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",