bsb-arbor 6.0.1__tar.gz → 7.0.2__tar.gz

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bsb-arbor
-Version: 6.0.1
+Version: 7.0.2
 Summary: Arbor simulation adapter for the BSB framework.
 Author-email: Robin De Schepper <robin@alexandria.sc>, Dimitri Rodarie <dimitri.rodarie@unipv.it>
 Requires-Python: >=3.10,<4
@@ -8,8 +8,8 @@ Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 License-File: LICENSE
 Requires-Dist: numpy~=1.21
-Requires-Dist: bsb-core~=6.0
-Requires-Dist: arborize~=6.0
+Requires-Dist: bsb-core~=7.0
+Requires-Dist: arborize~=7.0
 Requires-Dist: arbor~=0.10; sys_platform != 'win32'
 
 [![Build Status](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb/actions/workflows/main.yml)

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/adapter.py

@@ -16,7 +16,7 @@ from bsb import (
     warn,
 )
 
-if typing.TYPE_CHECKING:
+if typing.TYPE_CHECKING:  # pragma: nocover
     from .simulation import ArborSimulation
 
 
@@ -69,6 +69,7 @@ class Population:
     This class manages a collection of cells from a specific cell model, handling their
     GID ranges and providing methods to access and manipulate subsets of the population.
     """
+
     def __init__(self, simdata, cell_model, offset):
         """
         Initialize a population of cells.
@@ -203,7 +204,9 @@ class Population:
                 start = i
                 stop = i + 1
             prev = i
+        ranges.append((start, stop))
         pop._ranges = ranges
+
         return pop
 
     def _subpop_one(self, item):
@@ -405,11 +408,13 @@ class ArborAdapter(SimulatorAdapter):
             report("MPI processes:", context.ranks, level=2)
             report("Threads per process:", context.threads, level=2)
             recipe = self.get_recipe(simulation, simdata)
+            self._duration = simulation.duration
             # Gap junctions are required for domain decomposition
             self.domain = arbor.partition_load_balance(recipe, context)
             self.gids = set(it.chain.from_iterable(g.gids for g in self.domain.groups))
             simdata.arbor_sim = arbor.simulation(recipe, context, self.domain)
-            self.prepare_samples(simulation, simdata)
+            self.implement_components(simulation)
+            self.load_controllers(simulation)
             report("prepared simulation", level=1)
             return simdata
         except Exception:
@@ -419,10 +424,6 @@ class ArborAdapter(SimulatorAdapter):
     def get_gid_manager(self, simulation, simdata):
         return GIDManager(simulation, simdata)
 
-    def prepare_samples(self, simulation, simdata):
-        for device in simulation.devices.values():
-            device.prepare_samples(simdata, comm=self.comm)
-
     def run(self, *simulations):
         if len(simulations) != 1:
             raise RuntimeError(
@@ -443,14 +444,19 @@ class ArborAdapter(SimulatorAdapter):
 
             start = time.time()
             report("running simulation", level=1)
-            arbor_sim.run(simulation.duration * U.ms, dt=simulation.resolution * U.ms)
-            report(f"completed simulation. {time.time() - start:.2f}s", level=1)
+
+            for t, checkpoint_controllers in self.get_next_checkpoint():
+                arbor_sim.run(t * U.ms, dt=simulation.resolution * U.ms)
+                self.execute_checkpoints(checkpoint_controllers)
+            report(f"Completed simulation. {time.time() - start:.2f}s", level=1)
             if simulation.profiling and arbor.config()["profiling"]:
                 report("printing profiler summary", level=2)
                 report(arbor.profiler_summary(), level=1)
             return [simdata.result]
         finally:
+            results = [self.simdata[sim].result for sim in simulations]
             del self.simdata[simulation]
+        return results
 
     def get_recipe(self, simulation, simdata=None):
         if simdata is None:
@@ -523,7 +529,7 @@ class ArborAdapter(SimulatorAdapter):
 
 def _all_bools(arr):
     try:
-        return all(isinstance(b, bool) for b in arr)
+        return all(np.issubdtype(type(b), np.bool_) for b in arr)
     except TypeError:
         # Not iterable
         return False
@@ -531,7 +537,7 @@ def _all_bools(arr):
 
 def _all_ints(arr):
     try:
-        return all(isinstance(b, int) for b in arr)
+        return all(np.issubdtype(type(b), np.integer) for b in arr)
     except TypeError:
         # Not iterable
         return False

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/cell.py

@@ -24,23 +24,23 @@ class ArborCell(CellModel):
     """Importable reference to the arborize model describing the cell type."""
 
