Merge main on feature/ref_parser

bsb_nest/adapter.py

@@ -15,10 +15,10 @@
 from neo import SpikeTrain
 from tqdm import tqdm
 
-from .exceptions import NestConnectError, NestModelError, NestModuleError
+from .exceptions import KernelWarning, NestConnectError, NestModelError, NestModuleError
 
 if typing.TYPE_CHECKING:
-    from bsb import Simulation
+    from .simulation import NestSimulation
 
 
 class NestResult(SimulationResult):
@@ -167,10 +167,12 @@ def create_devices(self, simulation):
         for device_model in simulation.devices.values():
             device_model.implement(self, simulation, simdata)
 
-    def set_settings(self, simulation: "Simulation"):
+    def set_settings(self, simulation: "NestSimulation"):
         nest.set_verbosity(simulation.verbosity)
         nest.resolution = simulation.resolution
         nest.overwrite_files = True
+        if simulation.seed is not None:
+            nest.rng_seed = simulation.seed
 
     def check_comm(self):
         if nest.NumProcesses() != MPI.get_size():

bsb_nest/cell.py

@@ -1,11 +1,13 @@
 import nest
-from bsb import CellModel, config, types
+from bsb import CellModel, config
+
+from .distributions import NestRandomDistribution, nest_parameter
 
 
 @config.node
 class NestCell(CellModel):
     model = config.attr(type=str, default="iaf_psc_alpha")
-    constants = config.dict(type=types.any_())
+    constants = config.dict(type=nest_parameter())
 
     def create_population(self, simdata):
         n = len(simdata.placement[self])
@@ -15,7 +17,12 @@ def create_population(self, simdata):
         return population
 
     def set_constants(self, population):
-        population.set(self.constants)
+        population.set(
+            {
+                k: (v() if isinstance(v, NestRandomDistribution) else v)
+                for k, v in self.constants.items()
+            }
+        )
 
     def set_parameters(self, population, simdata):
         ps = simdata.placement[self]

bsb_nest/connection.py

@@ -7,6 +7,7 @@
 from bsb import MPI, ConnectionModel, compose_nodes, config, types
 from tqdm import tqdm
 
+from .distributions import nest_parameter
 from .exceptions import NestConnectError
 
 
@@ -16,7 +17,7 @@ class NestSynapseSettings:
     weight = config.attr(type=float, required=True)
     delay = config.attr(type=float, required=True)
     receptor_type = config.attr(type=int)
-    constants = config.catch_all(type=types.any_())
+    constants = config.catch_all(type=nest_parameter())
 
 
 @config.node

bsb_nest/distributions.py

@@ -0,0 +1,62 @@
+import builtins
+import typing
+
+import errr
+import nest.random.hl_api_random as _distributions
+from bsb import DistributionCastError, TypeHandler, config, types
+
+if typing.TYPE_CHECKING:
+    from bsb import Scaffold
+
+_available_distributions = [d for d in _distributions.__all__]
+
+
+@config.node
+class NestRandomDistribution:
+    """
+    Class to handle NEST random distributions.
+    """
+
+    scaffold: "Scaffold"
+    distribution: str = config.attr(
+        type=types.in_(_available_distributions), required=True
+    )
+    """Distribution name. Should correspond to a function of nest.random.hl_api_random"""
+    parameters: dict[str, typing.Any] = config.catch_all(type=types.any_())
+    """Dictionary of parameters to assign to the distribution. Should correspond to NEST's"""
+
+    def __init__(self, **kwargs):
+        try:
+            self._distr = getattr(_distributions, self.distribution)(**self.parameters)
+        except Exception as e:
+            errr.wrap(
+                DistributionCastError, e, prepend=f"Can't cast to '{self.distribution}': "
+            )
+
+    def __call__(self):
+        return self._distr
+
+    def __getattr__(self, attr):
+        # hasattr does not work here. So we use __dict__
+        if "_distr" not in self.__dict__:
+            raise AttributeError("No underlying _distr found for distribution node.")
+        return getattr(self._distr, attr)
+
+
+class nest_parameter(TypeHandler):
+    """
+    Type validator. Type casts the value or node to a Nest parameter, that can be either a value or
+    a NestRandomDistribution.
+    """
+
+    def __call__(self, value, _key=None, _parent=None):
+        if isinstance(value, builtins.dict) and "distribution" in value.keys():
+            return NestRandomDistribution(**value, _key=_key, _parent=_parent)
+        return value
+
+    @property
+    def __name__(self):  # pragma: nocover
+        return "nest parameter"
+
+    def __inv__(self, value):
+        return value

