Access population config from the populations (#179)

CHANGELOG.rst

@@ -1,6 +1,13 @@
 Changelog
 =========
 
+Version v1.0.1
+--------------
+
+New Features
+~~~~~~~~~~~~
+- Access the population configs for node/edge populations via population_config property
+
 Version v1.0.0
 --------------
 

bluepysnap/circuit.py

@@ -21,6 +21,7 @@
 
 from bluepysnap.config import CircuitConfig
 from bluepysnap.edges import Edges
+from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.node_sets import NodeSets
 from bluepysnap.nodes import Nodes
 
@@ -49,6 +50,20 @@ def config(self):
         """Network config dictionary."""
         return self._config.to_dict()
 
+    def get_node_population_config(self, name):
+        """Get node population configuration."""
+        try:
+            return self._config.node_populations[name]
+        except KeyError as e:
+            raise BluepySnapError(f"Population config not found for node population: {name}") from e
+
+    def get_edge_population_config(self, name):
+        """Get edge population configuration."""
+        try:
+            return self._config.edge_populations[name]
+        except KeyError as e:
+            raise BluepySnapError(f"Population config not found for edge population: {name}") from e
+
     @cached_property
     def node_sets(self):
         """Returns the NodeSets object bound to the circuit."""

bluepysnap/config.py

@@ -17,6 +17,7 @@
 
 """SONATA network config parsing."""
 
+import copy
 import json
 from collections.abc import Iterable, Mapping
 from pathlib import Path
@@ -163,11 +164,55 @@ def to_dict(self):
 class CircuitConfig(Config):
     """Handle CircuitConfig."""
 
+    def __init__(self, *args):
+        """Initializes circuit config."""
+        super().__init__(*args)
+        self._populations = self._resolve_population_configs(self.to_dict())
+
     @classmethod
     def from_config(cls, config_path):
         """Instantiate the config class from circuit configuration."""
         return cls(config_path, libsonata.CircuitConfig)
 
+    @property
+    def node_populations(self):
+        """Access node population configs."""
+        return self._populations["nodes"]
+
+    @property
+    def edge_populations(self):
+        """Access edge population configs."""
+        return self._populations["edges"]
+
+    @staticmethod
+    def _resolve_population_configs(config):
+        """Resolves population configs for the node and edge populations."""
+        networks = config.get("networks") or {}
+        components = config.get("components") or {}
+
+        def resolve_network_populations(element_type):
+            populations = {}
+            type_file_key = f"{element_type}_file"
+            element_dicts = networks.get(element_type) or []
+
+            for elem_dict in element_dicts:
+                elem_pops = elem_dict.get("populations") or {}
+
+                for pop, cfg in elem_pops.items():
+                    populations[pop] = copy.deepcopy(components)
+                    populations[pop].update(cfg or {})
+
+                    # add h5 filepath for simpler access
+                    if type_file_key in elem_dict:
+                        populations[pop][type_file_key] = elem_dict[type_file_key]
+
+            return populations
+
+        return {
+            "nodes": resolve_network_populations("nodes"),
+            "edges": resolve_network_populations("edges"),
+        }
+
 
 class SimulationConfig(Config):
     """Handle SimulationConfig."""

bluepysnap/edges.py

@@ -114,6 +114,16 @@ def _dynamics_params_names(self):
     def _topology_property_names(self):
         return {Edge.SOURCE_NODE_ID, Edge.TARGET_NODE_ID}
 
+    @property
+    def population_config(self):
+        """Access the configuration for the population.
+
+        This configuration is extended with
+        * 'components' of the circuit config
+        * 'edges_file': the path the h5 file containing the population.
+        """
+        return self._circuit.get_edge_population_config(self.name)
+
     @property
     def property_names(self):
         """Set of available edge properties.
@@ -450,6 +460,7 @@ def pair_edges(self, source_node_id, target_node_id, properties=None):
 
     def _iter_connections(self, source_node_ids, target_node_ids, unique_node_ids, shuffle):
         """Iterate through `source_node_ids` -> `target_node_ids` connections."""
+
         # pylint: disable=too-many-branches,too-many-locals
         def _optimal_direction():
             """Choose between source and target node IDs for iterating."""
@@ -563,13 +574,10 @@ def iter_connections(
             omit_edge_count = lambda x: x[:2]
             return map(omit_edge_count, it)
 
-    @cached_property
+    @property
     def h5_filepath(self):
         """Get the H5 edges file associated with population."""
-        for edge_conf in self._circuit.config["networks"]["edges"]:
-            if self.name in edge_conf["populations"]:
-                return edge_conf["edges_file"]
-        raise BluepySnapError(f"h5_filepath not found for population '{self.name}'")
+        return self.population_config["edges_file"]
 
 
 class Edges(

bluepysnap/nodes.py

@@ -127,6 +127,16 @@ def target_in_edges(self):
             edge.name for edge in self._circuit.edges.values() if self.name == edge.target.name
         )
 
