Fix tests with libsonata 0.1.16 and warnings with pytest (#170)

bluepysnap/edges.py

@@ -569,11 +569,6 @@ def h5_filepath(self):
         for edge_conf in self._circuit.config["networks"]["edges"]:
             if self.name in edge_conf["populations"]:
                 return edge_conf["edges_file"]
-        for edge_conf in self._circuit.config["networks"]["edges"]:
-            h5_filepath = edge_conf["edges_file"]
-            storage = libsonata.EdgeStorage(h5_filepath)
-            if self.name in storage.population_names:  # pylint: disable=unsupported-membership-test
-                return h5_filepath
         raise BluepySnapError(f"h5_filepath not found for population '{self.name}'")
 
 

bluepysnap/nodes.py

@@ -20,7 +20,6 @@
 from collections.abc import Mapping, Sequence
 from copy import deepcopy
 
-import libsonata
 import numpy as np
 import pandas as pd
 from cached_property import cached_property
@@ -575,11 +574,6 @@ def h5_filepath(self):
         for node_conf in self._circuit.config["networks"]["nodes"]:
             if self.name in node_conf["populations"]:
                 return node_conf["nodes_file"]
-        for node_conf in self._circuit.config["networks"]["nodes"]:
-            h5_filepath = node_conf["nodes_file"]
-            storage = libsonata.NodeStorage(h5_filepath)
-            if self.name in storage.population_names:  # pylint: disable=unsupported-membership-test
-                return h5_filepath
         raise BluepySnapError(f"h5_filepath not found for population '{self.name}'")
 
 

tests/data/circuit_config.json

@@ -16,6 +16,9 @@
         "populations": {
             "default": {
                 "type": "biophysical"
+            },
+            "default2": {
+                "type": "biophysical"
             }
         }
       }
@@ -26,6 +29,9 @@
         "populations": {
             "default":{
                 "type": "chemical"
+            },
+            "default2":{
+                "type": "chemical"
             }
         }
       }

tests/test_circuit.py

@@ -7,14 +7,14 @@
 from bluepysnap.edges import EdgePopulation, Edges
 from bluepysnap.nodes import NodePopulation, Nodes
 
-from utils import TEST_DATA_DIR, copy_test_data, edit_config
+from utils import TEST_DATA_DIR, copy_test_data, edit_config, skip_if_libsonata_0_1_16
 
 
 def test_all():
     circuit = test_module.Circuit(str(TEST_DATA_DIR / "circuit_config.json"))
     assert circuit.config["networks"]["nodes"][0] == {
         "nodes_file": str(TEST_DATA_DIR / "nodes.h5"),
-        "populations": {"default": {"type": "biophysical"}},
+        "populations": {"default": {"type": "biophysical"}, "default2": {"type": "biophysical"}},
     }
     assert isinstance(circuit.nodes, Nodes)
     assert isinstance(circuit.edges, Edges)
@@ -29,21 +29,25 @@ def test_all():
     )
 
 
+@skip_if_libsonata_0_1_16
 def test_duplicate_node_populations():
     with copy_test_data() as (_, config_path):
         with edit_config(config_path) as config:
             config["networks"]["nodes"].append(config["networks"]["nodes"][0])
 
-        with pytest.raises(SonataError, match="Duplicate population"):
+        match = "Duplicate population|Population default is declared twice"
+        with pytest.raises(SonataError, match=match):
             test_module.Circuit(config_path)
 
 
+@skip_if_libsonata_0_1_16
 def test_duplicate_edge_populations():
     with copy_test_data() as (_, config_path):
         with edit_config(config_path) as config:
             config["networks"]["edges"].append(config["networks"]["edges"][0])
 
-        with pytest.raises(SonataError, match="Duplicate population"):
+        match = "Duplicate population|Population default is declared twice"
+        with pytest.raises(SonataError, match=match):
             test_module.Circuit(config_path)
 
 

tests/test_circuit_ids.py

@@ -19,7 +19,7 @@ def _multi_index():
 
 
 class TestCircuitNodeId:
-    def setup(self):
+    def setup_method(self):
         self.test_obj = test_module.CircuitNodeId("pop", 1)
 
     def test_init(self):
@@ -32,7 +32,7 @@ def test_accessors(self):
 
 
 class TestCircuitEdgeId:
-    def setup(self):
+    def setup_method(self):
         self.test_obj = test_module.CircuitEdgeId("pop", 1)
 
     def test_init(self):
@@ -62,7 +62,7 @@ def _circuit_ids(self, populations, ids):
         index.names = ["population", self.id_name]
         return index
 
-    def setup(self):
+    def setup_method(self):
         self.test_obj_unsorted = self.ids_cls(_multi_index(), sort_index=False)
         self.test_obj_sorted = self.ids_cls(_multi_index())
 

tests/test_circuit_validation.py

@@ -115,6 +115,8 @@ def test_missing_data_config_no_population_for_edge(to_remove):
         assert errors == {
             Error(Error.FATAL, 'No node population for "/edges/default/source_node_id"'),
             Error(Error.FATAL, 'No node population for "/edges/default/target_node_id"'),
+            Error(Error.FATAL, 'No node population for "/edges/default2/source_node_id"'),
+            Error(Error.FATAL, 'No node population for "/edges/default2/target_node_id"'),
         }
 