bsb_nest/simulation.py

@@ -12,9 +12,15 @@ class NestSimulation(Simulation):
     """
 
     modules = config.list(type=str)
+    """List of NEST modules to load at the beginning of the simulation"""
     threads = config.attr(type=types.int(min=1), default=1)
+    """Number of threads to use during simulation"""
     resolution = config.attr(type=types.float(min=0.0), required=True)
+    """Simulation time step size in milliseconds"""
     verbosity = config.attr(type=str, default="M_ERROR")
+    """NEST verbosity level"""
+    seed = config.attr(type=int, default=None)
+    """Random seed for the simulations"""
 
     cell_models = config.dict(type=NestCell, required=True)
     connection_models = config.dict(type=NestConnection, required=True)

tests/test_nest.py

@@ -2,7 +2,7 @@
 
 import nest
 import numpy as np
-from bsb import BootError, ConfigurationError
+from bsb import BootError, CastError, ConfigurationError
 from bsb.config import Configuration
 from bsb.core import Scaffold
 from bsb.services import MPI
@@ -345,3 +345,90 @@ def test_dc_generator(self):
             v_ms[int(50 / resolution) + 1 : int(60 / resolution) + 1] > -70,
             "Current injected should raise membrane potential",
         )
+
+    def test_nest_randomness(self):
+        nest.ResetKernel()
+        nest.resolution = 0.1
+        nest.rng_seed = 1234
+        # gif_cond_exp implements a random spiking process.
+        # So it's perfect to test the seed
+        A = nest.Create(
+            "gif_cond_exp",
+            1,
+            params={"I_e": 200.0, "V_m": nest.random.normal(mean=-70, std=20.0)},
+        )
+        spikeA = nest.Create("spike_recorder")
+        nest.Connect(A, spikeA)
+        nest.Simulate(1000.0)
+        spike_times_nest = spikeA.get("events")["times"]
+        print(spike_times_nest)
+
+        conf = {
+            "name": "test",
+            "storage": {"engine": "hdf5"},
+            "network": {"x": 1, "y": 1, "z": 1},
+            "partitions": {"B": {"type": "layer", "thickness": 1}},
+            "cell_types": {"A": {"spatial": {"radius": 1, "count": 1}}},
+            "placement": {
+                "placement_A": {
+                    "strategy": "bsb.placement.strategy.FixedPositions",
+                    "cell_types": ["A"],
+                    "partitions": ["B"],
+                    "positions": [[1, 1, 1]],
+                }
+            },
+            "connectivity": {},
+            "after_connectivity": {},
+            "simulations": {
+                "test": {
+                    "simulator": "nest",
+                    "duration": 1000,
+                    "resolution": 0.1,
+                    "seed": 1234,
+                    "cell_models": {
+                        "A": {
+                            "model": "gif_cond_exp",
+                            "constants": {
+                                "I_e": 200.0,
+                                "V_m": {
+                                    "distribution": "normal",
+                                    "mean": -70,
+                                    "std": 20.0,
+                                },
+                            },
+                        }
+                    },
+                    "connection_models": {},
+                    "devices": {
+                        "record_A_spikes": {
+                            "device": "spike_recorder",
+                            "delay": 0.5,
+                            "targetting": {
+                                "strategy": "cell_model",
+                                "cell_models": ["A"],
+                            },
+                        }
+                    },
+                }
+            },
+        }
+        cfg = Configuration(conf)
+        netw = Scaffold(cfg, self.storage)
+        netw.compile()
+        results = netw.run_simulation("test")
+        spike_times_bsb = results.spiketrains[0]
+        self.assertClose(np.array(spike_times_nest), np.array(spike_times_bsb))
+        self.assertEqual(
+            cfg.__tree__()["simulations"]["test"]["cell_models"]["A"]["constants"]["V_m"],
+            {
+                "distribution": "normal",
+                "mean": -70,
+                "std": 20.0,
+            },
+        )
+        # Test with an unknown distribution
+        conf["simulations"]["test"]["cell_models"]["A"]["constants"]["V_m"][
+            "distribution"
+        ] = "bean"
+        with self.assertRaises(CastError):
+            Configuration(conf)