Added cleanup_h5 to utils.py

src/mdevaluate/utils.py

@@ -3,6 +3,7 @@ Collection of utility functions.
 """
 import functools
 from time import time as pytime
+from subprocess import run
 from types import FunctionType
 
 import numpy as np
@@ -500,3 +501,18 @@ def timing(function):
         return result
 
     return wrap
+
+def cleanup_h5(hdf5_file) -> None:
+    hdf5_temp_file = f"{hdf5_file[:-3]}_temp.h5"
+    run(
+        [
+            "ptrepack",
+            "--chunkshape=auto",
+            "--propindexes",
+            "--complevel=9",
+            "--complib=blosc",
+            hdf5_file,
+            hdf5_temp_file,
+        ]
+    )
+    run(["mv", hdf5_temp_file, hdf5_file])