Reduce dependency to mocks for tests (#70)

* useful to test node accessors with something different than
  node_ids or node_ids list

tests/test_edges.py

@@ -11,10 +11,11 @@
 from bluepysnap.bbp import Synapse
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import Edge
+from bluepysnap.node_sets import NodeSets
 
 import bluepysnap.edges as test_module
 
-from utils import TEST_DATA_DIR
+from utils import TEST_DATA_DIR, create_node_population
 
 
 def index_as_uint64(values):
@@ -74,27 +75,24 @@ def test_population(self):
 class TestEdgePopulation(object):
 
     @staticmethod
-    def mocking_nodes(pop_name):
-        node_population = Mock()
-        node_population.name = pop_name
-        node_population.ids = lambda x: x
-        return node_population
-
-    @staticmethod
-    def create_population(filepath, pop_name):
+    def create_edge_population(filepath, pop_name):
         config = {
             'edges_file': filepath,
             'edge_types_file': None,
         }
-        node_population = TestEdgePopulation.mocking_nodes("default")
         circuit = Mock()
-        circuit.nodes = {node_population.name: node_population}
-
+        create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default", circuit=circuit,
+                               node_sets=NodeSets(str(TEST_DATA_DIR / 'node_sets.json')))
         storage = test_module.EdgeStorage(config, circuit)
-        return storage.population(pop_name)
+        pop = storage.population(pop_name)
+
+        # check if the source and target populations are in the circuit nodes
+        assert pop.source.name in pop._edge_storage.circuit.nodes
+        assert pop.target.name in pop._edge_storage.circuit.nodes
+        return pop
 
     def setup(self):
-        self.test_obj = TestEdgePopulation.create_population(
+        self.test_obj = TestEdgePopulation.create_edge_population(
             str(TEST_DATA_DIR / "edges.h5"), 'default')
 
     def test_basic(self):
@@ -447,7 +445,7 @@ def test_iter_connections_10(self):
             )
 
     def test_iter_connection_unique(self):
-        test_obj = TestEdgePopulation.create_population(
+        test_obj = TestEdgePopulation.create_edge_population(
             str(TEST_DATA_DIR / "edges_complete_graph.h5"), 'default')
         it = test_obj.iter_connections([0, 1, 2], [0, 1, 2])
         assert sorted(it) == [(0, 1), (0, 2), (1, 0), (1, 2), (2, 0), (2, 1)]

tests/test_morph.py

@@ -14,22 +14,13 @@
 from bluepysnap.sonata_constants import Node
 from bluepysnap.exceptions import BluepySnapError
 
-from utils import TEST_DATA_DIR, copy_circuit, edit_config
+from utils import TEST_DATA_DIR, copy_circuit, edit_config, create_node_population
 
 
 class TestMorphHelper(object):
 
-    @staticmethod
-    def create_population(filepath, pop_name):
-        config = {
-            'nodes_file': filepath,
-            'node_types_file': None,
-        }
-        circuit = Mock()
-        return NodeStorage(config, circuit).population(pop_name)
-
     def setup(self):
-        self.nodes = self.create_population(
+        self.nodes = create_node_population(
             str(TEST_DATA_DIR / 'nodes_quaternions.h5'),
             "default")
         self.morph_path = TEST_DATA_DIR / 'morphologies'
@@ -118,7 +109,7 @@ def test_get_morphology_simple_rotation(self):
         npt.assert_almost_equal(expected, actual[:2])
 
     def test_get_morphology_standard_rotation(self):
-        nodes = self.create_population(
+        nodes = create_node_population(
             str(TEST_DATA_DIR / 'nodes.h5'),
             "default")
         test_obj = test_module.MorphHelper(str(self.morph_path), nodes)

tests/test_nodes.py

@@ -17,7 +17,7 @@
 
 import bluepysnap.nodes as test_module
 
-from utils import TEST_DATA_DIR
+from utils import TEST_DATA_DIR, create_node_population
 
 
 class TestNodeStorage:
@@ -57,21 +57,10 @@ def test_load_population_data(self):
 
 class TestNodePopulation:
 