 
@@ -290,6 +292,16 @@ def test_no_bio_component_dirs():
                     "must to be defined for 'biophysical' population 'default'"
                 ),
             ),
+            Error(
+                Error.FATAL, "'biophysical_neuron_models_dir' not defined for population 'default2'"
+            ),
+            Error(
+                Error.FATAL,
+                (
+                    "at least one of 'morphologies_dir' or 'alternate_morphologies' "
+                    "must to be defined for 'biophysical' population 'default2'"
+                ),
+            ),
         }
 
 
@@ -483,6 +495,14 @@ def test_no_edge_all_node_ids():
                 Error.FATAL,
                 "/edges/default/target_node_id does not have node ids in its node population",
             ),
+            Error(
+                Error.FATAL,
+                "/edges/default2/source_node_id does not have node ids in its node population",
+            ),
+            Error(
+                Error.FATAL,
+                "/edges/default2/target_node_id does not have node ids in its node population",
+            ),
         }
 
 
@@ -530,5 +550,6 @@ def test_no_duplicate_population_names():
             config["networks"]["nodes"].append(config["networks"]["nodes"][0])
         errors = validate(str(config_copy_path))
         assert errors == {
-            Error(Error.FATAL, 'Already have population "default" in config for type "nodes"')
+            Error(Error.FATAL, 'Already have population "default" in config for type "nodes"'),
+            Error(Error.FATAL, 'Already have population "default2" in config for type "nodes"'),
         }

tests/test_edges.py

@@ -50,7 +50,7 @@ def test_estimate_range_size_4():
 
 
 class TestEdges:
-    def setup(self):
+    def setup_method(self):
         circuit = Circuit(str(TEST_DATA_DIR / "circuit_config.json"))
         self.test_obj = test_module.Edges(circuit)
 
@@ -809,7 +809,7 @@ def get_edge_population(circuit_path, pop_name):
         circuit = Circuit(circuit_path)
         return test_module.EdgePopulation(circuit, pop_name)
 
-    def setup(self):
+    def setup_method(self):
         self.test_obj = TestEdgePopulation.get_edge_population(
             str(TEST_DATA_DIR / "circuit_config.json"), "default"
         )
@@ -1365,7 +1365,7 @@ def test_iter_connection_unique(self):
                     {
                         "edge_types_file": None,
                         "edges_file": str(Path(config_dir) / "edges_complete_graph.h5"),
-                        "populations": {},
+                        "populations": {"default": {"type": "chemical"}},
                     }
                 ]
 
@@ -1395,20 +1395,6 @@ def test_iter_connection_unique(self):
     def test_h5_filepath_from_config(self):
         assert self.test_obj.h5_filepath == str(TEST_DATA_DIR / "edges.h5")
 
-    def test_h5_filepath_from_libsonata(self):
-        with copy_test_data() as (config_dir, config_path):
-            edge_path = str(Path(config_dir) / "edges.h5")
-            with edit_config(config_path) as config:
-                config["networks"]["edges"] = [
-                    {
-                        "edge_types_file": None,
-                        "edges_file": edge_path,
-                        "populations": {"fake": {}},
-                    }
-                ]
-            test_obj = test_module.Edges(Circuit(config_path))
-            assert test_obj["default"].h5_filepath == edge_path
-
     def test_no_h5_filepath(self):
         with pytest.raises(BluepySnapError, match="h5_filepath not found for population"):
             self.test_obj.name = "fake"

tests/test_frame_report.py

@@ -17,7 +17,7 @@
 
 
 class TestFrameReport:
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.FrameReport(self.simulation, "soma_report")
         self.test_obj_info = test_module.FrameReport(self.simulation, "section_report")
@@ -85,7 +85,7 @@ def test_iter(self):
 
 
 class TestCompartmentReport:
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.CompartmentReport(self.simulation, "section_report")
 
@@ -132,7 +132,7 @@ def test_filter(self):
 
 
 class TestSomaReport:
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.SomaReport(self.simulation, "soma_report")
 
@@ -184,7 +184,7 @@ def test_filter(self):
 
 
 class TestPopulationFrameReport:
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.FrameReport(self.simulation, "section_report")["default"]
 
