bsb-nest 0.0.0b0__tar.gz → 0.0.0b2__tar.gz

bsb_nest-0.0.0b2/PKG-INFO

@@ -0,0 +1,23 @@
+Metadata-Version: 2.1
+Name: bsb-nest
+Version: 0.0.0b2
+Summary: NEST simulation adapter for the BSB framework.
+Author-email: Robin De Schepper <robingilbert.deschepper@unipv.it>
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Requires-Dist: bsb-core>=4.0.0b4,<=4.0.0b9999
+Requires-Dist: pre-commit~=3.5 ; extra == "dev"
+Requires-Dist: black~=24.1.1 ; extra == "dev"
+Requires-Dist: isort~=5.12 ; extra == "dev"
+Requires-Dist: bump-my-version~=0.18 ; extra == "dev"
+Requires-Dist: bsb-core[parallel] ; extra == "parallel"
+Requires-Dist: bsb-test>=0.0.0b9,<=0.0.0b9999 ; extra == "test"
+Requires-Dist: coverage~=7.0 ; extra == "test"
+Requires-Dist: bsb-hdf5>=1.0.0b0 ; extra == "test"
+Requires-Dist: bsb-arbor==0.0.0b1 ; extra == "test"
+Provides-Extra: dev
+Provides-Extra: parallel
+Provides-Extra: test
+
+# bsb-nest
+

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/__init__.py

@@ -2,11 +2,11 @@
 NEST simulation adapter for the BSB framework.
 """
 
-from bsb.simulation import SimulationBackendPlugin
+from bsb import SimulationBackendPlugin
+
+from . import devices
 from .adapter import NestAdapter
 from .simulation import NestSimulation
-from . import devices
-
 
 __plugin__ = SimulationBackendPlugin(Simulation=NestSimulation, Adapter=NestAdapter)
-__version__ = "0.0.0b0"
+__version__ = "0.0.0-b2"

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/adapter.py

@@ -1,31 +1,30 @@
 import sys
-from neo import SpikeTrain
 import typing
-import time
-import functools
-from tqdm import tqdm
 
-from bsb.simulation.adapter import SimulatorAdapter, SimulationData
-from bsb.simulation.results import SimulationResult
-from bsb.reporting import report, warn
-from bsb.exceptions import (
-    KernelWarning,
-    NestModuleError,
-    NestModelError,
-    NestConnectError,
+import nest
+from bsb import (
+    MPI,
+    AdapterError,
+    AdapterProgress,
+    SimulationData,
+    SimulationResult,
+    SimulatorAdapter,
+    report,
+    warn,
 )
-from bsb.services import MPI
+from neo import SpikeTrain
+from tqdm import tqdm
+
+from .exceptions import NestConnectError, NestModelError, NestModuleError
 
 if typing.TYPE_CHECKING:
-    from bsb.simulation import Simulation
+    from bsb import Simulation
 
 
 class NestResult(SimulationResult):
     def record(self, nc, **annotations):
-        import bsb_nest
-
-        recorder = bsb_nest.Create("spike_recorder", params={"record_to": "memory"})
-        bsb_nest.Connect(nc, recorder)
+        recorder = nest.Create("spike_recorder", params={"record_to": "memory"})
+        nest.Connect(nc, recorder)
 
         def flush(segment):
             events = recorder.events[0]
@@ -34,7 +33,7 @@ class NestResult(SimulationResult):
                 SpikeTrain(
                     events["times"],
                     waveforms=events["senders"],
-                    t_stop=bsb_nest.biological_time,
+                    t_stop=nest.biological_time,
                     units="ms",
                     **annotations,
                 )
@@ -48,16 +47,6 @@ class NestAdapter(SimulatorAdapter):
         self.simdata = dict()
         self.loaded_modules = set()
 
-    @property
-    @functools.cache
-    def nest(self):
-        report("Importing  NEST...", level=2)
-        import bsb_nest
-
-        self.check_comm()
-
-        return bsb_nest
-
     def simulate(self, simulation):
         try:
             self.reset_kernel()
@@ -85,32 +74,35 @@ class NestAdapter(SimulatorAdapter):
             raise
 
     def reset_kernel(self):
-        self.nest.ResetKernel()
+        nest.ResetKernel()
         # Reset which modules we should consider explicitly loaded by the user
         # to appropriately warn them when they load them twice.
         self.loaded_modules = set()
 
