From 6b8109c431fcfd3a5655cd59e1236e0cfdf90744 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Feb 2024 10:22:19 +0000 Subject: [PATCH 1/5] Regenerated --- examples/LEMS_SimExample3.xml | 2 +- examples/LEMS_SimExample4.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml index da92cef..d5abac4 100644 --- a/examples/LEMS_SimExample3.xml +++ b/examples/LEMS_SimExample3.xml @@ -2,7 +2,7 @@ diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml index 08796f8..683c2b1 100644 --- a/examples/LEMS_SimExample4.xml +++ b/examples/LEMS_SimExample4.xml @@ -2,7 +2,7 @@ From bd191f539bc1fecdbace59b57467dee72dda1470 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Feb 2024 10:30:19 +0000 Subject: [PATCH 2/5] Tested param sweep file --- neuromllite/sweep/ParameterSweep.py | 32 +++++++++++++++-------------- neuromllite/sweep/cleanup.sh | 5 +++++ 2 files changed, 22 insertions(+), 15 deletions(-) create mode 100755 neuromllite/sweep/cleanup.sh diff --git a/neuromllite/sweep/ParameterSweep.py b/neuromllite/sweep/ParameterSweep.py index 52f167a..23cc99e 100644 --- a/neuromllite/sweep/ParameterSweep.py +++ b/neuromllite/sweep/ParameterSweep.py @@ -301,7 +301,7 @@ def _run_all(self): if i % downscale == 0 ] - param_name = self.vary.keys()[0] + param_name = list(self.vary.keys())[0] pval = get_value_in_si(params[param_name]) if self.hm_x == None: self.hm_x = tt @@ -344,7 +344,7 @@ def run(self): z = np.array(self.hm_z) print_v( - "Plotting x: %s->%s (%i), y: %s->%s (%i), z: %s->%s (%i)" + "Plotting x: %s->%s (%i), y: %s->%s (%i), z: %s->%s (%s)" % ( self.hm_x[0], self.hm_x[-1], @@ -354,7 +354,7 @@ def run(self): len(self.hm_y), z.min(), z.max(), - z.size, + z.shape, ) ) @@ -362,6 +362,7 @@ def run(self): # yvals = np.array(self.hm_y) if not self.heatmap_lims: + plot0 = self.hm_ax.pcolormesh( np.array(self.hm_x), np.array(self.hm_y), z, cmap=self.colormap ) @@ -379,7 +380,7 @@ def run(self): # self.hm_ax.set_yticklabels(['ff%s'%i for i in range(len(self.hm_y))]) plt.xlabel("Time (ms)") - plt.ylabel("%s " % self.vary.keys()[0]) + plt.ylabel("%s " % list(self.vary.keys())[0]) plt.xlim([self.hm_x[0], self.hm_x[-1]]) plt.ylim([self.hm_y[0], self.hm_y[-1]]) title = "Values of %s" % self.vary.keys() @@ -585,7 +586,7 @@ def run_once(self, job_dir, **kwargs): if a in network.parameters: print_v(" Setting %s to %s in network..." % (a, kwargs[a])) network.parameters[a] = kwargs[a] - elif a in sim.fields: + elif a in sim.allowed_fields: print_v(" Setting %s to %s in simulator..." % (a, kwargs[a])) setattr(sim, a, kwargs[a]) else: @@ -612,8 +613,8 @@ def run_once(self, job_dir, **kwargs): if "-2d" in sys.argv: fixed = {"dt": 0.025} vary = { - "stim_amp": ["%spA" % (i) for i in xrange(-40, 220, 40)], - "stim_del": ["%sms" % (i) for i in xrange(10, 40, 10)], + "stim_amp": ["%spA" % (i) for i in range(-40, 220, 40)], + "stim_del": ["%sms" % (i) for i in range(10, 40, 10)], } vary = { @@ -622,7 +623,7 @@ def run_once(self, job_dir, **kwargs): } vary = { - "stim_amp": ["%spA" % (i) for i in xrange(-40, 220, 20)], + "stim_amp": ["%spA" % (i) for i in range(-40, 220, 20)], "stim_del": ["%sms" % (i) for i in [10, 20]], } @@ -671,9 +672,9 @@ def run_once(self, job_dir, **kwargs): elif "-hh" in sys.argv: fixed = {"dt": 0.025} - vary = {"stim_amp": ["%spA" % (i) for i in xrange(-200, 1500, 10)]} - vary = {"stim_amp": ["%spA" % (i) for i in xrange(-100, 1800, 20)]} - # vary = {'stim_amp':['%spA'%(i) for i in xrange(-100,500,5)]} + vary = {"stim_amp": ["%spA" % (i) for i in range(-200, 1500, 10)]} + vary = {"stim_amp": ["%spA" % (i) for i in range(-100, 1800, 20)]} + # vary = {'stim_amp':['%spA'%(i) for i in range(-100,500,5)]} simulator = "jNeuroML_NetPyNE" simulator = "NetPyNE" @@ -707,10 +708,11 @@ def run_once(self, job_dir, **kwargs): plt.show() elif "-dt" in sys.argv: - fixed = {"stim_amp": "500pA"} + fixed = {"stim_amp": "500pA", "duration": 300} vary = {"dt": [0.025, 0.02, 0.015, 0.01, 0.005, 0.0025]} vary = {"dt": [0.1, 0.05, 0.025, 0.01, 0.005, 0.0025, 0.001]} + #vary = {"dt": [0.1, 0.05, 0.025]} simulator = "jNeuroML_NetPyNE" simulator = "NetPyNE" @@ -805,11 +807,11 @@ def run_once(self, job_dir, **kwargs): quick = False # quick=True - vary = {"stim_amp": ["%spA" % (i / 10.0) for i in xrange(-10, 20, 2)]} - vary = {"stim_amp": ["%spA" % (i / 10.0) for i in xrange(-10, 20, 5)]} + vary = {"stim_amp": ["%spA" % (i / 10.0) for i in range(-10, 20, 2)]} + vary = {"stim_amp": ["%spA" % (i / 10.0) for i in range(-10, 20, 5)]} vary = {"weightInput": [1, 2, 5, 10]} vary = {"weightInput": [1, 2, 3, 20]} - vary = {"eta": [i / 100.0 for i in xrange(0, 200, 20)]} + vary = {"eta": [i / 100.0 for i in range(0, 200, 20)]} # vary = {'eta':['100Hz']} # vary = {'stim_amp':['1.5pA']} diff --git a/neuromllite/sweep/cleanup.sh b/neuromllite/sweep/cleanup.sh new file mode 100755 index 0000000..109c440 --- /dev/null +++ b/neuromllite/sweep/cleanup.sh @@ -0,0 +1,5 @@ +#!/bin/bash +set -ex + +rm -rf ParamSweep_* *.dat *.txt *kes *.png + From 3f649c9bfe7cd77a094ee337e340345571b93164 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Feb 2024 11:12:54 +0000 Subject: [PATCH 3/5] Update gha versions --- .github/workflows/ci.yml | 4 ++-- .github/workflows/python-publish.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1dd19e1..f0902d2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,9 +19,9 @@ jobs: HDF5_DISABLE_VERSION_CHECK: 1 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 0fe16bc..85cc411 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -18,9 +18,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies From c3cf3923da79df5f3fb37917f713b823a817153b Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Feb 2024 11:19:15 +0000 Subject: [PATCH 4/5] To v0.5.9 --- examples/Example10_Lorenz.json | 2 +- examples/Example11_Synapses.json | 2 +- examples/Example11_Synapses.net.nml | 2 +- examples/Example12_MultiComp.json | 2 +- examples/Example1_TestNetwork.json | 2 +- examples/Example2_TestNetwork.json | 2 +- examples/Example2_TestNetwork.net.nml | 2 +- examples/Example3_Network.json | 2 +- examples/Example3_Network.net.nml | 2 +- examples/Example4_PyNN.json | 2 +- examples/Example4_PyNN.net.nml | 2 +- examples/Example4_PyNN.yaml | 2 +- examples/Example6_PyNN.json | 2 +- examples/Example6_PyNN.net.nml | 2 +- examples/Example6_PyNN_noinputs.json | 2 +- examples/Example6_PyNN_noinputs.net.nml | 2 +- examples/Example7_Brunel2000.json | 2 +- examples/Example7_Brunel2000.net.nml | 2 +- examples/Example8_Extension.json | 2 +- examples/Example9_HindmarshRose.json | 2 +- examples/SimExample10.json | 2 +- examples/SimExample11.json | 2 +- examples/SimExample12_MultiComp.json | 2 +- examples/SimExample3.json | 2 +- examples/SimExample4.json | 2 +- examples/SimExample4.yaml | 2 +- examples/SimExample6_PyNN.json | 2 +- examples/SimExample7.json | 2 +- examples/SimExample8.json | 2 +- examples/SimExample9.json | 2 +- examples/arbor/ArborExample.json | 2 +- examples/arbor/ArborExample.yaml | 2 +- examples/arbor/SimArborExample.json | 2 +- examples/arbor/SimArborExample.yaml | 2 +- examples/spikeratetest/SimSpikers.json | 2 +- examples/spikeratetest/Spikers.json | 2 +- neuromllite/__init__.py | 2 +- 37 files changed, 37 insertions(+), 37 deletions(-) diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json index 065cecf..f1fc935 100644 --- a/examples/Example10_Lorenz.json +++ b/examples/Example10_Lorenz.json @@ -1,6 +1,6 @@ { "Example10_Lorenz": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 10: Lorenz", "parameters": { "N": 1, diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json index 1800533..c826fc0 100644 --- a/examples/Example11_Synapses.json +++ b/examples/Example11_Synapses.json @@ -1,6 +1,6 @@ { "Example11_Synapses": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 11: synaptic properties", "parameters": { "input_amp": 0.23, diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.net.nml index 7d37090..c2571ab 100644 --- a/examples/Example11_Synapses.net.nml +++ b/examples/Example11_Synapses.