Record interface dependencies

src/miv_simulator/interface/connections.py

@@ -30,7 +30,7 @@ class Config(BaseModel):
         value_chunk_size: int = 1000
         cache_size: int = 1
         write_size: int = 1
-        ranks_: int = 8
+        ranks: int = 8
 
     def config_from_file(self, filename: str) -> Dict:
         return from_yaml(filename)

src/miv_simulator/interface/distances.py

@@ -29,7 +29,7 @@ class Config(BaseModel):
         chunk_size: int = 1000
         value_chunk_size: int = 1000
         cache_size: int = 50
-        ranks_: int = 8
+        ranks: int = 8
 
     def __call__(self):
         logging.basicConfig(level=logging.INFO)

src/miv_simulator/interface/network_architecture.py

@@ -1,16 +1,28 @@
-from typing import Optional, Tuple, Dict
+from typing import Optional, Tuple, Dict, Union
 import os
 import logging
 
 from machinable import Component
 from machinable.element import normversion
-from machinable.types import VersionType
 from miv_simulator import config, simulator
 from miv_simulator.utils import io as io_utils, from_yaml
 from mpi4py import MPI
 from pydantic import BaseModel, Field, ConfigDict
 
 
+def _join(*args):
+    uses = []
+    for arg in args:
+        if arg is None:
+            continue
+        elif isinstance(arg, (list, tuple)):
+            uses.extend(arg)
+        else:
+            uses.append(arg)
+
+    return uses
+
+
 class NetworkArchitecture(Component):
     """Creates the network architecture by generating the soma coordinates within specified layer geometry."""
 
@@ -34,7 +46,7 @@ class Config(BaseModel):
         io_size: int = -1
         chunk_size: int = 1000
         value_chunk_size: int = 1000
-        ranks_: int = 1
+        ranks: int = 8
 
     def config_from_file(self, filename: str) -> Dict:
         return from_yaml(filename)
@@ -64,7 +76,7 @@ def __call__(self) -> None:
             value_chunk_size=self.config.value_chunk_size,
         )
 
-    def measure_distances(self, version: VersionType = None):
+    def measure_distances(self, version=None, uses=None):
         return self.derive(
             "miv_simulator.interface.distances",
             [
@@ -83,12 +95,10 @@ def measure_distances(self, version: VersionType = None):
                 }
             ]
             + normversion(version),
-            uses=self,
+            uses=_join(self, uses),
         )
 
-    def generate_synapse_forest(
-        self, version: VersionType = None
-    ) -> "Component":
+    def generate_synapse_forest(self, version=None, uses=None) -> "Component":
         return self.derive(
             "miv_simulator.interface.synapse_forest",
             [
@@ -97,17 +107,17 @@ def generate_synapse_forest(
                 }
             ]
             + normversion(version),
-            uses=self,
+            uses=_join(self, uses),
         )
 
-    def distribute_synapses(self, version: VersionType = None):
+    def distribute_synapses(self, version=None, uses=None):
         return self.derive(
             "miv_simulator.interface.synapses",
             [] + normversion(version),
-            uses=self,
+            uses=_join(self, uses),
         )
 
-    def generate_connections(self, version: VersionType = None):
+    def generate_connections(self, version=None, uses=None):
         return self.derive(
             "miv_simulator.interface.connections",
             [
@@ -118,5 +128,5 @@ def generate_connections(self, version: VersionType = None):
                 }
             ]
             + normversion(version),
-            uses=self,
+            uses=_join(self, uses),
         )

src/miv_simulator/interface/synapse_forest.py

@@ -27,3 +27,4 @@ def __call__(self) -> None:
             population=self.config.population,
             morphology=self.config.morphology,
         )
+        print("generate_synapse_forest() completed")

src/miv_simulator/interface/synapses.py

@@ -23,8 +23,7 @@ class Config(BaseModel):
         write_size: int = 1
         chunk_size: int = 1000
         value_chunk_size: int = 1000
-        ranks_: int = 8
-        nodes_: int = 1
+        ranks: int = 8
 
     def config_from_file(self, filename: str) -> Dict:
         return from_yaml(filename)

src/miv_simulator/simulator/generate_synapse_forest.py

@@ -11,6 +11,22 @@ def _bin_check(bin: str) -> None:
         raise FileNotFoundError(f"{bin} not found. Did you add it to the PATH?")
 
 
+def _run(cmd):
+    try:
+        subprocess.check_output(
+            cmd,
+            stderr=subprocess.STDOUT,
+        )
+    except subprocess.CalledProcessError as e:
+        error_message = e.output.decode()
+        print(f"{os.getcwd()}$:")
+        print(" ".join(cmd))
+        print("Error:", error_message)
+        raise subprocess.CalledProcessError(
+            e.returncode, e.cmd, output=error_message
+        )
+
+
 def generate_synapse_forest(
     filepath: str,
     tree_output_filepath: str,
@@ -21,33 +37,28 @@ def generate_synapse_forest(
     # create tree
     if not os.path.isfile(tree_output_filepath):
         _bin_check("neurotrees_import")
-        assert (
-            subprocess.run(
-                [
-                    "neurotrees_import",
-                    population,
-                    tree_output_filepath,
-                    morphology,
-                ]
-            ).returncode
-            == 0
+        _run(
+            [
+                "neurotrees_import",
+                population,
+                tree_output_filepath,
+                morphology,
+            ]
         )
-        assert (
-            subprocess.run(
-                [
-                    "h5copy",
-                    "-p",
-                    "-s",
-                    "/H5Types",
-                    "-d",
-                    "/H5Types",
-                    "-i",
-                    filepath,
-                    "-o",
-                    tree_output_filepath,
-                ]
-            ).returncode
-            == 0
+
+        _run(
+            [
+                "h5copy",
+                "-p",
+                "-s",
+                "/H5Types",
+                "-d",
+                "/H5Types",
+                "-i",
+                filepath,
+                "-o",
+                tree_output_filepath,
+            ]
         )
 
     if not os.path.isfile(output_filepath):
@@ -61,17 +72,14 @@ def generate_synapse_forest(
             offset = f["H5Types"]["Populations"][idx][0]
 
         _bin_check("neurotrees_copy")
-        assert (
-            subprocess.run(
-                [
-                    "neurotrees_copy",
-                    "--fill",
-                    "--output",
-                    output_filepath,
-                    tree_output_filepath,
-                    population,
-                    str(offset),
-                ]
-            ).returncode
-            == 0
+        _run(
+            [
+                "neurotrees_copy",
+                "--fill",
+                "--output",
+                output_filepath,
+                tree_output_filepath,
+                population,
+                str(offset),
+            ]
         )