bsb-arbor 0.0.0b0__tar.gz → 0.0.0b1__tar.gz

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bsb-arbor
-Version: 0.0.0b0
+Version: 0.0.0b1
 Summary: Arbor simulation adapter for the BSB framework
 Author-email: Robin De Schepper <robingilbert.deschepper@unipv.it>
 Description-Content-Type: text/markdown
@@ -8,7 +8,9 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 or later (G
 Requires-Dist: bsb-core>=4.0.0b0,<=4.0.0b9999
 Requires-Dist: arbor~=0.9
 Requires-Dist: arborize[arbor]>=4.0.0b1
+Requires-Dist: bsb-core[parallel] ; extra == "test"
 Requires-Dist: bsb-test>=0.0.0b0 ; extra == "test"
+Requires-Dist: coverage~=7.0 ; extra == "test"
 Provides-Extra: test
 
 # bsb-arbor

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/__init__.py

@@ -3,9 +3,10 @@ Arbor simulation adapter for the BSB framework
 """
 
 from bsb.simulation import SimulationBackendPlugin
-from .simulation import ArborSimulation
-from .adapter import ArborAdapter
+
 from . import devices
+from .adapter import ArborAdapter
+from .simulation import ArborSimulation
 
-__version__ = "0.0.0b0"
+__version__ = "0.0.0b1"
 __plugin__ = SimulationBackendPlugin(Simulation=ArborSimulation, Adapter=ArborAdapter)

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/adapter.py

@@ -1,14 +1,13 @@
 import itertools
+import itertools as it
+import time
 import typing
 
-from bsb.reporting import report, warn
+import arbor
 from bsb.exceptions import AdapterError, UnknownGIDError
+from bsb.reporting import report, warn
 from bsb.services import MPI
 from bsb.simulation.adapter import SimulationData, SimulatorAdapter
-import itertools as it
-import time
-import arbor
-
 from bsb.storage import Chunk
 
 if typing.TYPE_CHECKING:
@@ -79,7 +78,9 @@ class Population:
         return ranges
 
     def __iter__(self):
-        yield from itertools.chain.from_iterable(range(r[0], r[1]) for r in self._ranges)
+        yield from itertools.chain.from_iterable(
+            range(r[0], r[1]) for r in self._ranges
+        )
 
 
 class GIDManager:
@@ -266,7 +267,12 @@ class ArborAdapter(SimulatorAdapter):
         for device in simulation.devices.values():
             device.prepare_samples(simdata)
 
-    def run(self, simulation):
+    def run(self, *simulations):
+        if len(simulations) != 1:
+            raise RuntimeError(
+                "Can not run multiple simultaneous simulations. Composition not implemented."
+            )
+        simulation = simulations[0]
         try:
             simdata = self.simdata[simulation]
             arbor_sim = simdata.arbor_sim
@@ -285,7 +291,7 @@ class ArborAdapter(SimulatorAdapter):
             if simulation.profiling and arbor.config()["profiling"]:
                 report("printing profiler summary", level=2)
                 report(arbor.profiler_summary(), level=1)
-            return simdata.result
+            return [simdata.result]
         finally:
             del self.simdata[simulation]
 

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/cell.py

@@ -1,11 +1,11 @@
 import abc
 import typing
 
+import arbor
 from bsb import config
 from bsb.config import types
 from bsb.exceptions import ConfigurationError
 from bsb.simulation.cell import CellModel
-import arbor
 
 from .adapter import SingleReceiverCollection
 

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/connection.py

@@ -1,8 +1,7 @@
+import arbor
 import tqdm
-
 from bsb import config
 from bsb.simulation.connection import ConnectionModel
-import arbor
 
 
 class Receiver:
@@ -63,5 +62,7 @@ class ArborConnection(ConnectionModel):
 
     def gap_junction(self, conn):
         l = arbor.cell_local_label(f"gap_{conn.to_compartment.id}")
-        g = arbor.cell_global_label(int(conn.from_id), f"gap_{conn.from_compartment.id}")
+        g = arbor.cell_global_label(
+            int(conn.from_id), f"gap_{conn.from_compartment.id}"
+        )
         return arbor.gap_junction_connection(g, l, self.weight)

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/device.py

@@ -1,12 +1,11 @@
 import abc
 
+import arbor
 from bsb import config
 from bsb.config import types
 from bsb.simulation.device import DeviceModel
 from bsb.simulation.targetting import Targetting
 
-import arbor
-
 
 @config.dynamic(attr_name="device", auto_classmap=True, classmap_entry=None)
 class ArborDevice(DeviceModel):

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/devices/__init__.py

@@ -1,3 +1,3 @@
 from .poisson_generator import PoissonGenerator
-from .spike_recorder import SpikeRecorder
 from .probe import Probe
+from .spike_recorder import SpikeRecorder

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/devices/poisson_generator.py

@@ -1,7 +1,8 @@
+import arbor
 from bsb import config
+
 from ..connection import Receiver
 from ..device import ArborDevice
-import arbor
 
 
 @config.node

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/devices/probe.py

@@ -1,6 +1,7 @@
-from ..device import ArborDevice
-from bsb.exceptions import ConfigurationError
 import arbor
+from bsb.exceptions import ConfigurationError
+
+from ..device import ArborDevice
 
 
 class Probe(ArborDevice):

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/devices/spike_recorder.py

@@ -1,7 +1,7 @@
 import neo
-
 from bsb import config
 from bsb.services import MPI
+
 from ..device import ArborDevice
 
 

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/bsb_arbor/simulation.py

@@ -2,6 +2,7 @@ import psutil
 from bsb import config
 from bsb.config import types
 from bsb.simulation.simulation import Simulation
+
 from .cell import ArborCell
 from .connection import ArborConnection
 from .device import ArborDevice

{bsb_arbor-0.0.0b0 → bsb_arbor-0.0.0b1}/pyproject.toml

@@ -22,4 +22,4 @@ arbor = "bsb_arbor"
 name = "bsb_arbor"
 
 [project.optional-dependencies]
-test = ["bsb-test>=0.0.0b0"]
+test = ["bsb-core[parallel]", "bsb-test>=0.0.0b0", "coverage~=7.0"]

bsb_arbor-0.0.0b0/.github/workflows/main.yml

@@ -1,40 +0,0 @@
-name: Test BSB Arbor adapter
-
-on: [ push, pull_request ]
-
-jobs:
-  build:
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ "3.9", "3.10", "3.11" ]
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install apt dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install openmpi-bin libopenmpi-dev
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-            ${{ runner.os }}-
-      - name: Install dependencies & self
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e . --no-deps
-          pip install -r requirements.txt --prefer-binary
-          pip install -e .
-      - name: Run tests & coverage
-        run: |
-          coverage run -p -m unittest
-          mpiexec -n 2 coverage run -p -m unittest
-          bash <(curl -s https://codecov.io/bash)

bsb_arbor-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_arbor-0.0.0b0/requirements.txt

@@ -1,5 +0,0 @@
-arbor==0.9
-mpi4py==3.1.5
-bsb-core>=4.0.0b0
-bsb-test==0.0.0b2
-coverage==7.3.3

bsb_arbor-0.0.0b0/tests/test_arbor.py

@@ -1,34 +0,0 @@
-from bsb.config import from_file
-from bsb.core import Scaffold
-from bsb.services import MPI
-from bsb_test import RandomStorageFixture, get_config_path
-import unittest
-
-
-@unittest.skipIf(MPI.get_size() > 1, "Skipped during parallel testing.")
-class TestArbor(RandomStorageFixture, unittest.TestCase, engine_name="hdf5"):
-    def test_brunel(self):
-        cfg = from_file(get_config_path("test_brunel_wbsb.json"))
-        simcfg = cfg.simulations.test_arbor
-
-        network = Scaffold(cfg, self.storage)
-        network.compile()
-        result = network.run_simulation("test_arbor")
-
-        spiketrains = result.block.segments[0].spiketrains
-        sr_exc, sr_inh = None, None
-        for st in spiketrains:
-            if st.annotations["device"] == "sr_exc":
-                sr_exc = st
-            elif st.annotations["device"] == "sr_inh":
-                sr_inh = st
-
-        self.assertIsNotNone(sr_exc)
-        self.assertIsNotNone(sr_inh)
-
-        rate_ex = len(sr_exc) / simcfg.duration * 1000.0 / sr_exc.annotations["pop_size"]
-        rate_in = len(sr_inh) / simcfg.duration * 1000.0 / sr_inh.annotations["pop_size"]
-
-        # These are temporary circular values, taken from the output. May be incorrect.
-        self.assertAlmostEqual(rate_in, 34.2, delta=1)
-        self.assertAlmostEqual(rate_ex, 34.2, delta=1)