diff --git a/Dockerfile-brian2 b/Dockerfile-brian2 index 5aa3b9c..ff071ee 100644 --- a/Dockerfile-brian2 +++ b/Dockerfile-brian2 @@ -1,8 +1,8 @@ # Base OS FROM ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:latest -ARG VERSION=0.0.15 -ARG SIMULATOR_VERSION="2.5.0.1" +ARG VERSION=0.0.16 +ARG SIMULATOR_VERSION="2.5.0.3" # metadata LABEL \ diff --git a/Dockerfile-netpyne b/Dockerfile-netpyne index acfdfa5..ca6b713 100644 --- a/Dockerfile-netpyne +++ b/Dockerfile-netpyne @@ -1,7 +1,7 @@ # Base OS FROM ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:latest -ARG VERSION=0.0.15 +ARG VERSION=0.0.16 ARG SIMULATOR_VERSION="1.0.0.2" # metadata diff --git a/Dockerfile-neuron b/Dockerfile-neuron index 8e40a9a..28f47de 100644 --- a/Dockerfile-neuron +++ b/Dockerfile-neuron @@ -1,8 +1,8 @@ # Base OS FROM ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:latest -ARG VERSION=0.0.15 -ARG SIMULATOR_VERSION="8.0.0" +ARG VERSION=0.0.16 +ARG SIMULATOR_VERSION="8.0.2" # metadata LABEL \ diff --git a/Dockerfile-pyneuroml b/Dockerfile-pyneuroml index 4432190..40e2e6c 100644 --- a/Dockerfile-pyneuroml +++ b/Dockerfile-pyneuroml @@ -1,8 +1,8 @@ # Base OS FROM python:3.9-slim-buster -ARG VERSION=0.0.15 -ARG SIMULATOR_VERSION="0.5.18" +ARG VERSION=0.0.16 +ARG SIMULATOR_VERSION="0.5.20" # metadata LABEL \ diff --git a/biosimulators-brian2.json b/biosimulators-brian2.json index 7975129..fb14f13 100644 --- a/biosimulators-brian2.json +++ b/biosimulators-brian2.json @@ -1,14 +1,14 @@ { "id": "brian2", "name": "Brian 2", - "version": "2.5.0.1", + "version": "2.5.0.3", "description": "Clock-driven simulator for spiking neural networks", "urls": [{ "type": "Home page", "url": "https://briansimulator.org" }], "image": { - "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.5.0.1", + "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/brian2:2.5.0.3", "format": { "namespace": "EDAM", "id": "format_3973", diff --git a/biosimulators-neuron.json b/biosimulators-neuron.json index af9eb34..3000470 100644 --- a/biosimulators-neuron.json +++ b/biosimulators-neuron.json @@ -1,7 +1,7 @@ { "id": "neuron", "name": "NEURON", - "version": "8.0.0", + "version": "8.0.2", "description": "Empirically-based simulator for modeling neurons and networks of neurons.", "urls": [ { @@ -10,7 +10,7 @@ } ], "image": { - "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0", + "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2", "format": { "namespace": "EDAM", "id": "format_3973", diff --git a/biosimulators-pyneuroml.json b/biosimulators-pyneuroml.json index deb4c19..4259e87 100644 --- a/biosimulators-pyneuroml.json +++ b/biosimulators-pyneuroml.json @@ -1,7 +1,7 @@ { "id": "pyneuroml", "name": "pyNeuroML", - "version": "0.5.18", + "version": "0.5.20", "description": "Python package for reading, writing, simulating and analysing NeuroML2/LEMS models.", "urls": [ { @@ -10,7 +10,7 @@ } ], "image": { - "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:0.5.18", + "url": "ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:0.5.20", "format": { "namespace": "EDAM", "id": "format_3973", diff --git a/biosimulators_pyneuroml/_version.py b/biosimulators_pyneuroml/_version.py index 8ecd910..19c6940 100644 --- a/biosimulators_pyneuroml/_version.py +++ b/biosimulators_pyneuroml/_version.py @@ -1 +1 @@ -__version__ = '0.0.15' +__version__ = '0.0.16' diff --git a/biosimulators_pyneuroml/utils.py b/biosimulators_pyneuroml/utils.py index 2325f30..09509a2 100644 --- a/biosimulators_pyneuroml/utils.py +++ b/biosimulators_pyneuroml/utils.py @@ -142,7 +142,7 @@ def set_sim_in_lems_xml(simulation_xml, task, variables, simulator=Simulator.pyn simulation = task.simulation # modify simulation - if simulator in [Simulator.brian2, Simulator.netpyne]: + if simulator in [Simulator.netpyne]: length = simulation.output_end_time + (simulation.output_end_time - simulation.output_start_time) * 1 / simulation.number_of_steps steps = (simulation.output_end_time - simulation.output_start_time) / simulation.number_of_steps else: @@ -421,10 +421,7 @@ def read_lems_output_files(output_file_configs, output_files_dirname='.', simula :obj:`dict` of :obj:`str` => :obj:`pandas.DataFrame`: dictionary that maps the id of each output file to a Pandas data frame with its value """ - if simulator == Simulator.brian2: - sep = ' ' - else: - sep = '\t' + sep = '\t' results = {} for output_file_config in output_file_configs: diff --git a/requirements.txt b/requirements.txt index 2fdf1c1..3cb5cb5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,7 @@ biosimulators_utils[neuroml,lems,logging] >= 0.1.147 kisao lxml +netpyne <= 1.0.0.2 numpy psutil -pyneuroml >= 0.5.18, < 0.5.19 +pyneuroml >= 0.5.20 diff --git a/tests/test_core_main.py b/tests/test_core_main.py index e34bff7..cdc26d3 100644 --- a/tests/test_core_main.py +++ b/tests/test_core_main.py @@ -258,7 +258,10 @@ def _build_combine_archive(self, algorithm=None): def _assert_variable_results(self, task, variables, results): sim = task.simulation self.assertTrue(set(results.keys()), set([var.id for var in variables])) - numpy.testing.assert_allclose(results['time'], numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1)) + numpy.testing.assert_allclose( + results['time'], + numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1) + ) for result in results.values(): self.assertEqual(result.shape, (sim.number_of_points + 1,)) self.assertFalse(numpy.any(numpy.isnan(result)))