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tarellitarelli
committedFeb 20, 2018
Rename to netpyne
·
1.1.00.1
1 parent 754d878 commit 5aa8e3e

25 files changed

+68
-68
lines changed
 

‎Dockerfile

+2-2
Original file line numberDiff line numberDiff line change
@@ -37,8 +37,8 @@ ENV PATH="/home/jovyan/work/nrn-7.4/x86_64/bin:${PATH}"
3737
RUN /bin/bash -c "source activate snakes && python setup.py install"
3838
RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
3939
RUN unzip $netpyneuiBranch.zip
40-
WORKDIR NEURON-UI-$netpyneuiBranch/utilities
40+
WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
4141
RUN /bin/bash -c "source activate snakes && python --version"
4242
RUN /bin/bash -c "source activate snakes && exec python install.py"
43-
RUN cd ../neuron_ui/tests && /bin/bash -c "source activate snakes && python -m unittest netpyne_model_interpreter_test"
43+
RUN cd ../netpyne_ui/tests && /bin/bash -c "source activate snakes && python -m unittest netpyne_model_interpreter_test"
4444
CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"

‎Dockerfile_pip

+1-1
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,6 @@ RUN make
1515
RUN make install
1616
WORKDIR src/nrnpython
1717
RUN python setup.py install
18-
RUN pip install neuron_ui
18+
RUN pip install netpyne_ui
1919
CMD exec jupyter nbextension enable --py jupyter_geppetto
2020
CMD exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''

‎README.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ jupyter nbextension enable --py jupyter_geppetto
3434
NetPyNE-UI
3535
```
3636

37-
#### Install from sources (for developers and for using your own NEURON models)
37+
#### Install from sources (for developers and for using your own NetPyNE models)
3838
```
3939
git clone https://github.com/MetaCell/NetPyNE-UI.git
4040
cd utilities

‎README.rst

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ The UI connects to
1212
through a `Geppetto <http://git.geppetto.org>`__ extension for `Jupyter
1313
Notebook <http://jupyter.org/>`__.
1414

15-
See the `Repo <https://github.com/MetaCell/NEURON-UI>`__ and `Wiki <https://github.com/MetaCell/NEURON-UI/wiki>`__ for more
15+
See the `Repo <https://github.com/MetaCell/NetPyNE-UI>`__ and `Wiki <https://github.com/MetaCell/NetPyNE-UI/wiki>`__ for more
1616
=======
1717
NetPyNE-UI
1818
=========

‎netpyne_ui/analysis.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
import logging
2-
from neuron_ui import neuron_utils
2+
from netpyne_ui import neuron_utils
33
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
44

55

‎netpyne_ui/cell_builder.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,9 @@
33
Neuron Cell Builder
44
"""
55
import logging
6-
from neuron_ui import neuron_utils
7-
from neuron_ui import neuron_geometries_utils
8-
from neuron_ui.singleton import Singleton
6+
from netpyne_ui import neuron_utils
7+
from netpyne_ui import neuron_geometries_utils
8+
from netpyne_ui.singleton import Singleton
99
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
1010
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
1111

‎netpyne_ui/models/CA3_pyramidal.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
import pkg_resources
44

55
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
6-
from neuron_ui import neuron_utils
7-
from neuron_ui import neuron_geometries_utils
6+
from netpyne_ui import neuron_utils
7+
from netpyne_ui import neuron_geometries_utils
88

99
class CA3_pyramidal:
1010

@@ -13,7 +13,7 @@ def __init__(self):
1313

1414
neuron_utils.createProject(name='CA3 Pyramidal Neuron')
1515

16-
resource_package = "neuron_ui"
16+
resource_package = "netpyne_ui"
1717
resource_path = '/'.join(('models', 'geo-cell1zr.hoc'))
1818
filepath = pkg_resources.resource_filename(resource_package, resource_path)
1919

‎netpyne_ui/models/PTcell.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
import pkg_resources
44

55
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
6-
from neuron_ui import neuron_utils
7-
from neuron_ui import neuron_geometries_utils
6+
from netpyne_ui import neuron_utils
7+
from netpyne_ui import neuron_geometries_utils
88

