Replace standardise_mom6_filenames.sh with a new script

payu_config/archive.sh

@@ -2,4 +2,4 @@
 # Copyright 2025 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
 # SPDX-License-Identifier: Apache-2.0
 
-source $(dirname "$0")/archive_scripts/standardise_mom6_filenames.sh
+python3 $(dirname "$0")/archive_scripts/standardise_mom_filenames.py

payu_config/archive_scripts/standardise_mom_filenames.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+# Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0.
+#
+# Standardise file naming for MOM output files in access-om by removing the underscore
+# before date/time suffixes and replacing subsequent underscores with hyphens, e.g.,
+# replacing '_YYYY_MM' with 'YYYY-MM'.
+# This was written assuming it would be used as a payu "userscript" at the "archive" stage,
+# but alternatively a path to an "archive" directory can be provided.
+# For more details, see https://github.com/COSIMA/om3-scripts/issues/32
+
+import argparse
+import glob
+import os
+import re
+import sys
+
+
+def standardised_filename(path):
+    """Return the standardised filename for a MOM output file, or None if no rename is needed.
+
+    Files ending in *_<digits>[_<digits>...].nc[...] are renamed so that the first
+    underscore before the digit groups is removed and subsequent ones are replaced with '-'.
+    For example:
+        file._2023.nc       -> file.2023.nc
+        file._2023_01.nc    -> file.2023-01.nc
+        file._2023_01_15.nc -> file.2023-01-15.nc
+    """
+    dirpath = os.path.dirname(path)
+    basename = os.path.basename(path)
+
+    # Split the .nc extension
+    ext_match = re.match(r"^(.*?)(\.nc.*)$", basename)
+    if not ext_match:
+        return None
+    stem, ext = ext_match.groups()
+
+    # Match the trailing block of underscore-separated digit groups
+    suffix_match = re.match(r"^(.*?)(_\d+(?:_\d+)*)$", stem)
+    if not suffix_match:
+        return None
+    base, suffix = suffix_match.groups()
+
+    # Remove the leading underscore and replace any remaining ones with '-'
+    new_suffix = suffix[1:].replace("_", "-")
+
+    new_basename = base + new_suffix + ext
+    if new_basename == basename:
+        return None
+
+    return os.path.join(dirpath, new_basename)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Standardise file naming for MOM output files."
+    )
+    parser.add_argument(
+        "-d",
+        metavar="DIRECTORY",
+        dest="out_dir",
+        help="Process files in the specified experiment 'DIRECTORY'.",
+    )
+    args = parser.parse_args()
+
+    if args.out_dir:
+        if not os.path.isdir(args.out_dir):
+            print(f"{args.out_dir} does not exist")
+            sys.exit(1)
+        out_dirs = [args.out_dir]
+    else:
+        out_dirs = sorted(glob.glob("archive/output*"), reverse=True)
+
+    # Support ACCESS-OM3 and ACCESS-OM2 output files
+    file_patterns = [
+        "access-om3.mom6.*.nc*",
+        "ocean/access-om2.mom5.*.nc*",
+    ]
+
+    for dir_path in out_dirs:
+        for pattern in file_patterns:
+            for current_file in glob.glob(f"{dir_path}/{pattern}"):
+                if not os.path.isfile(current_file):
+                    continue
+                new_file = standardised_filename(current_file)
+                if new_file is None:
+                    continue
+                if os.path.exists(new_file):
+                    print(f"Skipping {current_file}: {new_file} already exists")
+                    continue
+                os.rename(current_file, new_file)
+
+
+if __name__ == "__main__":
+    main()