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example11_Synapses Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json index 8fdbfc3..45d65f6 100644 --- a/examples/Example12_MultiComp.json +++ b/examples/Example12_MultiComp.json @@ -1,6 +1,6 @@ { "Example12_MultiComp": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 12: Multicompartmental cells...", "parameters": { "N": 20, diff --git a/examples/Example1_TestNetwork.json b/examples/Example1_TestNetwork.json index 0fde5be..be8655b 100644 --- a/examples/Example1_TestNetwork.json +++ b/examples/Example1_TestNetwork.json @@ -1,6 +1,6 @@ { "TestNetwork": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.", "populations": { "pop0": { diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json index e900634..8a45b5b 100644 --- a/examples/Example2_TestNetwork.json +++ b/examples/Example2_TestNetwork.json @@ -1,6 +1,6 @@ { "Example2_TestNetwork": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.", "cells": { "hhcell": { diff --git a/examples/Example2_TestNetwork.net.nml b/examples/Example2_TestNetwork.net.nml index 0d65062..56c0694 100644 --- a/examples/Example2_TestNetwork.net.nml +++ b/examples/Example2_TestNetwork.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example2_TestNetwork Generation seed: 1234 diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json index 1b58f99..cae5535 100644 --- a/examples/Example3_Network.json +++ b/examples/Example3_Network.json @@ -1,6 +1,6 @@ { "Example3_Network": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.", "cells": { "hhcell": { diff --git a/examples/Example3_Network.net.nml b/examples/Example3_Network.net.nml index c251a6e..8cb1d6b 100644 --- a/examples/Example3_Network.net.nml +++ b/examples/Example3_Network.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example3_Network Generation seed: 1234 diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json index a3a5693..2e71485 100644 --- a/examples/Example4_PyNN.json +++ b/examples/Example4_PyNN.json @@ -1,6 +1,6 @@ { "Example4_PyNN": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 4: a network with PyNN cells & inputs", "parameters": { "input_amp": 0.99 diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.net.nml index c12e585..0869fd4 100644 --- a/examples/Example4_PyNN.net.nml +++ b/examples/Example4_PyNN.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example4_PyNN Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml index bdb808a..207e1ce 100644 --- a/examples/Example4_PyNN.yaml +++ b/examples/Example4_PyNN.yaml @@ -1,5 +1,5 @@ Example4_PyNN: - version: NeuroMLlite v0.5.8 + version: NeuroMLlite v0.5.9 notes: 'Example 4: a network with PyNN cells & inputs' parameters: input_amp: 0.99 diff --git a/examples/Example6_PyNN.json b/examples/Example6_PyNN.json index fdac4b0..ebc7db9 100644 --- a/examples/Example6_PyNN.json +++ b/examples/Example6_PyNN.json @@ -1,6 +1,6 @@ { "Example6_PyNN": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Another network for PyNN - work in progress...", "parameters": { "N_scaling": 0.005, diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.net.nml index 97050c1..8692b8f 100644 --- a/examples/Example6_PyNN.net.nml +++ b/examples/Example6_PyNN.