don't use monkey patch actually

lindi/h5py_patch/__init__.py → lindi/File/File.py

@@ -1,20 +1,16 @@
 from typing import Literal
 import os
 import h5py
-from h5py import File as OriginalH5pyFile
 from ..LindiH5pyFile.LindiH5pyFile import LindiH5pyFile
 from ..LindiStagingStore.StagingArea import StagingArea
 from ..LocalCache.LocalCache import LocalCache
 
 
-# We need to use this metaclass so that isinstance(f, h5py.File) works when f is
-# a LindiH5pyFile or OriginalH5pyFile
-class InstanceCheckMeta(type):
-    def __instancecheck__(cls, instance):
-        return isinstance(instance, OriginalH5pyFile) or isinstance(instance, LindiH5pyFile)
-
-
-class File(metaclass=InstanceCheckMeta):
+class File(h5py.File):
+    """
+    A drop-in replacement for h5py.File that is either a lindi.LindiH5pyFile or
+    h5py.File depending on whether the file name ends with .lindi.json or not.
+    """
     def __new__(cls, name, mode: Literal['r', 'r+', 'w', 'w-', 'x', 'a'] = 'r', **kwds):
         if isinstance(name, str) and name.endswith('.lindi.json'):
             # should we raise exceptions on select unsupported kwds? or just go with the flow?
@@ -35,12 +31,4 @@ def __new__(cls, name, mode: Literal['r', 'r+', 'w', 'w-', 'x', 'a'] = 'r', **kw
                 local_cache=local_cache
             )
         else:
-            return OriginalH5pyFile(name, mode=mode, **kwds)
-
-
-def apply_h5py_patch():
-    h5py.File = File
-
-
-# by virtue of importing we apply the patch
-apply_h5py_patch()
+            return h5py.File(name, mode=mode, **kwds)

lindi/__init__.py

@@ -2,3 +2,4 @@
 from .LindiH5pyFile import LindiH5pyFile, LindiH5pyGroup, LindiH5pyDataset, LindiH5pyHardLink, LindiH5pySoftLink  # noqa: F401
 from .LindiStagingStore import LindiStagingStore, StagingArea  # noqa: F401
 from .LocalCache.LocalCache import LocalCache  # noqa: F401
+from .File.File import File  # noqa: F401

tests/test_patch.py → tests/test_lindi_file.py

@@ -1,18 +1,16 @@
-import lindi.h5py_patch  # noqa: F401
 import tempfile
 import numpy as np
 import h5py
-from h5py import File
+import lindi
 
 
-def test_patch():
+def test_lindi_file():
     with tempfile.TemporaryDirectory() as tmpdir:
         fname = f'{tmpdir}/test.lindi.json'
-        with File(fname, 'w') as f:
-            assert isinstance(f, File)
+        with lindi.File(fname, 'w') as f:
             f.create_dataset('data', data=np.arange(500000, dtype=np.uint32), chunks=(100000,))
 
-        with File(fname, 'r') as f:
+        with lindi.File(fname, 'r') as f:
             ds = f['data']
             assert isinstance(ds, h5py.Dataset)
             assert ds.shape == (500000,)
@@ -22,4 +20,4 @@ def test_patch():
 
 
 if __name__ == '__main__':
-    test_patch()
+    test_lindi_file()