99
class PTcell:
1010

@@ -13,7 +13,7 @@ def __init__(self):
1313

1414
neuron_utils.createProject(name='PTcell Neuron')
1515

16-
resource_package = "neuron_ui"
16+
resource_package = "netpyne_ui"
1717
resource_path = '/'.join(('models', 'PTcell.hoc'))
1818
filepath = pkg_resources.resource_filename(resource_package, resource_path)
1919

‎netpyne_ui/models/ring.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
from .ball_and_stick import BallAndStick
33
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
44
from math import pi, cos, sin
5-
from neuron_ui import neuron_utils
6-
from neuron_ui import neuron_geometries_utils
5+
from netpyne_ui import neuron_utils
6+
from netpyne_ui import neuron_geometries_utils
77
import logging
88
# from neuronpy.util import spiketrain
99

‎netpyne_ui/models/simple_cell.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
import logging
22
from neuron import h
33
from IPython.core.debugger import Tracer
4-
from neuron_ui import neuron_utils, neuron_geometries_utils
4+
from netpyne_ui import neuron_utils, neuron_geometries_utils
55
from math import sqrt, pow
66

77
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G

‎netpyne_ui/models/simple_network_old.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
from neuron import h
22
from pylab import sin,cos,pi
33
#from matplotlib import pyplot
4-
from neuron_ui import neuron_utils
4+
from netpyne_ui import neuron_utils
55

66
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
77

‎netpyne_ui/models/verysimple_cell.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
from __future__ import print_function
22
from neuron import h
3-
from neuron_ui import neuron_utils
4-
from neuron_ui import neuron_geometries_utils
3+
from netpyne_ui import neuron_utils
4+
from netpyne_ui import neuron_geometries_utils
55

66
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
77

‎netpyne_ui/netpyne_geppetto.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
import time
1414

1515

16-
from neuron_ui import neuron_utils
16+
from netpyne_ui import neuron_utils
1717
from netpyne import specs, sim, analysis
1818
from netpyne.metadata import metadata, api
1919
from netpyne_model_interpreter import NetPyNEModelInterpreter
@@ -248,7 +248,7 @@ def run(self):
248248
# TODO With this line it hangs in some setups. Figure out if it's needed
249249
# h.nrniv_bind_thread(threading.current_thread().ident);
250250
self.started = True
251-
while True:# from neuron_ui import neuron_utils
251+
while True:# from netpyne_ui import neuron_utils
252252
self.fun()
253253
time.sleep(self.interval)
254254

@@ -340,4 +340,4 @@ def GeppettoInit():
340340
GeppettoJupyterModelSync.current_model.original_model = json.dumps({'netParams': netParams.__dict__,
341341
'simConfig': simConfig.__dict__,
342342
'metadata': metadata.metadata,
343-
'requirement': 'from neuron_ui.netpyne_geppetto import *'})
343+
'requirement': 'from netpyne_ui.netpyne_geppetto import *'})

‎netpyne_ui/neuron_geppetto.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,9 @@
99
from neuron import h
1010
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
1111
from jupyter_geppetto.geppetto_comm import GeppettoJupyterGUISync
12-
from neuron_ui.sample_models import SampleModels
13-
from neuron_ui.neuron_menu import NeuronMenu
14-
from neuron_ui import neuron_utils
12+
from netpyne_ui.sample_models import SampleModels
13+
from netpyne_ui.neuron_menu import NeuronMenu
14+
from netpyne_ui import neuron_utils
1515

1616
class LoopTimer(threading.Thread):
1717
"""

‎netpyne_ui/neuron_menu.py

+5-5
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
22
import importlib
33
from . import neuron_utils
44
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
5-
from neuron_ui.singleton import Singleton
6-
from neuron_ui.point_process import PointProcess
7-
from neuron_ui.space_plot import SpacePlot
8-
from neuron_ui.cell_builder import CellBuilder
9-
from neuron_ui.run_control import RunControl
5+
from netpyne_ui.singleton import Singleton
6+
from netpyne_ui.point_process import PointProcess
7+
from netpyne_ui.space_plot import SpacePlot
8+
from netpyne_ui.cell_builder import CellBuilder
9+
from netpyne_ui.run_control import RunControl
1010

1111

1212
@Singleton

‎netpyne_ui/neuron_utils.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
import logging
2-
from neuron_ui import neuron_geometries_utils
2+
from netpyne_ui import neuron_geometries_utils
33
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
44

