From b9e2f3839b6f5cee6c05f1504692801b203c58c6 Mon Sep 17 00:00:00 2001 From: Robin De Schepper Date: Tue, 13 Feb 2024 16:08:44 +0100 Subject: [PATCH] fix ci --- .github/workflows/main.yaml | 6 +++--- .pre-commit-config.yaml | 2 +- bsb_neuron/__init__.py | 3 ++- bsb_neuron/devices/__init__.py | 6 +++--- bsb_neuron/devices/current_clamp.py | 3 ++- bsb_neuron/devices/ion_recorder.py | 7 +++++-- bsb_neuron/devices/spike_generator.py | 1 + bsb_neuron/devices/synapse_recorder.py | 3 ++- bsb_neuron/devices/voltage_recorder.py | 5 +++-- bsb_neuron/simulation.py | 1 + pyproject.toml | 2 +- 11 files changed, 24 insertions(+), 15 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index dd20ee2..04ecad1 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -8,12 +8,12 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11"] steps: - - uses: actions/checkout@v3.5.0 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4.3.0 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 33716ff..748ece2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/psf/black-pre-commit-mirror - rev: 23.11.0 + rev: 24.1.1 hooks: - id: black - repo: https://github.com/pycqa/isort diff --git a/bsb_neuron/__init__.py b/bsb_neuron/__init__.py index 301a458..ddf8f7b 100644 --- a/bsb_neuron/__init__.py +++ b/bsb_neuron/__init__.py @@ -3,9 +3,10 @@ """ from bsb.simulation import SimulationBackendPlugin + +from . import devices from .adapter import NeuronAdapter from .simulation import NeuronSimulation -from . import devices __version__ = "0.0.0b2" __plugin__ = SimulationBackendPlugin(Simulation=NeuronSimulation, Adapter=NeuronAdapter) diff --git a/bsb_neuron/devices/__init__.py b/bsb_neuron/devices/__init__.py index 9301027..ce2852e 100644 --- a/bsb_neuron/devices/__init__.py +++ b/bsb_neuron/devices/__init__.py @@ -1,6 +1,6 @@ -from .spike_generator import SpikeGenerator from .current_clamp import CurrentClamp +from .ion_recorder import IonRecorder +from .spike_generator import SpikeGenerator +from .synapse_recorder import SynapseRecorder from .voltage_clamp import VoltageClamp from .voltage_recorder import VoltageRecorder -from .synapse_recorder import SynapseRecorder -from .ion_recorder import IonRecorder diff --git a/bsb_neuron/devices/current_clamp.py b/bsb_neuron/devices/current_clamp.py index c71b342..3cd0bf6 100644 --- a/bsb_neuron/devices/current_clamp.py +++ b/bsb_neuron/devices/current_clamp.py @@ -1,7 +1,8 @@ from bsb import config +from bsb.reporting import warn from bsb.simulation.targetting import LocationTargetting + from ..device import NeuronDevice -from bsb.reporting import warn @config.node diff --git a/bsb_neuron/devices/ion_recorder.py b/bsb_neuron/devices/ion_recorder.py index dfddc86..b386581 100644 --- a/bsb_neuron/devices/ion_recorder.py +++ b/bsb_neuron/devices/ion_recorder.py @@ -1,6 +1,7 @@ -from ..device import NeuronDevice import numpy as np +from ..device import NeuronDevice + class IonRecorder(NeuronDevice): defaults = { @@ -60,5 +61,7 @@ class IonicCurrentRecorder(_IonicRecorder, slug="current", record=_record_i): pass -class IonicConcentrationRecorder(_IonicRecorder, slug="concentration", record=_record_c): +class IonicConcentrationRecorder( + _IonicRecorder, slug="concentration", record=_record_c +): pass diff --git a/bsb_neuron/devices/spike_generator.py b/bsb_neuron/devices/spike_generator.py index 024a249..2335ab9 100644 --- a/bsb_neuron/devices/spike_generator.py +++ b/bsb_neuron/devices/spike_generator.py @@ -1,6 +1,7 @@ from bsb import config from bsb.config import types from bsb.simulation.targetting import LocationTargetting + from ..device import NeuronDevice diff --git a/bsb_neuron/devices/synapse_recorder.py b/bsb_neuron/devices/synapse_recorder.py index 17ae983..1d5b40c 100644 --- a/bsb_neuron/devices/synapse_recorder.py +++ b/bsb_neuron/devices/synapse_recorder.py @@ -1,5 +1,6 @@ -from bsb.simulation.targetting import LocationTargetting from bsb import config +from bsb.simulation.targetting import LocationTargetting + from ..device import NeuronDevice diff --git a/bsb_neuron/devices/voltage_recorder.py b/bsb_neuron/devices/voltage_recorder.py index fa4074f..c716f12 100644 --- a/bsb_neuron/devices/voltage_recorder.py +++ b/bsb_neuron/devices/voltage_recorder.py @@ -1,6 +1,7 @@ -from ..device import NeuronDevice -from bsb.simulation.targetting import LocationTargetting from bsb import config +from bsb.simulation.targetting import LocationTargetting + +from ..device import NeuronDevice @config.node diff --git a/bsb_neuron/simulation.py b/bsb_neuron/simulation.py index 02c067d..953b094 100644 --- a/bsb_neuron/simulation.py +++ b/bsb_neuron/simulation.py @@ -1,6 +1,7 @@ from bsb import config from bsb.config import types from bsb.simulation.simulation import Simulation + from .cell import NeuronCell from .connection import NeuronConnection from .device import NeuronDevice diff --git a/pyproject.toml b/pyproject.toml index 375a11b..df62530 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ dynamic = ["version", "description"] dependencies = [ "bsb-core>=4.0.0b0,<=4.0.0b9999", "nrn-patch>=4.0.0b3,<=4.0.0b9999", - "arborize[neuron]>=4.0.0b1,<=4.0.0b9999" + "arborize[neuron]>=4.0.0b3,<=4.0.0b9999" ] [project.entry-points."bsb.simulation_backends"]