@@ -197,7 +197,7 @@ def test__resolve(self):
 
 
 class TestPopulationCompartmentReport:
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.CompartmentReport(self.simulation, "section_report")["default"]
         timestamps = np.linspace(0, 0.9, 10)
@@ -292,7 +292,7 @@ def test_node_ids(self):
 
 
 class TestPopulationSomaReport(TestPopulationCompartmentReport):
-    def setup(self):
+    def setup_method(self):
         self.simulation = Simulation(str(TEST_DATA_DIR / "simulation_config.json"))
         self.test_obj = test_module.SomaReport(self.simulation, "soma_report")["default"]
         timestamps = np.linspace(0, 0.9, 10)

tests/test_morph.py

@@ -15,7 +15,7 @@
 
 
 class TestMorphHelper:
-    def setup(self):
+    def setup_method(self):
         self.nodes = create_node_population(str(TEST_DATA_DIR / "nodes_quaternions.h5"), "default")
         self.morph_path = TEST_DATA_DIR / "morphologies"
         self.test_obj = test_module.MorphHelper(str(self.morph_path), self.nodes)

tests/test_node_sets.py

@@ -10,7 +10,7 @@
 
 
 class TestNodeSets:
-    def setup(self):
+    def setup_method(self):
         self.test_obj = test_module.NodeSets(str(TEST_DATA_DIR / "node_sets_file.json"))
 
     def test_init(self):

tests/test_nodes.py

@@ -24,7 +24,7 @@
 
 
 class TestNodes:
-    def setup(self):
+    def setup_method(self):
         circuit = Circuit(str(TEST_DATA_DIR / "circuit_config.json"))
         self.test_obj = test_module.Nodes(circuit)
 
@@ -420,7 +420,7 @@ def test_get(self):
 
 
 class TestNodePopulation:
-    def setup(self):
+    def setup_method(self):
         self.test_obj = Circuit(str(TEST_DATA_DIR / "circuit_config.json")).nodes["default"]
 
     def test_basic(self):
@@ -997,20 +997,6 @@ def test_models(self):
     def test_h5_filepath_from_config(self):
         assert self.test_obj.h5_filepath == str(TEST_DATA_DIR / "nodes.h5")
 
-    def test_h5_filepath_from_libsonata(self):
-        with copy_test_data() as (config_dir, config_path):
-            node_path = str(Path(config_dir) / "nodes.h5")
-            with edit_config(config_path) as config:
-                config["networks"]["nodes"] = [
-                    {
-                        "node_types_file": None,
-                        "nodes_file": node_path,
-                        "populations": {"fake": {}},
-                    }
-                ]
-            test_obj = test_module.Nodes(Circuit(config_path))
-            assert test_obj["default"].h5_filepath == node_path
-
     def test_no_h5_filepath(self):
         with pytest.raises(BluepySnapError, match="h5_filepath not found for population"):
             self.test_obj.name = "fake"

tests/test_schemas.py

@@ -137,38 +137,45 @@ def test_validate_config_ok_missing_optional_fields(to_remove):
 
 
 @pytest.mark.parametrize(
-    ("to_remove", "expected"),
+    ("to_remove_list", "expected"),
     (
         (
-            ["networks", "nodes", 0, "populations", "default"],
+            [
+                ["networks", "nodes", 0, "populations", "default"],
+                ["networks", "nodes", 0, "populations", "default2"],
+            ],
             "networks.nodes[0].populations: too few properties",
         ),
         (
-            ["networks", "edges", 0, "populations", "default"],
+            [
+                ["networks", "edges", 0, "populations", "default"],
+                ["networks", "edges", 0, "populations", "default2"],
+            ],
             "networks.edges[0].populations: too few properties",
         ),
         (
-            ["networks", "nodes", 0, "populations"],
+            [["networks", "nodes", 0, "populations"]],
             "networks.nodes[0]: 'populations' is a required property",
         ),
         (
-            ["networks", "edges", 0, "populations"],
+            [["networks", "edges", 0, "populations"]],
             "networks.edges[0]: 'populations' is a required property",
         ),
-        (["networks", "nodes", 0], "networks.nodes: [] is too short"),
-        (["networks", "edges", 0], "networks.edges: [] is too short"),
-        (["networks", "nodes"], "networks: 'nodes' is a required property"),
-        (["networks", "edges"], "networks: 'edges' is a required property"),
-        (["networks"], "'networks' is a required property"),
+        ([["networks", "nodes", 0]], "networks.nodes: [] is too short"),
+        ([["networks", "edges", 0]], "networks.edges: [] is too short"),
+        ([["networks", "nodes"]], "networks: 'nodes' is a required property"),
+        ([["networks", "edges"]], "networks: 'edges' is a required property"),
+        ([["networks"]], "'networks' is a required property"),
     ),
 )
-def test_validate_config_error(to_remove, expected):
+def test_validate_config_error(to_remove_list, expected):
     with copy_test_data() as (_, config_copy_path):
         with edit_config(config_copy_path) as config:
-            c = config
-            for key in to_remove[:-1]:
-                c = c[key]
-            del c[to_remove[-1]]
+            for to_remove in to_remove_list:
+                c = config
+                for key in to_remove[:-1]:
+                    c = c[key]
+                del c[to_remove[-1]]
         errors = test_module.validate_circuit_schema(str(config_copy_path), config)
 
         assert len(errors) == 1