55
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync

‎netpyne_ui/point_process.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,9 @@
33
Neuron Point Process
44
"""
55
import logging
6-
from neuron_ui import neuron_utils
7-
from neuron_ui import neuron_geometries_utils
8-
from neuron_ui.singleton import Singleton
6+
from netpyne_ui import neuron_utils
7+
from netpyne_ui import neuron_geometries_utils
8+
from netpyne_ui.singleton import Singleton
99
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
1010

1111
from neuron import h

‎netpyne_ui/run_control.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -3,10 +3,10 @@
33
Neuron Run Control Panel
44
"""
55
import logging
6-
from neuron_ui import neuron_utils
6+
from netpyne_ui import neuron_utils
77
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
88
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
9-
from neuron_ui.singleton import Singleton
9+
from netpyne_ui.singleton import Singleton
1010

1111
from neuron import h
1212
h.load_file("stdrun.hoc")

‎netpyne_ui/sample_models.py

+4-4
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
import logging
22
import importlib
3-
from neuron_ui import neuron_utils
3+
from netpyne_ui import neuron_utils
44
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
5-
from neuron_ui.singleton import Singleton
5+
from netpyne_ui.singleton import Singleton
66
import jupyter_client
77

88

@@ -49,7 +49,7 @@ def loadModule(self, triggeredComponent, args):
4949
logging.debug('Loading model ' +
5050
triggeredComponent.extraData['module'])
5151
module = importlib.import_module(
52-
"neuron_ui.models." + triggeredComponent.extraData['module'])
52+
"netpyne_ui.models." + triggeredComponent.extraData['module'])
5353
GeppettoJupyterModelSync.current_python_model = getattr(
5454
module, triggeredComponent.extraData['model'])()
5555
else:
@@ -64,7 +64,7 @@ def loadModule(self, triggeredComponent, args):
6464
km.load_connection_file()
6565
kk = km.shutdown(True)
6666
km.execute('import importlib')
67-
km.execute('python_module = importlib.import_module("neuron_ui.models.' + triggeredComponent.extraData['module'] +'")')
67+
km.execute('python_module = importlib.import_module("netpyne_ui.models.' + triggeredComponent.extraData['module'] +'")')
6868
km.execute('GeppettoJupyterModelSync.current_python_model = getattr( python_module, "' + triggeredComponent.extraData['model'] + '")()')
6969
km.execute('GeppettoJupyterModelSync.events_controller.triggerEvent("spinner:hide")')
7070

‎netpyne_ui/space_plot.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,8 @@
66
from jupyter_geppetto.geppetto_comm import GeppettoCoreAPI as G
77
from jupyter_geppetto.geppetto_comm import GeppettoJupyterModelSync
88
from neuron import h
9-
from neuron_ui import neuron_utils
10-
from neuron_ui.singleton import Singleton
9+
from netpyne_ui import neuron_utils
10+
from netpyne_ui.singleton import Singleton
1111

1212

1313
@Singleton

‎netpyne_ui/tests/netpyne_model_interpreter_test.py

+14-14
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
netpyne.__gui__ = False
44
from netpyne import specs, sim
55
import os
6-
from neuron_ui.netpyne_model_interpreter import NetPyNEModelInterpreter
6+
from netpyne_ui.netpyne_model_interpreter import NetPyNEModelInterpreter
77
import neuron
88
import subprocess
99

@@ -60,42 +60,42 @@ def test_tut1(self):
6060
print "------------------------------------"
6161
print "Tutorial 1 Instantiation:"
6262
print "------------------------------------"
63-
from neuron_ui.tests.tut1 import netParams, simConfig
63+
from netpyne_ui.tests.tut1 import netParams, simConfig
6464
self.getGeppettoModel(netParams, simConfig)
6565

6666
def test_tut1_simulation(self):
6767
print "------------------------------------"
6868
print "Tutorial 1 Simulation:"
6969
print "------------------------------------"
70-
from neuron_ui.tests.tut1 import netParams, simConfig
70+
from netpyne_ui.tests.tut1 import netParams, simConfig
7171
self.updateGeppettoModel(netParams, simConfig)
7272

