Add Config helper to simplify config file validation

src/miv_simulator/config.py

@@ -1,4 +1,4 @@
-import os
+import copy
 from pydantic import (
     BaseModel as _BaseModel,
     Field,
@@ -300,3 +300,70 @@ def probabilities_sum_to_one(x):
 
 
 CellDistributions = Dict[PopulationName, CellDistribution]
+
+SynapticProjections = Dict[
+    PostSynapticPopulationName,
+    List[PreSynapticPopulationName],
+]
+
+sentinel = object()
+
+
+class Config:
+    def __init__(self, data: Dict) -> None:
+        self._data = copy.deepcopy(data)
+
+        # compatibility
+        self.get("Cell Types.STIM", {}).setdefault("synapses", {})
+
+    @classmethod
+    def from_yaml(cls, filepath: str) -> "Config":
+        from miv_simulator.utils import from_yaml
+
+        return cls(from_yaml(filepath))
+
+    def get(self, path: str, default=sentinel, splitter: str = "."):
+        d = self._data
+        for key in path.split(splitter):
+            if key not in d:
+                if default is not sentinel:
+                    return default
+
+            d = d[key]
+
+        return d
+
+    @property
+    def cell_distributions(self) -> CellDistributions:
+        return self.get("Geometry.Cell Distribution")
+
+    @property
+    def layer_extents(self) -> LayerExtents:
+        return self.get("Geometry.Parametric Surface.Layer Extents")
+
+    @property
+    def geometry_rotation(self) -> Rotation:
+        return self.get("Geometry.Parametric Surface.Rotation", (0.0, 0.0, 0.0))
+
+    @property
+    def geometry_origin(self) -> Origin:
+        return self.get(
+            "Geometry.Parametric Surface.Origin",
+            {"U": "median", "V": "median", "L": "max"},
+        )
+
+    @property
+    def axon_extents(self) -> AxonExtents:
+        return self.get("Connection Generator.Axon Extent")
+
+    @property
+    def synapses(self) -> Synapses:
+        return self.get("Connection Generator.Synapses")
+
+    @property
+    def projections(self) -> SynapticProjections:
+        return {post: list(pre.keys()) for post, pre in self.synapses.items()}
+
+    @property
+    def cell_types(self) -> CellTypes:
+        return self.get("Cell Types")

src/miv_simulator/geometry/geometry.py

@@ -538,7 +538,7 @@ def interp_soma_distances(
     return soma_distances
 
 
-# !deprecated, use distance interpolant
+# !for imperative API, use distance interpolant
 def make_distance_interpolant(
     comm, geometry_config, make_volume, resolution=[30, 30, 10], nsample=1000
 ):
@@ -696,7 +696,7 @@ def RBFInterpolant(
     return origin_ranges, ip_dist_u, ip_dist_v
 
 
-# !deprecated, use measure_soma_distances
+# !for imperative API, use measure_soma_distances
 def measure_distances(
     comm,
     geometry_config,

src/miv_simulator/interface/h5_types.py

@@ -11,10 +11,7 @@ class Config(BaseModel):
         model_config = ConfigDict(extra="forbid")
 
         cell_distributions: config.CellDistributions = Field("???")
-        projections: Dict[
-            config.PostSynapticPopulationName,
-            List[config.PreSynapticPopulationName],
-        ] = Field("???")
+        projections: config.SynapticProjections = Field("???")
 
     def config_from_file(self, filename: str) -> Dict:
         return from_yaml(filename)

src/miv_simulator/plotting.py

@@ -401,7 +401,7 @@ def plot_coordinates(
     return ax
 
 
-# !deprecated, needs refactoring
+# !needs refactoring
 def plot_coords_in_volume(
     populations,
     coords_path,

src/miv_simulator/simulator/distribute_synapses.py

@@ -31,7 +31,7 @@ def mpi_excepthook(type, value, traceback):
 sys.excepthook = mpi_excepthook
 
 
-# !deprecated, use update_synapse_statistics instead
+# !for imperative API, use update_synapse_statistics instead
 def update_syn_stats(env, syn_stats_dict, syn_dict):
     return update_synapse_statistics(syn_dict, syn_stats_dict)
 
@@ -114,7 +114,7 @@ def local_syn_summary(syn_stats_dict):
     return str.join("\n", res)
 
 
-# !deprecated, use check_synapses instead
+# !for imperative API, use check_synapses instead
 def check_syns(
     gid,
     morph_dict,
@@ -179,7 +179,7 @@ def check_synapses(
         )
 
 
-# !deprecated, use distribute_synapses instead
+# !for imperative API, use distribute_synapses instead
 def distribute_synapse_locations(
     config,
     template_path,

src/miv_simulator/simulator/generate_connections.py

@@ -34,7 +34,7 @@ def mpi_excepthook(type, value, traceback):
 sys.excepthook = mpi_excepthook
 
 
-# !deprecated, use distance connections instead
+# !for imperative API, use distance connections instead
 def generate_distance_connections(
     config,
     include,
@@ -209,7 +209,7 @@ def generate_connections(
             f"Generating connectivity for populations {destination_populations}..."
         )
 
-    # !deprecated, does not seem applicable any longer
+    # !for imperative API, does not seem applicable any longer
     # if len(soma_distances) == 0:
     #     (origin_ranges, ip_dist_u, ip_dist_v) = make_distance_interpolant(
     #         env, resolution=resolution, nsample=interp_chunk_size

src/miv_simulator/simulator/generate_network_architecture.py

@@ -136,7 +136,7 @@ def rho(x):
     return in_nodes
 
 
-# !deprecated, use generate_network_architecture() instead
+# !for imperative API, use generate_network_architecture() instead
 def generate_soma_coordinates(
     config: str,
     types_path: str,

src/miv_simulator/utils/utils.py

@@ -370,7 +370,7 @@ def write_to_yaml(file_path, data, convert_scalars=False):
         )
 
 
-# !deprecated, use from_yaml instead
+# !for imperative API, use from_yaml instead
 def read_from_yaml(
     file_path: str, include_loader: None = None
 ) -> Dict[str, Dict[str, Dict[str, Union[Dict[str, float], Dict[str, int]]]]]: