Restructure simulator module to allow for direct library-like usage

docs/api/simulator.rst

@@ -6,10 +6,8 @@ Simulator
 .. autosummary::
    :toctree: _toctree
 
-   distribute_synapse_locations
-   generate_distance_connections
-   generate_input_features
-   generate_input_spike_trains
-   generate_soma_coordinates
-   make_h5types
+   distribute_synapses
+   generate_connections
+   generate_network_architecture
+   generate_synapse_forest
    measure_distances

src/miv_simulator/config.py

@@ -13,6 +13,8 @@
 
 # Definitions
 
+SWCFilePath = str
+
 
 class SWCTypesDef(IntEnum):
     soma = 1

src/miv_simulator/interface/distance_connections.py → src/miv_simulator/interface/connections.py

@@ -4,14 +4,13 @@
 
 from machinable import Component
 from pydantic import BaseModel, Field
-from miv_simulator import config
+from miv_simulator import config, simulator
 from typing import Optional, Dict
-from miv_simulator.simulator import distance_connections
 from miv_simulator.utils import from_yaml
 from mpi4py import MPI
 
 
-class DistanceConnections(Component):
+class Connections(Component):
     class Config(BaseModel):
         filepath: str = Field("???")
         forest_filepath: str = Field("???")
@@ -44,7 +43,7 @@ def output_filepath(self):
 
     def __call__(self):
         logging.basicConfig(level=logging.INFO)
-        distance_connections(
+        simulator.generate_connections(
             filepath=self.config.filepath,
             forest_filepath=self.config.forest_filepath,
             include_forest_populations=self.config.include_forest_populations,

src/miv_simulator/interface/measure_distances.py → src/miv_simulator/interface/distances.py

@@ -5,8 +5,7 @@
 
 from machinable import Component
 from machinable.config import Field
-from miv_simulator.simulator import measure_distances
-from miv_simulator import config
+from miv_simulator import config, simulator
 from mpi4py import MPI
 
 
@@ -32,7 +31,7 @@ class Config(BaseModel):
 
     def __call__(self):
         logging.basicConfig(level=logging.INFO)
-        measure_distances(
+        simulator.measure_distances(
             filepath=self.config.filepath,
             geometry_filepath=self.config.geometry_filepath,
             coordinate_namespace=self.config.coordinate_namespace,

src/miv_simulator/interface/create_h5.py → src/miv_simulator/interface/h5_types.py

@@ -1,14 +1,12 @@
 from machinable import Component
-from machinable.element import normversion
-from machinable.types import VersionType
 from pydantic import BaseModel, Field
 from miv_simulator import config
 from mpi4py import MPI
 from miv_simulator.utils import io as io_utils, from_yaml
 from typing import Dict
 
 
-class CreateH5(Component):
+class H5Types(Component):
     class Config(BaseModel):
         cell_distributions: config.CellDistributions = Field("???")
         synapses: config.Synapses = Field("???")

src/miv_simulator/interface/legacy/derive_spike_trains.py

@@ -4,7 +4,7 @@
 import numpy as np
 from machinable import Component
 from pydantic import Field, BaseModel
-from miv_simulator.simulator import (
+from miv_simulator.input_spike_trains import (
     generate_input_spike_trains,
     import_input_spike_train,
 )

src/miv_simulator/interface/legacy/input_features.py

@@ -4,7 +4,7 @@
 from pydantic import Field, BaseModel
 from machinable.element import normversion
 from machinable.types import VersionType
-from miv_simulator.simulator import generate_input_features
+from miv_simulator.input_features import generate_input_features
 
 
 class InputFeatures(Component):

src/miv_simulator/interface/legacy/prepare_data.py

@@ -42,17 +42,17 @@ def __call__(self):
         self.distance_connections = {}
         self.synapse_forest = {}
         for dependency in self.uses:
-            if dependency.module == "miv_simulator.interface.create_network":
+            if (
+                dependency.module
+                == "miv_simulator.interface.network_architecture"
+            ):
                 self.network = dependency
             elif (
                 dependency.module
                 == "miv_simulator.interface.legacy.derive_spike_trains"
             ):
                 self.spike_trains = dependency
-            elif (
-                dependency.module
-                == "miv_simulator.interface.distance_connections"
-            ):
+            elif dependency.module == "miv_simulator.interface.connections":
                 populations = read_population_names(
                     dependency.config.forest_filepath
                 )
@@ -74,10 +74,7 @@ def __call__(self):
                         f"defined in {self.synapse_forest[dependency.config.population]}"
                     )
                 self.synapse_forest[dependency.config.population] = dependency
-            elif (
-                dependency.module
-                == "miv_simulator.interface.distribute_synapses"
-            ):
+            elif dependency.module == "miv_simulator.interface.synapses":
                 if dependency.config.population in self.synapses:
                     # check for duplicates
                     raise ValueError(

src/miv_simulator/interface/create_network.py → src/miv_simulator/interface/network_architecture.py

@@ -5,17 +5,14 @@
 from machinable import Component
 from machinable.element import normversion
 from machinable.types import VersionType
-from miv_simulator import config
-from miv_simulator.simulator.soma_coordinates import (
-    generate as generate_soma_coordinates,
-)
+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
 
 
-class CreateNetwork(Component):
-    """Creates neural H5 type definitions and soma coordinates within specified layer geometry."""
+class NetworkArchitecture(Component):
+    """Creates the network architecture by generating the soma coordinates within specified layer geometry."""
 
     class Config(BaseModel):
         filepath: str = Field("???")
@@ -45,7 +42,7 @@ def on_write_meta_data(self):
 
     def __call__(self) -> None:
         logging.basicConfig(level=logging.INFO)
-        generate_soma_coordinates(
+        simulator.generate_network_architecture(
             output_filepath=self.config.filepath,
             cell_distributions=self.config.cell_distributions,
             layer_extents=self.config.layer_extents,
@@ -67,7 +64,7 @@ def __call__(self) -> None:
 
     def measure_distances(self, version: VersionType = None):
         return self.derive(
-            "miv_simulator.interface.measure_distances",
+            "miv_simulator.interface.distances",
             [
                 {
                     "filepath": self.config.filepath,
@@ -87,7 +84,9 @@ def measure_distances(self, version: VersionType = None):
             uses=self,
         )
 
-    def synapse_forest(self, version: VersionType = None) -> "Component":
+    def generate_synapse_forest(
+        self, version: VersionType = None
+    ) -> "Component":
         return self.derive(
             "miv_simulator.interface.synapse_forest",
             [
@@ -101,14 +100,14 @@ def synapse_forest(self, version: VersionType = None) -> "Component":
 
     def distribute_synapses(self, version: VersionType = None):
         return self.derive(
-            "miv_simulator.interface.distribute_synapses",
+            "miv_simulator.interface.synapses",
             [] + normversion(version),
             uses=self,
         )
 
-    def distance_connections(self, version: VersionType = None):
+    def generate_connections(self, version: VersionType = None):
         return self.derive(
-            "miv_simulator.interface.distance_connections",
+            "miv_simulator.interface.connections",
             [
                 {
                     "filepath": self.config.filepath,

src/miv_simulator/interface/synapse_forest.py

@@ -1,26 +1,13 @@
-import os
-import shutil
-import subprocess
-
-import h5py
 from machinable import Component
-from miv_simulator import config
+from miv_simulator import config, simulator
 from pydantic import BaseModel, Field
 
 
-def _bin_check(bin: str) -> None:
-    if not shutil.which(bin):
-        raise FileNotFoundError(f"{bin} not found. Did you add it to the PATH?")
-
-
-SWCFilePath = str
-
-
 class GenerateSynapseForest(Component):
     class Config(BaseModel):
         filepath: str = Field("???")
         population: config.PopulationName = Field("???")
-        morphology: SWCFilePath = Field("???")
+        morphology: config.SWCFilePath = Field("???")
 
     @property
     def tree_output_filepath(self) -> str:
@@ -31,60 +18,10 @@ def output_filepath(self) -> str:
         return self.local_directory("forest.h5")
 
     def __call__(self) -> None:
-        # create tree
-        if not os.path.isfile(self.tree_output_filepath):
-            _bin_check("neurotrees_import")
-            assert (
-                subprocess.run(
-                    [
-                        "neurotrees_import",
-                        self.config.population,
-                        self.tree_output_filepath,
-                        self.config.morphology,
-                    ]
-                ).returncode
-                == 0
-            )
-            assert (
-                subprocess.run(
-                    [
-                        "h5copy",
-                        "-p",
-                        "-s",
-                        "/H5Types",
-                        "-d",
-                        "/H5Types",
-                        "-i",
-                        self.config.filepath,
-                        "-o",
-                        self.tree_output_filepath,
-                    ]
-                ).returncode
-                == 0
-            )
-
-        if not os.path.isfile(self.output_filepath):
-            # determine population ranges
-            with h5py.File(self.config.filepath, "r") as f:
-                idx = list(
-                    reversed(
-                        f["H5Types"]["Population labels"].dtype.metadata["enum"]
-                    )
-                ).index(self.config.population)
-                offset = f["H5Types"]["Populations"][idx][0]
-
-            _bin_check("neurotrees_copy")
-            assert (
-                subprocess.run(
-                    [
-                        "neurotrees_copy",
-                        "--fill",
-                        "--output",
-                        self.output_filepath,
-                        self.tree_output_filepath,
-                        self.config.population,
-                        str(offset),
-                    ]
-                ).returncode
-                == 0
-            )
+        simulator.generate_synapse_forest(
+            filepath=self.config.filepath,
+            tree_output_filepath=self.tree_output_filepath,
+            output_filepath=self.output_filepath,
+            population=self.config.population,
+            morphology=self.config.morphology,
+        )

src/miv_simulator/interface/distribute_synapses.py → src/miv_simulator/interface/synapses.py

@@ -9,22 +9,18 @@
 from mpi4py import MPI
 
 
-class DistributeSynapses(Component):
+class Synapses(Component):
     class Config(BaseModel):
         forest_filepath: str = Field("???")
         cell_types: config.CellTypes = Field("???")
         population: str = Field("???")
         distribution: str = "uniform"
         mechanisms_path: str = "./mechanisms"
         template_path: str = "./templates"
-        dt: float = 0.025
-        tstop: float = 0.0
-        celsius: Optional[float] = 35.0
         io_size: int = -1
         write_size: int = 1
         chunk_size: int = 1000
         value_chunk_size: int = 1000
-        use_coreneuron: bool = False
         ranks_: int = 8
         nodes_: int = 1
 
@@ -44,15 +40,11 @@ def __call__(self):
             distribution=self.config.distribution,
             mechanisms_path=self.config.mechanisms_path,
             template_path=self.config.template_path,
-            dt=self.config.dt,
-            tstop=self.config.tstop,
-            celsius=self.config.celsius,
             output_filepath=self.output_filepath,
             io_size=self.config.io_size,
             write_size=self.config.write_size,
             chunk_size=self.config.chunk_size,
             value_chunk_size=self.config.value_chunk_size,
-            use_coreneuron=self.config.use_coreneuron,
             seed=self.seed,
             dry_run=False,
         )

src/miv_simulator/simulator/__init__.py

@@ -1,20 +1,12 @@
-from miv_simulator.simulator.distribute_synapse_locations import (
-    distribute_synapse_locations,
-    distribute_synapses,
-)
-from miv_simulator.simulator.generate_distance_connections import (
-    generate_distance_connections,
-    distance_connections,
-)
-from miv_simulator.simulator.generate_input_features import (
-    generate_input_features,
-)
-from miv_simulator.simulator.generate_input_spike_trains import (
-    generate_input_spike_trains,
-    import_input_spike_train,
+__doc__ = """Contains the end-user public API of the MiV-Simulator"""
+
+from miv_simulator.utils.io import create_neural_h5
+from miv_simulator.simulator.generate_network_architecture import (
+    generate_network_architecture,
 )
-from miv_simulator.simulator.soma_coordinates import generate_soma_coordinates
 from miv_simulator.simulator.measure_distances import measure_distances
-
-# !deprecated, use io_utils directly
-from miv_simulator.simulator.make_h5types import make_h5types
+from miv_simulator.simulator.generate_synapse_forest import (
+    generate_synapse_forest,
+)
+from miv_simulator.simulator.distribute_synapses import distribute_synapses
+from miv_simulator.simulator.generate_connections import generate_connections