fix: explicitly set h5py read mode in routines and tests

Upcoming versions of h5py will change the default access mode, so we
should be explicitly setting what we want to do. This will remove the
warnings in the tests.

caput/memh5.py

@@ -461,6 +461,7 @@ def from_hdf5(cls, filename, distributed=False, hints=True, comm=None, **kwargs)
             distributed = False
 
         if not distributed or not hints:
+            kwargs["mode"] = "r"
             with h5py.File(filename, **kwargs) as f:
                 self = cls(distributed=distributed, comm=comm)
                 deep_group_copy(f, self)
@@ -469,7 +470,7 @@ def from_hdf5(cls, filename, distributed=False, hints=True, comm=None, **kwargs)
 
         return self
 
-    def to_hdf5(self, filename, hints=True, **kwargs):
+    def to_hdf5(self, filename, mode="w", hints=True, **kwargs):
         """Replicate object on disk in an hdf5 file.
 
         Any keyword arguments are passed on to the constructor for `h5py.File`.
@@ -484,13 +485,13 @@ def to_hdf5(self, filename, hints=True, **kwargs):
         """
 
         if not self.distributed:
-            with h5py.File(filename, **kwargs) as f:
+            with h5py.File(filename, mode, **kwargs) as f:
                 deep_group_copy(self, f)
         else:
             if h5py.get_config().mpi:
-                _distributed_group_to_hdf5_parallel(self, filename, **kwargs)
+                _distributed_group_to_hdf5_parallel(self, filename, mode, **kwargs)
             else:
-                _distributed_group_to_hdf5_serial(self, filename, **kwargs)
+                _distributed_group_to_hdf5_serial(self, filename, mode, **kwargs)
 
     def create_group(self, name):
         """Create a group within the storage tree."""
@@ -1301,7 +1302,7 @@ def __init__(self, data_group=None, distributed=False, comm=None):
         # Otherwise, presume it is an HDF5 Group-like object (which includes
         # MemGroup and h5py.Group).
         else:
-            data_group, toclose = get_h5py_File(data_group)
+            data_group, toclose = get_h5py_File(data_group, mode="a")
 
         if distributed and isinstance(data_group, h5py.Group):
             raise ValueError(
@@ -1478,8 +1479,11 @@ def from_file(
             if isinstance(file_, h5py.Group):
                 file_ = file_.filename
 
+            if "mode" in kwargs:
+                del kwargs["mode"]
+
             data = MemGroup.from_hdf5(
-                file_, distributed=distributed, comm=comm, mode="r", **kwargs
+                file_, distributed=distributed, comm=comm, **kwargs
             )
             toclose = False
         else:
@@ -1488,6 +1492,7 @@ def from_file(
                 data = file_
                 toclose = False
             else:
+                kwargs.setdefault("mode", "a")
                 data = h5py.File(file_, **kwargs)
                 toclose = True
 
@@ -2059,7 +2064,7 @@ def format_abs_path(path):
     return out
 
 
-def _distributed_group_to_hdf5_serial(group, fname, hints=True, **kwargs):
+def _distributed_group_to_hdf5_serial(group, fname, mode, hints=True, **kwargs):
     """Private routine to copy full data tree from distributed memh5 object
     into an HDF5 file.
 
@@ -2073,18 +2078,13 @@ def _distributed_group_to_hdf5_serial(group, fname, hints=True, **kwargs):
 
     comm = group.comm
 
-    # Create a copy of the kwargs with no mode argument so that we can override it
-    kwargs_nomode = kwargs.copy()
-    if "mode" in kwargs:
-        del kwargs_nomode["mode"]
-
     # Create group (or file)
     if comm.rank == 0:
 
         # If this is the root group, create the file and copy the file level
         # attrs
         if group.name == "/":
-            with h5py.File(fname, "w", **kwargs) as f:
+            with h5py.File(fname, mode, **kwargs) as f:
                 copyattrs(group.attrs, f.attrs)
 
                 if hints:
@@ -2098,15 +2098,16 @@ def _distributed_group_to_hdf5_serial(group, fname, hints=True, **kwargs):
 
     comm.Barrier()
 
-    # Write out groups and distributed datasets, these operations must be done collectively
+    # Write out groups and distributed datasets, these operations must be done
+    # collectively
     # Sort to ensure insertion order is identical
     for key in sorted(group):
 
         entry = group[key]
 
         # Groups are written out by recursing
         if is_group(entry):
-            _distributed_group_to_hdf5_serial(entry, fname, **kwargs)
+            _distributed_group_to_hdf5_serial(entry, fname, mode, **kwargs)
 
         # Write out distributed datasets (only the data, the attributes are written below)
         elif isinstance(entry, MemDatasetDistributed):
@@ -2126,7 +2127,7 @@ def _distributed_group_to_hdf5_serial(group, fname, hints=True, **kwargs):
     # Write out common datasets, and the attributes on distributed datasets
     if comm.rank == 0:
 
-        with h5py.File(fname, "r+", **kwargs_nomode) as f:
+        with h5py.File(fname, "r+", **kwargs) as f:
 
             for key, entry in group.items():
 
@@ -2174,7 +2175,7 @@ def _distributed_group_to_hdf5_serial(group, fname, hints=True, **kwargs):
     comm.Barrier()
 
 
-def _distributed_group_to_hdf5_parallel(group, fname, hints=True, **kwargs):
+def _distributed_group_to_hdf5_parallel(group, fname, mode, hints=True, **kwargs):
     """Private routine to copy full data tree from distributed memh5 object
     into an HDF5 file.
     This version paralellizes all IO."""
@@ -2250,7 +2251,6 @@ def _copy_to_file(memgroup, h5group):
                 copyattrs(item.attrs, dset.attrs)
 
     # Open file on all ranks
-    mode = kwargs.get("mode", "w")
     with misc.open_h5py_mpi(fname, mode, comm=group.comm) as f:
         if not f.is_mpi:
             raise RuntimeError("Could not create file %s in MPI mode" % fname)

caput/tests/test_memh5.py

@@ -87,7 +87,7 @@ class TestH5Files(unittest.TestCase):
     fname = "tmp_test_memh5.h5"
 
     def setUp(self):
-        with h5py.File(self.fname) as f:
+        with h5py.File(self.fname, "w") as f:
             l1 = f.create_group("level1")
             l2 = l1.create_group("level2")
             d1 = l1.create_dataset("large", data=np.arange(100))
@@ -118,9 +118,8 @@ def assertAttrsEqual(self, a, b):
                 self.assertEqual(this_a, this_b)
 
     def test_h5_sanity(self):
-        f = h5py.File(self.fname)
-        self.assertGroupsEqual(f, f)
-        f.close()
+        with h5py.File(self.fname, "r") as f:
+            self.assertGroupsEqual(f, f)
 
     def test_to_from_hdf5(self):
         m = memh5.MemGroup.from_hdf5(self.fname)
@@ -189,10 +188,10 @@ def test_io(self):
         # self.assertIsInstance(tsc3['dset'].parent, TempSubClass)
         tsc3.close()
 
-        with memh5.MemDiskGroup.from_file(self.fname, ondisk=True) as tsc4:
+        with memh5.MemDiskGroup.from_file(self.fname, mode="r", ondisk=True) as tsc4:
             self.assertRaises(IOError, h5py.File, self.fname, "w")
 
-        with memh5.MemDiskGroup.from_file(self.fname, ondisk=False) as tsc4:
+        with memh5.MemDiskGroup.from_file(self.fname, mode="r", ondisk=False) as tsc4:
             f = h5py.File(self.fname, "w")
             f.close()