fix: Let writing data to file at flush

examples/nest-simulation/tests/test_examples.py

@@ -62,7 +62,7 @@ def test_json_example(self):
         self.scaffold.compile()
         self._test_scaffold_results()
         results = self.scaffold.run_simulation("basal_activity")
-        self._test_simulation_results(results.spiketrains)
+        self._test_simulation_results(results.block.segments[0].spiketrains)
 
     def test_yaml_example(self):
         self.cfg = parse_configuration_file(
@@ -72,7 +72,7 @@ def test_yaml_example(self):
         self.scaffold.compile()
         self._test_scaffold_results()
         results = self.scaffold.run_simulation("basal_activity")
-        self._test_simulation_results(results.spiketrains)
+        self._test_simulation_results(results.block.segments[0].spiketrains)
 
     def test_python_example(self):
         import scripts.guide_nest  # noqa: F401

examples/neuron-simulation/tests/test_examples.py

@@ -67,7 +67,7 @@ def test_json_example(self):
         self.scaffold.compile()
         self._test_scaffold_results()
         results = self.scaffold.run_simulation("neuronsim")
-        self._test_simulation_results(results.analogsignals)
+        self._test_simulation_results(results.block.segments[0].analogsignals)
 
     def test_yaml_example(self):
         self.cfg = parse_configuration_file(
@@ -77,7 +77,7 @@ def test_yaml_example(self):
         self.scaffold.compile()
         self._test_scaffold_results()
         results = self.scaffold.run_simulation("neuronsim")
-        self._test_simulation_results(results.analogsignals)
+        self._test_simulation_results(results.block.segments[0].analogsignals)
 
     def test_python_example(self):
         import scripts.guide_neuron  # noqa: F401

packages/bsb-arbor/bsb_arbor/adapter.py

@@ -25,11 +25,11 @@ class ArborSimulationData(SimulationData):
     Container class for simulation data.
     """
 
-    def __init__(self, simulation):
+    def __init__(self, simulation, filename):
         """
         Container class for simulation data.
         """
-        super().__init__(simulation)
+        super().__init__(simulation, filename=filename)
         self.arbor_sim: arbor.simulation = None
 
 
@@ -375,11 +375,13 @@ def __init__(self, comm=None):
         super().__init__(comm)
         self.simdata: dict[ArborSimulation, ArborSimulationData] = {}
 
-    def prepare(self, simulation: "ArborSimulation") -> ArborSimulationData:
+    def prepare(
+        self, simulation: "ArborSimulation", filename=None
+    ) -> ArborSimulationData:
         """
         Prepares the arbor simulation engine with the given simulation.
         """
-        simdata = self._create_simdata(simulation)
+        simdata = self._create_simdata(simulation, filename)
         try:
             context = arbor.context(arbor.proc_allocation(threads=simulation.threads))
             if self.comm.get_size() > 1:
@@ -466,8 +468,8 @@ def get_recipe(self, simulation, simdata=None):
         self._cache_devices(simulation, simdata)
         return ArborRecipe(simulation, simdata)
 
-    def _create_simdata(self, simulation):
-        self.simdata[simulation] = simdata = ArborSimulationData(simulation)
+    def _create_simdata(self, simulation, filename):
+        self.simdata[simulation] = simdata = ArborSimulationData(simulation, filename)
         self._assign_chunks(simulation, simdata)
         return simdata
 

packages/bsb-core/bsb/cli/commands/_commands.py

@@ -229,13 +229,13 @@ def handler(self, context):
                 level=0,
             )
         try:
-            result = network.run_simulation(sim_name)
+            network.run_simulation(sim_name, output_filename=root / f"{uuid4()}.nio")
         except NodeNotFoundError as e:
             append = ", " if len(network.simulations) else ""
             append += ", ".join(f"'{name}'" for name in extra_simulations)
             errr.wrap(type(e), e, append=append)
-        else:
-            result.write(root / f"{uuid4()}.nio", "ow")
+        # else:
+        #     result.write(root / f"{uuid4()}.nio", "ow")
 
     def get_options(self):
         return {

packages/bsb-core/bsb/core.py

@@ -449,7 +449,7 @@ def run_pipelines(self, fail_fast=True, pipelines=None):
                 pool.schedule(pipelines)
             pool.execute()
 
-    def run_simulation(self, simulation_name: str):
+    def run_simulation(self, simulation_name: str, output_filename: str = None):
         """
         Run a simulation starting from the default single-instance adapter.
 
@@ -460,7 +460,7 @@ def run_simulation(self, simulation_name: str):
         adapter = get_simulation_adapter(
             simulation.simulator, comm=self._comm.get_communicator()
         )
-        return adapter.simulate(simulation)[0]
+        return adapter.simulate(simulation, filename=output_filename)[0]
 
     def get_simulation(self, sim_name: str) -> Simulation:
         """

packages/bsb-core/bsb/simulation/adapter.py

@@ -66,7 +66,7 @@ def use_bar(self):
 
 
 class SimulationData:
-    def __init__(self, simulation: "Simulation", result=None):
+    def __init__(self, simulation: "Simulation", result=None, filename=None):
         self.chunks = None
         self.populations = dict()
         self.placement: dict[CellModel, PlacementSet] = {
@@ -75,7 +75,7 @@ def __init__(self, simulation: "Simulation", result=None):
         self.connections = dict()
         self.devices = dict()
         if result is None:
-            result = SimulationResult(simulation)
+            result = SimulationResult(simulation, filename=filename)
         self.result: SimulationResult = result
 
 
@@ -92,7 +92,7 @@ def __init__(self, comm=None):
         self._duration = None
         self.current_checkpoint = 0
 
-    def simulate(self, *simulations, post_prepare=None):
+    def simulate(self, *simulations, post_prepare=None, filename=None):
         """
         Simulate the given simulations.
 