     @abc.abstractmethod
-    def cache_population_data(self, simdata, ps: PlacementSet):
+    def cache_population_data(self, simdata, ps: PlacementSet):  # pragma: nocover
         pass
 
     @abc.abstractmethod
-    def discard_population_data(self):
+    def discard_population_data(self):  # pragma: nocover
         pass
 
     @abc.abstractmethod
-    def get_prefixed_catalogue(self):
+    def get_prefixed_catalogue(self):  # pragma: nocover
         pass
 
     @abc.abstractmethod
-    def get_cell_kind(self, gid):
+    def get_cell_kind(self, gid):  # pragma: nocover
         pass
 
     @abc.abstractmethod
-    def make_receiver_collection(self):
+    def make_receiver_collection(self):  # pragma: nocover
         pass
 
     def get_description(self, gid):

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/connection.py

@@ -1,6 +1,6 @@
 import arbor
 import tqdm
-from bsb import ConnectionModel, config
+from bsb import ConnectionModel, config, options
 
 
 class Receiver:
@@ -53,7 +53,9 @@ class ArborConnection(ConnectionModel):
             gj_on_gid.setdefault(conn.from_id, []).append(conn)
 
     def create_connections_on(self, conns_on_gid, conns, pop_pre, pop_post):
-        for pre_loc, post_loc in tqdm.tqdm(conns, total=len(conns), desc=self.name):
+        for pre_loc, post_loc in tqdm.tqdm(
+            conns, total=len(conns), desc=self.name, disable=options.verbosity < 2
+        ):
             conns_on_gid[post_loc[0] + pop_post.offset].append(
                 Receiver(self, pre_loc[0] + pop_pre.offset, pre_loc[1:], post_loc[1:])
             )

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/device.py

@@ -24,7 +24,7 @@ class ArborDevice(DeviceModel):
     def register_probe_id(self, gid, tag):
         self._probe_ids.append((gid, tag))
 
-    def prepare_samples(self, simdata, comm):
+    def implement(self, adapter, simulation, simdata):
         self._handles = [
             self.sample(simdata.arbor_sim, probe_id) for probe_id in self._probe_ids
         ]
@@ -42,9 +42,9 @@ class ArborDevice(DeviceModel):
         return dict(zip(attrs, (getattr(self, attr) for attr in attrs), strict=False))
 
     @abc.abstractmethod
-    def implement_probes(self, simdata, target):
+    def implement_probes(self, simdata, target):  # pragma: nocover
         pass
 
     @abc.abstractmethod
-    def implement_generators(self, simdata, target):
+    def implement_generators(self, simdata, target):  # pragma: nocover
         pass

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/devices/probe.py

@@ -16,15 +16,10 @@ class Probe(ArborDevice):
                 f"`{self.probe_type}` is not a valid probe type for `{self.name}`"
             )
 
-    def implement(self, target):
-        probe_args = ("where", "mechanism", "ion", "state")
-        kwargs = dict((k, getattr(self, k)) for k in probe_args if hasattr(self, k))
-        return [getattr(arbor, self.get_probe_name())(**kwargs)]
-
-    def prepare_samples(self, sim, comm):
-        super().prepare_samples(sim, comm)
+    def implement(self, adapter, simulation, simdata):
+        super().implement(adapter, simulation, simdata)
         for probe_id, handle in zip(self._probe_ids, self._handles, strict=False):
-            self.adapter.result.add(ProbeRecorder(self, sim, probe_id, handle))
+            self.adapter.result.add(ProbeRecorder(self, simdata, probe_id, handle))
 
 
 class ProbeRecorder:

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/bsb_arbor/devices/spike_recorder.py

@@ -9,9 +9,9 @@ class SpikeRecorder(ArborDevice, classmap_entry="spike_recorder"):
     def boot(self):
         self._gids = set()
 
-    def prepare_samples(self, simdata, comm):
-        super().prepare_samples(simdata, comm)
-        if not comm.get_rank():
+    def implement(self, adapter, simulation, simdata):
+        super().implement(adapter, simulation, simdata)
+        if not adapter.comm.get_rank():
 
             def record_device_spikes(segment):
                 spiketrain = list()

{bsb_arbor-6.0.1 → bsb_arbor-7.0.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "bsb-arbor"
-version = "6.0.1"
+version = "7.0.2"
 readme = "README.md"
 requires-python = ">=3.10,<4"
 dynamic = [ "description" ]
@@ -15,8 +15,8 @@ classifiers = [
 ]
 dependencies = [
   "numpy~=1.21",
-  "bsb-core~=6.0",
-  "arborize~=6.0",
+  "bsb-core~=7.0",
+  "arborize~=7.0",
   "arbor~=0.10; sys_platform != 'win32'"
 ]
 
@@ -46,7 +46,7 @@ branch = true
 source = [ "bsb_arbor" ]
 
 [tool.coverage.report]
-exclude_lines = [ "if TYPE_CHECKING:" ]
+exclude_lines = [ "if typing.TYPE_CHECKING:", "pragma: nocover" ]
 show_missing = true
 
 [tool.ruff]