Add remove_corrupt_h5 utility to clean up interrupted runs

.github/workflows/test_urls.yml

@@ -22,12 +22,12 @@ jobs:
     ping_urls:
       runs-on: ubuntu-latest
       steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: Install testing dependencies
         run: |

pyproject.toml

@@ -73,6 +73,7 @@ make_compton = "openmc_data.other.make_compton:main"
 make_stopping_powers = "openmc_data.other.make_stopping_powers:main"
 add_branching_ratios = "openmc_data.depletion.add_branching_ratios:main"
 combine_libraries = "openmc_data.other.combine_libraries:main"
+remove_corrupt_h5 = "openmc_data.other.remove_corrupt_h5:main"
 sample_sandy = "openmc_data.other.sample_sandy:main"
 reduce_chain = "openmc_data.depletion.reduce_chain:main"
 

src/openmc_data/other/remove_corrupt_h5.py

@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+"""Scan a directory of OpenMC HDF5 data files and remove any that are corrupt.
+
+Useful after an interrupted ``generate_*`` / ``convert_*`` run (e.g. Ctrl-C).
+Those scripts resume by skipping ENDF/ACE files whose output ``.h5`` already
+exists, checking only for existence -- not integrity. A file left half-written
+when the process was killed is therefore treated as "done" and silently kept in
+the library. Running this first deletes any unreadable ``.h5`` files so that a
+rerun regenerates them.
+
+Examples
+--------
+    # Remove any truncated/corrupt files (fast, opens each with h5py)
+    remove_corrupt_h5 tendl-2025-hdf5
+
+    # Also fully load each file with openmc (slower, neutron data only)
+    remove_corrupt_h5 tendl-2025-hdf5 --deep
+
+    # Report without deleting
+    remove_corrupt_h5 tendl-2025-hdf5 --dry-run
+"""
+import argparse
+import glob
+import os
+
+import h5py
+
+try:
+    import openmc.data
+except ModuleNotFoundError:
+    openmc = None
+
+
+def check_file(path, deep=False):
+    """Return an error string if ``path`` is corrupt, otherwise ``None``.
+
+    The default check opens the file with h5py, which catches the common
+    failure mode of a truncated write. ``deep=True`` additionally loads the
+    file with :class:`openmc.data.IncidentNeutron`.
+    """
+    try:
+        with h5py.File(path, "r"):
+            pass
+    except Exception as e:  # noqa: BLE001 - report any read failure
+        return str(e)
+    if deep:
+        if openmc is None:
+            raise ModuleNotFoundError(
+                "openmc is required for --deep validation but is not installed."
+            )
+        try:
+            openmc.data.IncidentNeutron.from_hdf5(path)
+        except Exception as e:  # noqa: BLE001 - report any load failure
+            return str(e)
+    return None
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+    parser.add_argument(
+        "directory", help="Directory containing the .h5 files to check"
+    )
+    parser.add_argument(
+        "--deep",
+        action="store_true",
+        help="Also fully load each file with openmc (slower, neutron data only)",
+    )
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Report corrupt files without deleting them",
+    )
+    args = parser.parse_args()
+
+    files = sorted(glob.glob(os.path.join(args.directory, "*.h5")))
+    print(f"Scanning {len(files)} .h5 files in {args.directory} ...")
+    removed = 0
+    for f in files:
+        reason = check_file(f, deep=args.deep)
+        if reason is not None:
+            action = "would remove" if args.dry_run else "removing"
+            print(f"{action} corrupt: {f} -> {reason}")
+            if not args.dry_run:
+                os.remove(f)
+            removed += 1
+    verb = "corrupt" if args.dry_run else "removed"
+    print(f"Done, {removed} {verb} file(s); {len(files) - removed} intact")
+
+
+if __name__ == "__main__":
+    main()