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example6_PyNN Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example6_PyNN_noinputs.json b/examples/Example6_PyNN_noinputs.json index 96b61aa..c793f72 100644 --- a/examples/Example6_PyNN_noinputs.json +++ b/examples/Example6_PyNN_noinputs.json @@ -1,6 +1,6 @@ { "Example6_PyNN_noinputs": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Another network for PyNN - work in progress...", "parameters": { "N_scaling": 0.005, diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.net.nml index b059cb8..36041b0 100644 --- a/examples/Example6_PyNN_noinputs.net.nml +++ b/examples/Example6_PyNN_noinputs.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example6_PyNN_noinputs Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example7_Brunel2000.json b/examples/Example7_Brunel2000.json index 8c3c453..2faca33 100644 --- a/examples/Example7_Brunel2000.json +++ b/examples/Example7_Brunel2000.json @@ -1,6 +1,6 @@ { "Example7_Brunel2000": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 7: based on network of Brunel 2000", "parameters": { "g": 4, diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.net.nml index 7f5f39e..34d24d2 100644 --- a/examples/Example7_Brunel2000.net.nml +++ b/examples/Example7_Brunel2000.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.8 + Generated by NeuroMLlite v0.5.9 Generated network: Example7_Brunel2000 Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json index 54e1c9c..486d4ac 100644 --- a/examples/Example8_Extension.json +++ b/examples/Example8_Extension.json @@ -1,6 +1,6 @@ { "Example8_Extension": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 8: general testing...", "parameters": { "N": 10, diff --git a/examples/Example9_HindmarshRose.json b/examples/Example9_HindmarshRose.json index aac74ca..4416e09 100644 --- a/examples/Example9_HindmarshRose.json +++ b/examples/Example9_HindmarshRose.json @@ -1,6 +1,6 @@ { "Example9_HindmarshRose": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example 9: HindmarshRose", "parameters": { "N": 1, diff --git a/examples/SimExample10.json b/examples/SimExample10.json index c2909f7..2386e97 100644 --- a/examples/SimExample10.json +++ b/examples/SimExample10.json @@ -1,6 +1,6 @@ { "SimExample10": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example10_Lorenz.json", "duration": 10000.0, "dt": 1.0, diff --git a/examples/SimExample11.json b/examples/SimExample11.json index 323c0b4..cce2c53 100644 --- a/examples/SimExample11.json +++ b/examples/SimExample11.json @@ -1,6 +1,6 @@ { "SimExample11": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example11_Synapses.json", "duration": 1000.0, "dt": 0.01, diff --git a/examples/SimExample12_MultiComp.json b/examples/SimExample12_MultiComp.json index f1c808b..8b5ae55 100644 --- a/examples/SimExample12_MultiComp.json +++ b/examples/SimExample12_MultiComp.json @@ -1,6 +1,6 @@ { "SimExample12_MultiComp": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example12_MultiComp.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample3.json b/examples/SimExample3.json index f921f10..803988d 100644 --- a/examples/SimExample3.json +++ b/examples/SimExample3.json @@ -1,6 +1,6 @@ { "SimExample3": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example3_Network.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample4.json b/examples/SimExample4.json index 1808ac5..ee2e618 100644 --- a/examples/SimExample4.json +++ b/examples/SimExample4.json @@ -1,6 +1,6 @@ { "SimExample4": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example4_PyNN.json", "duration": 1000.0, "dt": 0.01, diff --git a/examples/SimExample4.yaml b/examples/SimExample4.yaml index 2c8dfff..f1ef3fd 100644 --- a/examples/SimExample4.yaml +++ b/examples/SimExample4.yaml @@ -1,5 +1,5 @@ SimExample4: - version: NeuroMLlite v0.5.8 + version: NeuroMLlite v0.5.9 network: Example4_PyNN.yaml duration: 1000.0 dt: 0.01 diff --git a/examples/SimExample6_PyNN.json b/examples/SimExample6_PyNN.json index 3828e7e..53a7358 100644 --- a/examples/SimExample6_PyNN.json +++ b/examples/SimExample6_PyNN.json @@ -1,6 +1,6 @@ { "SimExample6_PyNN": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example6_PyNN.json", "duration": 100.0, "dt": 0.025, diff --git a/examples/SimExample7.json b/examples/SimExample7.json index 673b763..389ad06 100644 --- a/examples/SimExample7.json +++ b/examples/SimExample7.json @@ -1,6 +1,6 @@ { "SimExample7": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example7_Brunel2000.