Merge branch 'feature/spike_encoder' of https://github.com/GazzolaLab…

…/MiV-Simulator into feature/spike_encoder

pyproject.toml

@@ -14,7 +14,7 @@ packages = [
 python = ">=3.9,<3.12"
 numpy = "^1.22.4"
 scipy = "^1.8.1"
-mpi4py = "^3.1.3"
+mpi4py = "^3.1.5"
 h5py = "^3.7.0"
 Cython = "^0.29.30"
 PyYAML = "^6.0"
@@ -26,19 +26,8 @@ neuroh5 = {git = "https://github.com/iraikov/neuroh5.git"}
 future = "^0.18.3"
 matplotlib = "^3.6.0"
 quantities = "^0.13.0"
-sphinx = {version = "<6", optional = true}
-pydata-sphinx-theme = {version = "^0.12.0", optional = true}
-readthedocs-sphinx-search = {version = "^0.2.0", optional = true}
-sphinx-autodoc-typehints = {version = "^1.21.8", optional = true}
-numpydoc = {version = "^1.5.0", optional = true}
-sphinx-togglebutton = {version = "^0.3.2", optional = true}
-sphinx-copybutton = {version = "^0.5.1", optional = true}
-sphinx-click = {version = "^4.4.0", optional = true}
-sphinxcontrib-mermaid = {version = "^0.7.1", optional = true}
-update = {version = "^0.0.1", optional = true}
-myst-nb = {version = "^0.17.1", optional = true}
-myst-parser = {version = "^0.18.1", optional = true}
 pydantic = "^2.3.0"
+neuron = "^8.2.3"
 
 
 [tool.poetry.dev-dependencies]

src/miv_simulator/coding.py

@@ -5,7 +5,7 @@
 SpikeTimesLike = EventArray[NDArray[np.float_], "SpikeTimesLike ..."]
 """Potentially unsorted or scalar data that can be transformed into `SpikeTimes`"""
 
-SpikeTimes = EventArray[NDArray[np.float_], "SpikeTimes T ..."]
+SpikeTimes = EventArray[NDArray[np.float64], "SpikeTimes T ..."]
 """Sorted array of absolute spike times"""
 
 

src/miv_simulator/config.py

@@ -3,13 +3,14 @@
     BaseModel as _BaseModel,
     Field,
     conlist,
+    AfterValidator,
+    BeforeValidator,
 )
 from typing import Literal, Dict, Any, List, Tuple, Optional, Union, Callable
 from enum import IntEnum
 from collections import defaultdict
 import numpy as np
 from typing_extensions import Annotated
-from pydantic.functional_validators import AfterValidator, BeforeValidator
 
 # Definitions
 

src/miv_simulator/interface/connections.py

@@ -3,7 +3,7 @@
 import logging
 
 from machinable import Component
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 from miv_simulator import config, simulator
 from typing import Optional, Dict
 from miv_simulator.utils import from_yaml
@@ -12,6 +12,8 @@
 
 class Connections(Component):
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         filepath: str = Field("???")
         forest_filepath: str = Field("???")
         axon_extents: config.AxonExtents = Field("???")

src/miv_simulator/interface/distances.py

@@ -1,7 +1,7 @@
 from typing import Optional, Tuple
 
 import logging
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from machinable import Component
 from machinable.config import Field
@@ -11,6 +11,8 @@
 
 class MeasureDistances(Component):
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         filepath: str = Field("???")
         cell_distributions: config.CellDistributions = Field("???")
         layer_extents: config.LayerExtents = Field("???")

src/miv_simulator/interface/h5_types.py

@@ -1,5 +1,5 @@
 from machinable import Component
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 from miv_simulator import config
 from mpi4py import MPI
 from miv_simulator.utils import io as io_utils, from_yaml
@@ -8,6 +8,8 @@
 
 class H5Types(Component):
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         cell_distributions: config.CellDistributions = Field("???")
         synapses: config.Synapses = Field("???")
 

src/miv_simulator/interface/network_architecture.py

@@ -8,13 +8,15 @@
 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
+from pydantic import BaseModel, Field, ConfigDict
 
 
 class NetworkArchitecture(Component):
     """Creates the network architecture by generating the soma coordinates within specified layer geometry."""
 
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         filepath: str = Field("???")
         cell_distributions: config.CellDistributions = Field("???")
         synapses: config.Synapses = Field("???")

src/miv_simulator/interface/neuroh5_graph.py

@@ -1,7 +1,7 @@
 from machinable import Component
-from miv_simulator import simulator
 from neuroh5.io import read_population_names
 from typing import Dict
+from miv_simulator.utils.io import H5FileManager
 
 
 class NeuroH5Graph(Component):
@@ -12,7 +12,7 @@ def __init__(self, *args, **kwargs):
     @property
     def graph(self) -> None:
         if self._graph is None:
-            self._graph = simulator.nh5.Graph(self.local_directory())
+            self._graph = H5FileManager(self.local_directory())
         return self._graph
 
     def __call__(self) -> None:

src/miv_simulator/interface/synapse_forest.py

@@ -1,10 +1,12 @@
 from machinable import Component
 from miv_simulator import config, simulator
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 
 
 class GenerateSynapseForest(Component):
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         filepath: str = Field("???")
         population: config.PopulationName = Field("???")
         morphology: config.SWCFilePath = Field("???")

src/miv_simulator/interface/synapses.py

@@ -3,14 +3,16 @@
 from machinable import Component
 from miv_simulator import config
 from miv_simulator import simulator
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, ConfigDict
 from typing import Optional, Dict
 from miv_simulator.utils import from_yaml
 from mpi4py import MPI
 
 
 class Synapses(Component):
     class Config(BaseModel):
+        model_config = ConfigDict(extra="forbid")
+
         forest_filepath: str = Field("???")
         cell_types: config.CellTypes = Field("???")
         population: str = Field("???")

src/miv_simulator/simulator/__init__.py

@@ -1,14 +1,14 @@
 __doc__ = """Contains the end-user public API of the MiV-Simulator"""
 
-from miv_simulator.utils.io import create_neural_h5
+from miv_simulator.simulator.distribute_synapses import distribute_synapses
+from miv_simulator.simulator.generate_connections import generate_connections
 from miv_simulator.simulator.generate_network_architecture import (
     generate_network_architecture,
 )
-from miv_simulator.simulator.measure_distances import measure_distances
 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
-from miv_simulator.simulator import nh5
+from miv_simulator.simulator.measure_distances import measure_distances
+from miv_simulator.simulator.execution_environment import ExecutionEnvironment
+from miv_simulator.utils.io import create_neural_h5
 from miv_simulator.utils.neuron import configure_hoc