extract_science.py rebuild fix

CONTRIBUTORS.md

@@ -7,4 +7,5 @@
 | mo-marqh        | mark Hedley     | Met Office  | 2025-12-11 |
 | yaswant         | Yaswant Pradhan | Met Office  | 2025-12-16 |
 | oakleybrunt     | Oakley Brunt    | Met Office  | 2025-12-19 |
-| harry-shepherd | Harry Shepherd | Met Office | 2026-01-08 |
+| bblay-mo        | Byron Blay      | Met Office  | 2026-01-07 |
+| harry-shepherd  | Harry Shepherd  | Met Office  | 2026-01-08 |

build/extract/extract_science.py

@@ -1,3 +1,8 @@
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
 import argparse
 import subprocess
 import os
@@ -58,7 +63,8 @@ def clone_dependency(values: Dict, temp_dep: Path) -> None:
         run_command(command)
 
 
-def extract_files(dependency: str, values: Dict, files: List[str], working: Path):
+def extract_files(
+        dependency: str, values: Dict, files: List[str], working: Path):
     """
     Clone the dependency to a temporary location
     Then copy the desired files to the working directory
@@ -79,13 +85,15 @@ def extract_files(dependency: str, values: Dict, files: List[str], working: Path
     working_dep = working / dependency
 
     # make the working directory location
-    working_dep.mkdir(parents=True)
+    working_dep.mkdir(parents=True, exist_ok=True)
 
+    # copy new and updated files
     for extract_file in files:
         source_file = temp_dep / extract_file
         dest_file = working_dep / extract_file
-        run_command(f"mkdir -p {dest_file.parents[0]}")
-        copy_command = f"cp -r {source_file} {dest_file}"
+        dest_file.parent.mkdir(parents=True, exist_ok=True)
+        copy_command = \
+            f"cp -r -u --preserve=timestamps {source_file} {dest_file}"
         run_command(copy_command)
 
     rmtree(tempdir)
@@ -104,7 +112,8 @@ def parse_args() -> argparse.Namespace:
         help="The dependencies file for the apps working copy.",
     )
     parser.add_argument(
-        "-w", "--working", default=".", help="Location to perform extract steps in."
+        "-w", "--working", default=".",
+        help="Location to perform extract steps in."
     )
     parser.add_argument(
         "-e",