-    def run(self, simulation):
-        if simulation not in self.simdata:
-            raise RuntimeError("Can't run unprepared simulation")
+    def run(self, *simulations, comm=None):
+        unprepared = [sim for sim in simulations if sim not in self.simdata]
+        if unprepared:
+            raise AdapterError(f"Unprepared for simulations: {', '.join(unprepared)}")
         report("Simulating...", level=2)
-        tick = time.time()
-        simulation.start_progress(simulation.duration)
+        duration = max(sim.duration for sim in simulations)
+        progress = AdapterProgress(duration)
         try:
-            with self.nest.RunManager():
-                for oi, i in simulation.step_progress(simulation.duration, step=1):
-                    self.nest.Run(i - oi)
-                    simulation.progress(i)
+            with nest.RunManager():
+                for oi, i in progress.steps(step=1):
+                    nest.Run(i - oi)
+                    progress.tick(i)
         finally:
-            result = self.simdata[simulation].result
-            del self.simdata[simulation]
-        report(f"Simulation done. {time.time() - tick:.2f}s elapsed.", level=2)
-        return result
+            results = [self.simdata[sim].result for sim in simulations]
+            for sim in simulations:
+                del self.simdata[sim]
+        progress.complete()
+        report(f"Simulation done.", level=2)
+        return results
 
     def load_modules(self, simulation):
         for module in simulation.modules:
             try:
-                self.nest.Install(module)
+                nest.Install(module)
                 self.loaded_modules.add(module)
             except Exception as e:
                 if e.errorname == "DynamicModuleManagementError":
@@ -162,10 +154,10 @@ class NestAdapter(SimulatorAdapter):
             except KeyError:
                 raise NestModelError(f"No model found for {cs.post_type}")
             try:
-                simdata.connections[
-                    connection_model
-                ] = connection_model.create_connections(
-                    simdata, pre_nodes, post_nodes, cs
+                simdata.connections[connection_model] = (
+                    connection_model.create_connections(
+                        simdata, pre_nodes, post_nodes, cs
+                    )
                 )
             except Exception as e:
                 raise NestConnectError(f"{connection_model} error during connect.")
@@ -176,15 +168,13 @@ class NestAdapter(SimulatorAdapter):
             device_model.implement(self, simulation, simdata)
 
     def set_settings(self, simulation: "Simulation"):
-        self.nest.set_verbosity(simulation.verbosity)
-        self.nest.resolution = simulation.resolution
-        self.nest.overwrite_files = True
+        nest.set_verbosity(simulation.verbosity)
+        nest.resolution = simulation.resolution
+        nest.overwrite_files = True
 
     def check_comm(self):
-        import bsb_nest
-
-        if bsb_nest.NumProcesses() != MPI.get_size():
+        if nest.NumProcesses() != MPI.get_size():
             raise RuntimeError(
-                f"NEST is managing {bsb_nest.NumProcesses()} processes, but {MPI.get_size()}"
+                f"NEST is managing {nest.NumProcesses()} processes, but {MPI.get_size()}"
                 " were detected. Please check your MPI setup."
             )

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/cell.py

@@ -1,6 +1,5 @@
-from bsb import config
-from bsb.config import types
-from bsb.simulation.cell import CellModel
+import nest
+from bsb import CellModel, config, types
 
 
 @config.node
@@ -9,10 +8,8 @@ class NestCell(CellModel):
     constants = config.dict(type=types.any_())
 
     def create_population(self, simdata):
-        import bsb_nest
-
         n = len(simdata.placement[self])
-        population = bsb_nest.Create(self.model, n) if n else bsb_nest.NodeCollection([])
+        population = nest.Create(self.model, n) if n else nest.NodeCollection([])
         self.set_constants(population)
         self.set_parameters(population, simdata)
         return population

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/connection.py

@@ -1,15 +1,13 @@
 import functools
 import sys
 
+import nest
 import numpy as np
 import psutil
+from bsb import MPI, ConnectionModel, compose_nodes, config, types
 from tqdm import tqdm
 
-from bsb import config
-from bsb.config import types, compose_nodes
-from bsb.services import MPI
-from bsb.simulation.connection import ConnectionModel
-from bsb.exceptions import NestConnectError
+from .exceptions import NestConnectError
 
 
 @config.node
@@ -46,9 +44,7 @@ class LazySynapseCollection:
 
     @functools.cached_property
     def collection(self):
-        import bsb_nest
-
-        return bsb_nest.GetConnections(self._pre, self._post)
+        return nest.GetConnections(self._pre, self._post)
 