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample8.json b/examples/SimExample8.json index 6ac6391..f7acaa5 100644 --- a/examples/SimExample8.json +++ b/examples/SimExample8.json @@ -1,6 +1,6 @@ { "SimExample8": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example8_Extension.json", "duration": 1000.0, "dt": 0.025, diff --git a/examples/SimExample9.json b/examples/SimExample9.json index 654ecc6..7fe2760 100644 --- a/examples/SimExample9.json +++ b/examples/SimExample9.json @@ -1,6 +1,6 @@ { "SimExample9": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Example9_HindmarshRose.json", "duration": 1000000.0, "dt": 25.0, diff --git a/examples/arbor/ArborExample.json b/examples/arbor/ArborExample.json index e2a9d33..12c1362 100644 --- a/examples/arbor/ArborExample.json +++ b/examples/arbor/ArborExample.json @@ -1,6 +1,6 @@ { "ArborExample": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example for testing Arbor", "parameters": { "v_init": -50, diff --git a/examples/arbor/ArborExample.yaml b/examples/arbor/ArborExample.yaml index 7a76208..455263b 100644 --- a/examples/arbor/ArborExample.yaml +++ b/examples/arbor/ArborExample.yaml @@ -1,5 +1,5 @@ ArborExample: - version: NeuroMLlite v0.5.8 + version: NeuroMLlite v0.5.9 notes: Example for testing Arbor parameters: v_init: -50 diff --git a/examples/arbor/SimArborExample.json b/examples/arbor/SimArborExample.json index c36d797..a89098f 100644 --- a/examples/arbor/SimArborExample.json +++ b/examples/arbor/SimArborExample.json @@ -1,6 +1,6 @@ { "SimArborExample": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "ArborExample.json", "duration": 100.0, "dt": 0.01, diff --git a/examples/arbor/SimArborExample.yaml b/examples/arbor/SimArborExample.yaml index 64d6ad6..7836548 100644 --- a/examples/arbor/SimArborExample.yaml +++ b/examples/arbor/SimArborExample.yaml @@ -1,5 +1,5 @@ SimArborExample: - version: NeuroMLlite v0.5.8 + version: NeuroMLlite v0.5.9 network: ArborExample.yaml duration: 100.0 dt: 0.01 diff --git a/examples/spikeratetest/SimSpikers.json b/examples/spikeratetest/SimSpikers.json index 13f4839..6e1558d 100644 --- a/examples/spikeratetest/SimSpikers.json +++ b/examples/spikeratetest/SimSpikers.json @@ -1,6 +1,6 @@ { "SimSpikers": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "network": "Spikers.json", "duration": 10000.0, "dt": 0.025, diff --git a/examples/spikeratetest/Spikers.json b/examples/spikeratetest/Spikers.json index 6cfb51e..a8a71c9 100644 --- a/examples/spikeratetest/Spikers.json +++ b/examples/spikeratetest/Spikers.json @@ -1,6 +1,6 @@ { "Spikers": { - "version": "NeuroMLlite v0.5.8", + "version": "NeuroMLlite v0.5.9", "notes": "Example with spiking entities..", "parameters": { "N": 10, diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py index 2eefbe8..0c96744 100644 --- a/neuromllite/__init__.py +++ b/neuromllite/__init__.py @@ -1,6 +1,6 @@ import collections -__version__ = "0.5.8" +__version__ = "0.5.9" # import pyNN # import nest From 4fe5bb4a9cd2ecd0921e916f3fb0691c986db0ef Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Feb 2024 11:19:33 +0000 Subject: [PATCH 5/5] Add ppft requirement - needed for param sweep --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index ba65143..c76fd81 100644 --- a/setup.py +++ b/setup.py @@ -26,6 +26,7 @@ "tables", "h5py", "modelspec>=0.2.6", + "ppft" ], classifiers=[ "Intended Audience :: Science/Research",