updated Brian2, NEURON, pyNeuroML

biosimulators · Feb 22, 2022 · 5b7113b · 5b7113b
1 parent 99bf500
commit 5b7113b
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1 +1 @@
-__version__ = '0.0.15'
+__version__ = '0.0.16'
diff --git 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
@@ -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
@@ -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)))