 
 @config.dynamic(attr_name="model_strategy", required=False)
@@ -57,15 +53,15 @@ class NestConnection(compose_nodes(NestConnectionSettings, ConnectionModel)):
     synapse = config.attr(type=NestSynapseSettings, required=True)
 
     def create_connections(self, simdata, pre_nodes, post_nodes, cs):
-        import bsb_nest
+        import nest
 
         syn_spec = self.get_syn_spec()
-        if syn_spec["synapse_model"] not in bsb_nest.synapse_models:
+        if syn_spec["synapse_model"] not in nest.Models(mtype="synapses"):
             raise NestConnectError(
                 f"Unknown synapse model '{syn_spec['synapse_model']}'."
             )
         if self.rule is not None:
-            bsb_nest.Connect(pre_nodes, post_nodes, self.get_conn_spec(), syn_spec)
+            nest.Connect(pre_nodes, post_nodes, self.get_conn_spec(), syn_spec)
         else:
             MPI.barrier()
             for pre_locs, post_locs in self.predict_mem_iterator(
@@ -83,7 +79,7 @@ class NestConnection(compose_nodes(NestConnectionSettings, ConnectionModel)):
                 bw = syn_spec["weight"]
                 ssw["weight"] = [bw * m for m in multiplicity]
                 ssw["delay"] = [syn_spec["delay"]] * len(ssw["weight"])
-                bsb_nest.Connect(
+                nest.Connect(
                     [prel[x] for x in cell_pairs[:, 0]],
                     [postl[x] for x in cell_pairs[:, 1]],
                     "one_to_one",
@@ -96,7 +92,9 @@ class NestConnection(compose_nodes(NestConnectionSettings, ConnectionModel)):
     def predict_mem_iterator(self, pre_nodes, post_nodes, cs):
         avmem = psutil.virtual_memory().available
         predicted_all_mem = (
-            len(pre_nodes) * 8 * 2 + len(post_nodes) * 8 * 2 + len(cs) * 6 * 8 * (16 + 2)
+            len(pre_nodes) * 8 * 2
+            + len(post_nodes) * 8 * 2
+            + len(cs) * 6 * 8 * (16 + 2)
         ) * MPI.get_size()
         predicted_local_mem = predicted_all_mem / len(cs.get_local_chunks("out"))
         if predicted_local_mem > avmem / 2:

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/device.py

@@ -1,9 +1,7 @@
 import warnings
 
-from bsb import config
-from bsb.config import types, refs
-from bsb.simulation.device import DeviceModel
-from bsb.simulation.targetting import Targetting
+import nest
+from bsb import DeviceModel, Targetting, config, refs, types
 
 
 @config.node
@@ -30,18 +28,17 @@ class NestDevice(DeviceModel):
             node_collector = (
                 simdata.populations[model][targets]
                 for model, targets in simdata.populations.items()
-                if not self.targetting.cell_models or model in self.targetting.cell_models
+                if not self.targetting.cell_models
+                or model in self.targetting.cell_models
             )
-        return sum(node_collector, start=adapter.nest.NodeCollection())
+        return sum(node_collector, start=nest.NodeCollection())
 
     def connect_to_nodes(self, device, nodes):
-        import bsb_nest
-
         if len(nodes) == 0:
             warnings.warn(f"{self.name} has no targets")
         else:
             try:
-                bsb_nest.Connect(
+                nest.Connect(
                     device,
                     nodes,
                     syn_spec={"weight": self.weight, "delay": self.delay},
@@ -49,7 +46,7 @@ class NestDevice(DeviceModel):
             except Exception as e:
                 if "does not send output" not in str(e):
                     raise
-                bsb_nest.Connect(
+                nest.Connect(
                     nodes,
                     device,
                     syn_spec={"weight": self.weight, "delay": self.delay},
@@ -66,7 +63,7 @@ class ExtNestDevice(NestDevice, classmap_entry="external"):
     constants = config.dict(type=types.or_(types.number(), str))
 
     def implement(self, adapter, simulation, simdata):
-        simdata.devices[self] = device = adapter.nest.Create(
+        simdata.devices[self] = device = nest.Create(
             self.nest_model, params=self.constants
         )
         nodes = self.get_target_nodes(adapter, simdata)

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/devices/__init__.py

@@ -1,2 +1,2 @@
-from .spike_recorder import SpikeRecorder
 from .poisson_generator import PoissonGenerator
+from .spike_recorder import SpikeRecorder

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/devices/poisson_generator.py

@@ -1,6 +1,8 @@
+import nest
+from bsb import config
 from neo import SpikeTrain
+
 from ..device import NestDevice
-from bsb import config
 
 
 @config.node
@@ -8,14 +10,12 @@ class PoissonGenerator(NestDevice, classmap_entry="poisson_generator"):
     rate = config.attr(type=float, required=True)
 
     def implement(self, adapter, simulation, simdata):
-        import bsb_nest
-
         nodes = self.get_target_nodes(adapter, simulation, simdata)
         device = self.register_device(
-            simdata, bsb_nest.Create("poisson_generator", params={"rate": self.rate})
+            simdata, nest.Create("poisson_generator", params={"rate": self.rate})
         )
-        sr = bsb_nest.Create("spike_recorder")
-        bsb_nest.Connect(device, sr)
+        sr = nest.Create("spike_recorder")
+        nest.Connect(device, sr)
         self.connect_to_nodes(device, nodes)
 
         def recorder(segment):

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/devices/spike_recorder.py

@@ -1,7 +1,8 @@
+import nest
+from bsb import config
 from neo import SpikeTrain
 
 from ..device import NestDevice
-from bsb import config
 
 
 @config.node
@@ -9,10 +10,9 @@ class SpikeRecorder(NestDevice, classmap_entry="spike_recorder"):
     weight = config.provide(1)
 
     def implement(self, adapter, simulation, simdata):
-        import bsb_nest
 
         nodes = self.get_target_nodes(adapter, simulation, simdata)
-        device = self.register_device(simdata, bsb_nest.Create("spike_recorder"))
+        device = self.register_device(simdata, nest.Create("spike_recorder"))
         self.connect_to_nodes(device, nodes)
 
         def recorder(segment):

bsb_nest-0.0.0b2/bsb_nest/exceptions.py

@@ -0,0 +1,18 @@
+class KernelWarning(Warning):
+    pass
+
+
+class NestError(Exception):
+    pass
+
+class NestKernelError(NestError):
+    pass
+
+class NestModuleError(NestKernelError):
+    pass
+
+class NestModelError(NestError):
+    pass
+
+class NestConnectError(NestError):
+    pass

{bsb-nest-0.0.0b0 → bsb_nest-0.0.0b2}/bsb_nest/simulation.py

@@ -1,6 +1,5 @@
-from bsb import config
-from bsb.config import types
-from bsb.simulation.simulation import Simulation
+from bsb import Simulation, config, types
+
 from .cell import NestCell
 from .connection import NestConnection
 from .device import NestDevice
@@ -20,10 +19,3 @@ class NestSimulation(Simulation):
     cell_models = config.dict(type=NestCell, required=True)
     connection_models = config.dict(type=NestConnection, required=True)
     devices = config.dict(type=NestDevice, required=True)
-
-    def boot(self):
-        self.is_prepared = False
-        self.suffix = ""
-        self.multi = False
-        self.has_lock = False
-        self.global_identifier_map = {}

bsb_nest-0.0.0b2/pyproject.toml

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "bsb-nest"
+authors = [{name = "Robin De Schepper", email = "robingilbert.deschepper@unipv.it"}]
+readme = "README.md"
+license = {file = "LICENSE"}
+classifiers = ["License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)"]
+dynamic = ["version", "description"]
+dependencies = ["bsb-core>=4.0.0b4,<=4.0.0b9999"]
+
+[tool.flit.module]
+name = "bsb_nest"
+
+[project.entry-points."bsb.simulation_backends"]
+nest = "bsb_nest"
+
+[project.optional-dependencies]
+parallel = ["bsb-core[parallel]"]
+test = [
+    "bsb-test>=0.0.0b9,<=0.0.0b9999",
+    "coverage~=7.0",
+    "bsb-hdf5>=1.0.0b0",
+    # Required to load the Brunel config file
+    "bsb-arbor==0.0.0b1"
+]
+dev = [
+    "pre-commit~=3.5",
+    "black~=24.1.1",
+    "isort~=5.12",
+    "bump-my-version~=0.18"
+]
+
+[tool.black]
+line-length = 90
+
+[tool.isort]
+profile = "black"
+known_third_party = ["nest"]
+
+[tool.bumpversion]
+current_version = "0.0.0-b2"
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash seperator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = "--no-verify"
+
+[tool.bumpversion.parts.pre_l]
+values = ["dev", "a", "b", "rc", "final"]
+optional_value = "final"
+
+[[tool.bumpversion.files]]
+filename = "bsb_nest/__init__.py"

bsb-nest-0.0.0b0/.gitignore

@@ -1,126 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-.idea/

bsb-nest-0.0.0b0/PKG-INFO

@@ -1,11 +0,0 @@
-Metadata-Version: 2.1
-Name: bsb-nest
-Version: 0.0.0b0
-Summary: NEST simulation adapter for the BSB framework.
-Author-email: Robin De Schepper <robingilbert.deschepper@unipv.it>
-Description-Content-Type: text/markdown
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Requires-Dist: bsb-core>=4.0.0b0,<=4.0.0b9999
-
-# bsb-nest
-

bsb-nest-0.0.0b0/pyproject.toml

@@ -1,18 +0,0 @@
-[build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
-
-[project]
-name = "bsb-nest"
-authors = [{name = "Robin De Schepper", email = "robingilbert.deschepper@unipv.it"}]
-readme = "README.md"
-license = {file = "LICENSE"}
-classifiers = ["License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)"]
-dynamic = ["version", "description"]
-dependencies = ["bsb-core>=4.0.0b0,<=4.0.0b9999"]
-
-[tool.flit.module]
-name = "bsb_nest"
-
-[project.entry-points."bsb.simulation_backends"]
-nest = "bsb_nest"