fix smalln test and long standing weirdness with particle links

underlying problem with the acceptance of None or Ellipsis as indices

src/amuse/datamodel/incode_storage.py

@@ -105,6 +105,11 @@
 
 from amuse.rfi.async_request import ASyncRequestSequence, PoolDependentASyncRequest
 
+try:
+    from types import EllipsisType
+except:
+    EllipsisType = type(Ellipsis)
+
 class ParticleMappingMethod(AbstractCodeMethodWrapper):
     def __init__(self, method, attribute_names = None):
         AbstractCodeMethodWrapper.__init__(self, method)
@@ -898,7 +903,7 @@ def get_value_of(self, index, attribute):
 
     def get_values_in_store(self, indices_in_the_code, attributes):
 
-        if indices_in_the_code is None:
+        if indices_in_the_code is None or isinstance(indices_in_the_code, EllipsisType):
             indices_in_the_code = self.code_indices
 
         if len(indices_in_the_code) == 0:

src/amuse/io/store_v1.py

@@ -268,6 +268,9 @@ def get_values(self, indices):
             linked_set = self.loader.load_particles_from_group(referenced_group)
         else:
             linked_set = mapping_from_groupid_to_set[referenced_group.id]
+
+        if indices is None: 
+            indices=slice(None)
 
         keys = self.keys[:][indices]
         mask = self.masked[:][indices]

src/amuse/io/store_v2.py

@@ -290,6 +290,8 @@ def __init__(self, name, group, loader):
         self.loader = loader
 
     def get_values(self, indices):
+        if indices is None: 
+            indices=slice(None)
         kinds = self.kind_dataset[:][indices]
         references = self.ref_dataset[:][indices]
         keys = self.keys_dataset[:][indices]

test/core_tests/test_store.py

@@ -393,8 +393,8 @@ def test15(self):
 
     def test16(self):
         import h5py
-        print h5py.version.version
-        print h5py
+        #~ print h5py.version.version
+        #~ print h5py
         test_results_path = self.get_path_to_results()
         output_file = os.path.join(test_results_path, "test16"+self.store_version()+".hdf5")
         if os.path.exists(output_file):
@@ -758,6 +758,24 @@ def test30(self):
 
         self.assertEquals(output.new_attribute, 2 * output.mass)
 
+    def test31(self):
+        test_results_path = self.get_path_to_results()
+        output_file = os.path.join(test_results_path, "test31"+self.store_version()+".h5")
+        if os.path.exists(output_file):
+            os.remove(output_file)
+
+        p=Particles(10)
+        p.mass=numpy.arange(10)
+        q=Particles(3)
+        q[0].link=p[1]
+        q[1].link=p[3]
+        q[2].link=p[4]
+        io.write_set_to_file(q,output_file,"amuse",version=self.store_version())
+        r=io.read_set_from_file(output_file,"amuse")
+        self.assertEqual(len(r.link.shape),1)
+        self.assertEqual(r[0].link.mass,1)
+        self.assertEqual(r[1].link.mass,3)
+        self.assertEqual(r[2].link.mass,4)
 
 
 
@@ -1064,3 +1082,5 @@ def test61(self):
 
         os.remove(output_file)
 
+
+