+    @property
+    def population_config(self):
+        """Access the configuration for the population.
+
+        This configuration is extended with
+        * 'components' of the circuit config
+        * 'nodes_file': the path the h5 file containing the population.
+        """
+        return self._circuit.get_node_population_config(self.name)
+
     @property
     def property_names(self):
         """Set of available node properties.
@@ -568,13 +578,10 @@ def models(self):
 
         return NeuronModelsHelper(self._properties, self)
 
-    @cached_property
+    @property
     def h5_filepath(self):
         """Get the H5 nodes file associated with population."""
-        for node_conf in self._circuit.config["networks"]["nodes"]:
-            if self.name in node_conf["populations"]:
-                return node_conf["nodes_file"]
-        raise BluepySnapError(f"h5_filepath not found for population '{self.name}'")
+        return self.population_config["nodes_file"]
 
 
 class Nodes(

tests/test_circuit.py

@@ -5,6 +5,7 @@
 
 import bluepysnap.circuit as test_module
 from bluepysnap.edges import EdgePopulation, Edges
+from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.nodes import NodePopulation, Nodes
 
 from utils import TEST_DATA_DIR, copy_test_data, edit_config, skip_if_libsonata_0_1_16
@@ -28,6 +29,16 @@ def test_all():
         json.loads((TEST_DATA_DIR / "node_sets.json").read_text())
     )
 
+    fake_pop = "fake"
+    with pytest.raises(
+        BluepySnapError, match=f"Population config not found for node population: {fake_pop}"
+    ):
+        circuit.get_node_population_config(fake_pop)
+    with pytest.raises(
+        BluepySnapError, match=f"Population config not found for edge population: {fake_pop}"
+    ):
+        circuit.get_edge_population_config(fake_pop)
+
 
 @skip_if_libsonata_0_1_16
 def test_duplicate_node_populations():

tests/test_config.py

@@ -155,3 +155,48 @@ def test_simulation_config():
     )
     assert actual["conditions"]["celsius"] == 34.0
     assert actual["conditions"]["v_init"] == -80
+
+
+def test__resolve_population_configs():
+    node = {
+        "nodes_file": "nodes_path",
+        "populations": {"node_pop": {"changed_node": "changed", "added_this": "node_test"}},
+    }
+
+    edge = {
+        "edges_file": "edges_path",
+        "populations": {"edge_pop": {"changed_edge": "changed", "added_this": "edge_test"}},
+    }
+
+    config = {
+        "components": {
+            "unchanged": True,
+            "changed_node": "unchanged",
+            "changed_edge": "unchanged",
+        },
+        "networks": {
+            "nodes": [node],
+            "edges": [edge],
+        },
+    }
+    expected_node_pop = {
+        "unchanged": True,
+        "changed_node": "changed",
+        "changed_edge": "unchanged",
+        "added_this": "node_test",
+        "nodes_file": "nodes_path",
+    }
+    expected_edge_pop = {
+        "unchanged": True,
+        "changed_node": "unchanged",
+        "changed_edge": "changed",
+        "added_this": "edge_test",
+        "edges_file": "edges_path",
+    }
+    expected = {
+        "nodes": {"node_pop": expected_node_pop},
+        "edges": {"edge_pop": expected_edge_pop},
+    }
+    res = test_module.CircuitConfig._resolve_population_configs(config)
+
+    assert res == expected

tests/test_edges.py

@@ -692,7 +692,6 @@ def test_efferent_edges(self):
         )
 
     def test_pair_edges(self):
-
         # no connection between 0 and 2
         assert self.test_obj.pair_edges(0, 2, None) == CircuitEdgeIds.from_arrays([], [])
         actual = self.test_obj.pair_edges(0, 2, [Synapse.AXONAL_DELAY])
@@ -1394,8 +1393,3 @@ 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_no_h5_filepath(self):
-        with pytest.raises(BluepySnapError, match="h5_filepath not found for population"):
-            self.test_obj.name = "fake"
-            self.test_obj.h5_filepath

tests/test_nodes.py

@@ -996,8 +996,3 @@ 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_no_h5_filepath(self):
-        with pytest.raises(BluepySnapError, match="h5_filepath not found for population"):
-            self.test_obj.name = "fake"
-            self.test_obj.h5_filepath

tox.ini

@@ -63,7 +63,8 @@ max-line-length = 100
 [pydocstyle]
 # ignore the following
 #   - D413: no blank line after last section
-add-ignore = D413
+#   - D202: no blank line after docstring (handled by black, causes an issue if first line is '#pylint:disable')
+add-ignore = D413,D202
 convention = google
 
 [gh-actions]