support for h5py and json readers and writers

Author: jreadey

data/hdf5/dset_creationprop.h5

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 120
+# E402: module level import not at top of file
+# C901: too complex
+# F401: unused exports are necessary in __init__.py
+ignore = E402, C901, F401

data/json/nullspace_dset.json

@@ -491,6 +491,7 @@ def arrayToBytes(arr, encoding=None):
         data = encodeData(data)
     return data
 
+
 def bytesToArray(data, dt, shape, encoding=None):
     """
     Create numpy array based on byte representation
@@ -522,7 +523,7 @@ def bytesToArray(data, dt, shape, encoding=None):
 
     return arr
 
-  
+
 def getNumpyValue(value, dt=None, encoding=None):
     """
     Return value as numpy type for given dtype and encoding

setup.cfg

@@ -12,17 +12,31 @@
 
 import time
 
+
 def resize_dataset(dset_json, shape):
     shape_json = dset_json["shape"]
     shape_class = shape_json["class"]
     if shape_class != "H5S_SIMPLE":
         raise TypeError(f"dataset with shape class: {shape_class} cannot be resized")
-    if len(shape_class["dims"]) != len(shape):
+    if len(shape_json["dims"]) != len(shape):
         raise ValueError("Resize shape parameter doesn't match dataset's rank")
+    if "maxdims" not in shape_json:
+        raise ValueError("Dataset is not resizable")
+    dims = shape_json["dims"]
+    maxdims = shape_json["maxdims"]
+
     if shape_json["dims"] == list(shape):
         # no change, just return
         return
+    for i in range(len(dims)):
+        extent = shape[i]
+        if extent < 0:
+            raise ValueError("dimensions can't be negative")
+        if maxdims[i] == "H5S_UNLIMITED":
+            # any positive extent is ok
+            continue
+        if extent > maxdims[i]:
+            raise ValueError(f"extent for dimension {i} can't be larger than {maxdims[i]}")
+
     shape_json["dims"] = list(shape)
     dset_json["modified"] = time.time()
-        
-         

src/h5json/array_util.py

@@ -9,7 +9,7 @@
 # distribution tree.  If you do not have access to this file, you may        #
 # request a copy from help@hdfgroup.org.                                     #
 ##############################################################################
- 
+
 import h5py
 
 _HDF_FILTERS = {
@@ -53,4 +53,3 @@
 }
 
 _H5PY_COMPRESSION_FILTERS = ("gzip", "lzf", "szip")
-

src/h5json/dset_util.py

@@ -15,15 +15,16 @@
 
 from . import hdf5dtype
 
+
 def is_reference(val):
     """ Return True if the type or value is a Reference """
 
     if isinstance(val, object) and val.__class__.__name__ == "Reference":
         return True
     elif isinstance(val, type) and val.__name__ == "Reference":
         return True
- 
-    return False
+    else:
+        return False
 
 
 def is_regionreference(val):
@@ -59,7 +60,7 @@ def has_reference(dtype):
 
 def convert_dtype(srcdt, to_h5py=True):
     """Return a dtype based on input dtype, converting any Reference types from
-    h5py style to h5pyd and vice-versa.
+    h5py style to h5json and vice-versa.
     """
 
     if len(srcdt) > 0:
@@ -96,7 +97,7 @@ def convert_dtype(srcdt, to_h5py=True):
             if to_h5py:
                 tgt_dt = h5py.special_dtype(vlen=tgt_base)
             else:
-                tgt_dt = h5pyd.special_dtype(vlen=tgt_base)
+                tgt_dt = hdf5dtype.special_dtype(vlen=tgt_base)
         elif srcdt.kind == "U":
             # use vlen for unicode strings
             if to_h5py: