add ci, opt out of multisim

.bumpversion.cfg

@@ -0,0 +1,34 @@
+[bumpversion]
+current_version = 0.0.0b0
+files = bsb_arbor/__init__.py
+commit = True
+tag = True
+parse = ^
+	(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
+	((?P<prekind>a|alpha|b|beta|d|dev|rc)
+	(?P<pre>\d+)  # pre-release version num
+	)?
+	(\.(?P<postkind>post)(?P<post>\d+))?  # post-release
+serialize = 
+	{major}.{minor}.{patch}{prekind}{pre}.{postkind}{post}
+	{major}.{minor}.{patch}{prekind}{pre}
+	{major}.{minor}.{patch}{postkind}{post}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:prekind]
+optional_value = _
+values = 
+	_
+	dev
+	d
+	alpha
+	a
+	beta
+	b
+	rc
+
+[bumpversion:part:postkind]
+optional_value = _
+values = 
+	_
+	post

.github/workflows/black.yml

@@ -0,0 +1,15 @@
+name: Black
+
+on: [push, pull_request]
+
+jobs:
+  black:
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: psf/black@stable
+      with:
+        options: "--check --verbose"
+        version: "24.1.1"

.github/workflows/isort.yml

@@ -0,0 +1,20 @@
+name: Run isort
+on:
+  - push
+
+jobs:
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - name: Install apt dependencies
+        # Install `libopenmpi` for mpi4py
+        run: |
+          sudo apt update
+          sudo apt install openmpi-bin libopenmpi-dev
+      # Install dependencies for proper 1st/2nd/3rd party import sorting
+      - run: pip install -e .[parallel]
+      - uses: isort/isort-action@master

.github/workflows/main.yml

@@ -30,9 +30,7 @@ jobs:
       - 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 .
+          pip install -e .[test]
       - name: Run tests & coverage
         run: |
           coverage run -p -m unittest

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.1.1
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)

bsb_arbor/__init__.py

@@ -3,9 +3,10 @@
 """
 
 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"
 __plugin__ = SimulationBackendPlugin(Simulation=ArborSimulation, Adapter=ArborAdapter)

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 @@ def _get_ranges(self, chunks, ps, offset):
         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 @@ def prepare_samples(self, simulation, simdata):
         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 @@ def run(self, simulation):
             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/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/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 @@ def create_connections_from(self, conns_from_gid, conns, pop_pre, pop_post):
 
     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/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/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/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/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/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/simulation.py

@@ -2,6 +2,7 @@
 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

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"]

tests/test_arbor.py

@@ -1,8 +1,9 @@
+import unittest
+
 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.")
@@ -26,8 +27,12 @@ def test_brunel(self):
         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"]
+        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)