-    @staticmethod
-    def create_population(filepath, pop_name):
-        config = {
-            'nodes_file': filepath,
-            'node_types_file': None,
-        }
-        circuit = Mock()
-        circuit.node_sets = NodeSets(str(TEST_DATA_DIR / 'node_sets.json'))
-        storage = test_module.NodeStorage(config, circuit)
-        return storage.population(pop_name)
-
     def setup(self):
-        self.test_obj = TestNodePopulation.create_population(
-            str(TEST_DATA_DIR / 'nodes.h5'),
-            "default")
+        self.test_obj = create_node_population(
+            str(TEST_DATA_DIR / 'nodes.h5'), "default",
+            node_sets=NodeSets(str(TEST_DATA_DIR / 'node_sets.json')))
 
     def test_basic(self):
         assert self.test_obj._node_storage._h5_filepath == str(TEST_DATA_DIR / 'nodes.h5')
@@ -106,7 +95,7 @@ def test_property_values(self):
                 self.test_obj.property_values(Cell.MORPHOLOGY) ==
                 {'morph-A', 'morph-B', 'morph-C'}
         )
-        test_obj_library = TestNodePopulation.create_population(
+        test_obj_library = create_node_population(
             str(TEST_DATA_DIR / 'nodes_with_library.h5'),
             "default")
         assert test_obj_library.property_values("categorical") == {"A", "B", "C"}
@@ -235,7 +224,7 @@ def test_ids(self):
             _call({'no-such-node-property': 42})
 
     def test_node_ids_by_filter_complex_query(self):
-        test_obj = TestNodePopulation.create_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
+        test_obj = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
         data = pd.DataFrame({
             Cell.MTYPE: ['L23_MC', 'L4_BP', 'L6_BP', 'L6_BPC'],
         })
@@ -306,7 +295,7 @@ def test_get(self):
             _call([0, 999])  # one of node ids is invalid
 
     def test_get_with_library(self):
-        test_obj = TestNodePopulation.create_population(
+        test_obj = create_node_population(
             str(TEST_DATA_DIR / 'nodes_with_library.h5'),
             "default")
         assert test_obj.property_names == {"categorical", "string", "int", "float"}
@@ -370,7 +359,7 @@ def test_orientations(self):
         )
 
         # NodePopulation without rotation_angle[x|z]
-        _call_no_xz = TestNodePopulation.create_population(
+        _call_no_xz = create_node_population(
             str(TEST_DATA_DIR / 'nodes_no_xz_rotation.h5'),
             "default").orientations
         # 0 and 2 node_ids have x|z rotation angles equal to zero
@@ -387,7 +376,7 @@ def test_orientations(self):
         )
 
         # NodePopulation without rotation_angle
-        _call_no_rot = TestNodePopulation.create_population(
+        _call_no_rot = create_node_population(
             str(TEST_DATA_DIR / 'nodes_no_rotation.h5'),
             "default").orientations
 
@@ -401,7 +390,7 @@ def test_orientations(self):
         )
 
         # NodePopulation with quaternions
-        _call_quat = TestNodePopulation.create_population(
+        _call_quat = create_node_population(
             str(TEST_DATA_DIR / 'nodes_quaternions.h5'),
             "default").orientations
 
@@ -444,7 +433,7 @@ def test_orientations(self):
             )
         )
 
-        _call_missing_quat = TestNodePopulation.create_population(
+        _call_missing_quat = create_node_population(
             str(TEST_DATA_DIR / 'nodes_quaternions_w_missing.h5'),
             "default").orientations
 

tests/utils.py

@@ -4,6 +4,7 @@
 import tempfile
 import json
 import six
+import mock
 from contextlib import contextmanager
 from distutils.dir_util import copy_tree
 
@@ -12,6 +13,9 @@
 except ImportError:
     from pathlib2 import Path
 
+from bluepysnap.nodes import NodeStorage
+
+
 TEST_DIR = Path(__file__).resolve().parent
 TEST_DATA_DIR = TEST_DIR / 'data'
 
@@ -59,3 +63,29 @@ def edit_config(config_path):
     finally:
         with config_path.open('w') as f:
             f.write(six.u(json.dumps(config)))
+
+
+def create_node_population(filepath, pop_name, circuit=None, node_sets=None):
+    """Creates a node population.
+    Args:
+        filepath (str): path to the node file.
+        pop_name (str): population name inside the file.
+        circuit (Mock/Circuit): either a real circuit or a Mock containing the nodes.
+        node_sets: (Mock/NodeSets): either a real node_sets or a mocked node_sets.
+    Returns:
+        NodePopulation: return a node population.
+    """
+    config = {
+        'nodes_file': filepath,
+        'node_types_file': None,
+    }
+    if circuit is None:
+        circuit = mock.Mock()
+    if node_sets is not None:
+        circuit.node_sets = node_sets
+    node_pop = NodeStorage(config, circuit).population(pop_name)
+    if isinstance(circuit.nodes, dict):
+        circuit.nodes[node_pop.name] = node_pop
+    else:
+        circuit.nodes = {node_pop.name: node_pop}
+    return node_pop