, (ambiguous)
         ["ex1"],
         [
@@ -127,41 +126,34 @@ def test_tmp_file_structure(input, expected, example_cases):
             Path("packA/ex2/script3.py"),
         ],
     ),
-    (  # 3) copy list of examples from different packs (ambiguous)
-        ["ex1", "ex1"],
-        [
-            Path("packA/ex1/path1/script1.py"),
-            Path("packB/ex1/path2/script2.py"),
-        ],
-    ),
-    (  # 4) copy one example (unambiguous)
+    (  # 3) copy one example (unambiguous)
         ["ex2"],
         [
             Path("packA/ex2/script3.py"),
         ],
     ),
-    (  # 5) copy list of examples from same pack (unambiguous)
+    (  # 4) copy list of examples from same pack (unambiguous)
         ["ex3", "ex4"],
         [
             Path("packB/ex3/script4.py"),
             Path("packB/ex4/script5.py"),
         ],
     ),
-    (  # 6) copy list of examples from different packs (unambiguous)
+    (  # 5) copy list of examples from different packs (unambiguous)
         ["ex2", "ex3"],
         [
             Path("packA/ex2/script3.py"),
             Path("packB/ex3/script4.py"),
         ],
     ),
-    (  # 7) copy all examples from a pack
+    (  # 6) copy all examples from a pack
         ["packA"],
         [
             Path("packA/ex1/path1/script1.py"),
             Path("packA/ex2/script3.py"),
         ],
     ),
-    (  # 8) copy all examples from list of packs
+    (  # 7) copy all examples from list of packs
         ["packA", "packB"],
         [
             Path("packA/ex1/path1/script1.py"),
@@ -171,7 +163,7 @@ def test_tmp_file_structure(input, expected, example_cases):
             Path("packB/ex4/script5.py"),
         ],
     ),
-    (  # 9) copy all examples from all packs
+    (  # 8) copy all examples from all packs
         ["all"],
         [
             Path("packA/ex1/path1/script1.py"),
@@ -255,65 +247,77 @@ def test_copy_examples_location(input, expected_paths, example_cases):
 # 3) Path to directory already exists
 # 4) No input provided
 @pytest.mark.parametrize(
-    "bad_inputs,expected,path",
+    "bad_inputs,expected,path,is_warning",
     [
         (
             # 1) Input not found (example or pack).
             # Expected: Raise an error with the message.
             ["bad_example"],
             "No examples or packs found for input: 'bad_example'",
             None,
+            False,
         ),
         (
             # 2) Mixed good example and bad input.
             # Expected: Raise an error with the message.
             ["ex1", "bad_example"],
             "No examples or packs found for input: 'bad_example'",
             None,
+            False,
         ),
         (
             # 3) Mixed good pack and bad input.
             # Expected: Raise an error with the message.
             ["packA", "bad_example"],
             "No examples or packs found for input: 'bad_example'",
             None,
+            False,
         ),
         (
             # 4) Path to directory already exists.
             # Expected: Raise a warning with the message.
             ["ex1"],
             (
                 "Example directory(ies): 'ex1' already exist. "
-                " Current versions of existing files have "
+                "Current versions of existing files have "
                 "been left unchanged. To overwrite, please rerun "
                 "and specify --force."
             ),
             Path("docs/examples/"),
+            True,
         ),
     ],
 )
-def test_copy_examples_bad(bad_inputs, expected, path, example_cases):
+def test_copy_examples_bad(
+    bad_inputs, expected, path, is_warning, example_cases
+):
     examples_dir = example_cases / "case3"
     pm = PacksManager(root_path=examples_dir)
     target_dir = None if path is None else examples_dir / path
-    with pytest.raises(Exception, match=re.escape(expected)):
-        pm.copy_examples(bad_inputs, target_dir=target_dir)
+    if is_warning:
+        with pytest.warns(UserWarning, match=re.escape(expected)):
+            pm.copy_examples(bad_inputs, target_dir=target_dir)
+    else:
+        with pytest.raises(FileNotFoundError, match=re.escape(expected)):
+            pm.copy_examples(bad_inputs, target_dir=target_dir)
 
 
 def test_copy_examples_force(example_cases):
     examples_dir = example_cases / "case3"
     pm = PacksManager(root_path=examples_dir)
-    target_dir = examples_dir / "docs" / "examples"
-    pm.copy_examples(["packA"], target_dir=target_dir, force=True)
+    case5dir = example_cases / "case5" / "docs" / "examples"
+    pm.copy_examples(["packA"], target_dir=case5dir, force=True)
     expected_paths = [
+        Path("packA/ex1/path1/script1.py"),
         Path("packA/ex1/script1.py"),
-        Path("packA/ex2/solution/script2.py"),
+        Path("packA/ex2/solutions/script2.py"),
+        Path("packA/ex2/script3.py"),
     ]
-    actual = sorted(target_dir.rglob("*.py"))
-    expected = sorted([target_dir / path for path in expected_paths])
+    actual = sorted((case5dir / "packA").rglob("*.py"))
+    expected = sorted([case5dir / path for path in expected_paths])
     assert actual == expected
     for path in expected_paths:
-        copied_path = target_dir / path
+        copied_path = case5dir / path
         original_path = examples_dir / path
         if copied_path.is_file() and original_path.is_file():
             assert copied_path.read_text() == original_path.read_text()