ipython exit handler to close file handles of stale hdf5 files

pyphare/pyphare/core/ipython.py

@@ -0,0 +1,55 @@
+
+
+
+
+import weakref
+h5_weak_refs = {}
+
+def clean_dead_h5_weak_refs():
+    for h5_path, h5_weak_ref in h5_weak_refs.copy().items():
+        if h5_weak_ref["ref"]() is None:
+            del h5_weak_refs[h5_path]
+
+# https://stackoverflow.com/a/40222538/795574
+try:
+    def exit_register(fun, *args, **kwargs):
+        def callback():
+            fun()
+            ip.events.unregister('post_execute', callback)
+        ip.events.register('post_execute', callback)
+
+    ip = get_ipython() # should fail if not running under ipython
+
+    def add_h5_weak_ref(h5Filepath, h5File):
+        import pathlib, datetime, time
+        clean_dead_h5_weak_refs()
+
+        h5_weak_refs[h5Filepath] = {
+          "ref": weakref.ref(h5File),
+          "access": int(time.time()),
+          "path": pathlib.Path(h5Filepath)
+        }
+
+except NameError:
+
+    def add_h5_weak_ref(h5Filepath, h5File):
+        pass # empty function for normal (not jupyter) case
+
+    # forwarding import to keep functionality even if ipython is not in use
+    #  it's possible this isn't even needed, and we just want to execute the callback for only if
+    #    we're running under ipython, in that case, "exit_register" -> "ipython_exit_register" and
+    #     replace the next line with def ipython_exit_register(fun, *args, **kwargs): pass
+    from atexit import register as exit_register # lgtm [py/unused-import]
+
+
+
+
+@exit_register
+def close_h5_files_refs():
+    import pathlib, datetime, time
+    for h5_weak_ref_dict in list(h5_weak_refs.values()):
+        h5_ref = h5_weak_ref_dict["ref"]()
+        if h5_ref is not None:
+            mtime = int(h5_weak_ref_dict["path"].stat().st_mtime)
+            if mtime > h5_weak_ref_dict["access"] and h5_ref.__bool__():
+                h5_ref.close()

pyphare/pyphare/pharesee/hierarchy.py

@@ -11,7 +11,7 @@
 import matplotlib.pyplot as plt
 from ..core.phare_utilities import refinement_ratio, deep_copy
 
-
+from ..core.ipython import add_h5_weak_ref
 
 
 class PatchData:
@@ -1108,6 +1108,9 @@ def patch_has_datasets(h5_patch_grp):
 def hierarchy_fromh5(h5_filename, time, hier, silent=True):
     import h5py
     data_file = h5py.File(h5_filename, "r")
+
+    # ADD ref only for jupyter to close file handles without killing kernel
+    add_h5_weak_ref(h5_filename, data_file)
     basename = os.path.basename(h5_filename)
 
     root_cell_width = np.asarray(data_file.attrs["cell_width"])