@@ -113,7 +113,7 @@ def simulate(self, *simulations, post_prepare=None):
                 self._controllers.append(listener)
 
             for simulation in simulations:
-                data = self.prepare(simulation)
+                data = self.prepare(simulation, filename)
                 alldata.append(data)
                 for hook in simulation.post_prepare:
                     hook(self, simulation, data)
@@ -123,7 +123,7 @@ def simulate(self, *simulations, post_prepare=None):
             return self.collect(results)
 
     @abc.abstractmethod
-    def prepare(self, simulation):  # pragma: nocover
+    def prepare(self, simulation, filename=None):  # pragma: nocover
         """
         Reset the simulation backend and prepare for the given simulation.
 

packages/bsb-core/bsb/simulation/results.py

@@ -9,22 +9,37 @@
 
 
 class SimulationResult:
-    def __init__(self, simulation):
-        from neo import Block
+    def __init__(self, simulation, filename=None):
+        from neo import Block, io
 
         tree = simulation.__tree__()
         with contextlib.suppress(KeyError):
             del tree["post_prepare"]
-        self.block = Block(name=simulation.name, config=tree)
+        if filename:
+            self.filename = filename
+            self.name = simulation.name
+            io = io.NixIO(filename, mode="rw")
+            io.write(Block(name=self.name, nix_name=self.name, config=tree))
+            for i, nixblock in enumerate(io.nix_file.blocks):
+                if self.name == nixblock.name:
+                    self.block_id = i
+            io.close()
+        else:
+            self.block = Block(
+                name=simulation.name, nix_name=simulation.name, config=tree
+            )
+
         self.recorders = []
 
     @property
-    def spiketrains(self):
-        return self.block.segments[0].spiketrains
+    def analogsignals(self):
+        if hasattr(self, "block"):
+            return self.block.segments[0].analogsignals
 
     @property
-    def analogsignals(self):
-        return self.block.segments[0].analogsignals
+    def spiketrains(self):
+        if hasattr(self, "block"):
+            return self.block.segments[0].spiketrains
 
     def add(self, recorder):
         self.recorders.append(recorder)
@@ -36,21 +51,28 @@ def create_recorder(self, flush: typing.Callable[["neo.core.Segment"], None]):
         return recorder
 
     def flush(self):
-        from neo import Segment
+        from neo import Segment, io
 
         segment = Segment()
-        self.block.segments.append(segment)
         for recorder in self.recorders:
             try:
                 recorder.flush(segment)
             except Exception:
                 traceback.print_exc()
                 warn("Recorder errored out!")
+        if hasattr(self, "filename"):
+            io = io.NixIO(self.filename, mode="rw")
+            block = io.nix_file.blocks[self.block_id]
+            io._write_segment(segment, block)
+            io.close()
+        else:
+            self.block.segments.append(segment)
 
     def write(self, filename, mode):
         from neo import io
 
-        io.NixIO(filename, mode=mode).write(self.block)
+        if hasattr(self, "block"):
+            io.NixIO(filename, mode=mode).write(self.block)
 
 
 class SimulationRecorder:

packages/bsb-nest/bsb_nest/adapter.py

@@ -51,14 +51,16 @@ def __init__(self, comm=None):
         self.loaded_modules = set()
         self._prev_chkpoint = 0
 
-    def simulate(self, *simulations, post_prepare=None):
+    def simulate(self, *simulations, post_prepare=None, filename=None):
         try:
             self.reset_kernel()
-            return super().simulate(*simulations, post_prepare=post_prepare)
+            return super().simulate(
+                *simulations, post_prepare=post_prepare, filename=filename
+            )
         finally:
             self.reset_kernel()
 
-    def prepare(self, simulation):
+    def prepare(self, simulation, filename=None):
         """
         Prepare the simulation environment in NEST.
 
@@ -80,7 +82,7 @@ def prepare(self, simulation):
         :rtype: bsb.simulation.adapter.SimulationData
         """
         self.simdata[simulation] = SimulationData(
-            simulation, result=NestResult(simulation)
+            simulation, result=NestResult(simulation, filename)
         )
         try:
             report("Installing  NEST modules...", level=2)

packages/bsb-neuron/bsb_neuron/adapter.py

@@ -70,7 +70,7 @@ def engine(self):
 
         return engine
 
-    def prepare(self, simulation):
+    def prepare(self, simulation, filename=None):
         """
         Prepare the simulation environment and data structures for running a NEURON
         simulation.
@@ -90,7 +90,8 @@ def prepare(self, simulation):
         """
 
         self.simdata[simulation] = NeuronSimulationData(
-            simulation, result=NeuronResult(simulation)
+            simulation,
+            result=NeuronResult(simulation, filename=filename),
         )
         try:
             report("Preparing simulation", level=2)