7373
def test_tut2(self):
7474
print "------------------------------------"
7575
print "Tutorial 2 Instantiation:"
7676
print "------------------------------------"
77-
from neuron_ui.tests.tut2 import netParams, simConfig
77+
from netpyne_ui.tests.tut2 import netParams, simConfig
7878
self.getGeppettoModel(netParams, simConfig)
7979

8080
def test_tut2_simulation(self):
8181
print "------------------------------------"
8282
print "Tutorial 2 Simulation:"
8383
print "------------------------------------"
84-
from neuron_ui.tests.tut2 import netParams, simConfig
84+
from netpyne_ui.tests.tut2 import netParams, simConfig
8585
self.updateGeppettoModel(netParams, simConfig)
8686

8787
def test_tut3(self):
8888
print "------------------------------------"
8989
print "Tutorial 3 Instantiation:"
9090
print "------------------------------------"
91-
from neuron_ui.tests.tut3 import netParams, simConfig
91+
from netpyne_ui.tests.tut3 import netParams, simConfig
9292
self.getGeppettoModel(netParams, simConfig)
9393

9494
def test_tut3_simulation(self):
9595
print "------------------------------------"
9696
print "Tutorial 3 Simulation:"
9797
print "------------------------------------"
98-
from neuron_ui.tests.tut3 import netParams, simConfig
98+
from netpyne_ui.tests.tut3 import netParams, simConfig
9999
self.updateGeppettoModel(netParams, simConfig)
100100

101101
def test_tut4(self):
@@ -110,7 +110,7 @@ def test_tut4(self):
110110
os.chdir(owd)
111111
neuron.load_mechanisms(modelpath)
112112

113-
from neuron_ui.tests.tut4.tut4 import netParams, simConfig
113+
from netpyne_ui.tests.tut4.tut4 import netParams, simConfig
114114
self.getGeppettoModel(netParams, simConfig)
115115

116116
def test_tut4_simulation(self):
@@ -125,35 +125,35 @@ def test_tut4_simulation(self):
125125
os.chdir(owd)
126126
neuron.load_mechanisms(modelpath)
127127

128-
from neuron_ui.tests.tut4.tut4 import netParams, simConfig
128+
from netpyne_ui.tests.tut4.tut4 import netParams, simConfig
129129
self.updateGeppettoModel(netParams, simConfig)
130130

131131
def test_tut5(self):
132132
print "------------------------------------"
133133
print "Tutorial 5 Instantiation:"
134134
print "------------------------------------"
135-
from neuron_ui.tests.tut5 import netParams, simConfig
135+
from netpyne_ui.tests.tut5 import netParams, simConfig
136136
self.getGeppettoModel(netParams, simConfig)
137137

138138
def test_tut5_simulation(self):
139139
print "------------------------------------"
140140
print "Tutorial 5 Simulation:"
141141
print "------------------------------------"
142-
from neuron_ui.tests.tut5 import netParams, simConfig
142+
from netpyne_ui.tests.tut5 import netParams, simConfig
143143
self.updateGeppettoModel(netParams, simConfig)
144144

145145
def test_tut6(self):
146146
print "------------------------------------"
147147
print "Tutorial 6 Instantiation:"
148148
print "------------------------------------"
149-
from neuron_ui.tests.tut6 import netParams, simConfig
149+
from netpyne_ui.tests.tut6 import netParams, simConfig
150150
self.getGeppettoModel(netParams, simConfig)
151151

152152
def test_tut6_simulation(self):
153153
print "------------------------------------"
154154
print "Tutorial 6 Simulation:"
155155
print "------------------------------------"
156-
from neuron_ui.tests.tut6 import netParams, simConfig
156+
from netpyne_ui.tests.tut6 import netParams, simConfig
157157
self.updateGeppettoModel(netParams, simConfig)
158158

159159
def test_M1detailed(self):
@@ -169,7 +169,7 @@ def test_M1detailed(self):
169169
neuron.load_mechanisms(modpath)
170170
os.chdir(modelpath)
171171

172-
from neuron_ui.tests.M1detailed.init import netParams, cfg
172+
from netpyne_ui.tests.M1detailed.init import netParams, cfg
173173
self.getGeppettoModel(netParams, cfg)
174174

175175
os.chdir(owd)

‎netpyne_ui/tests/tut4/x86_64/izhi2007b.c

+1-1
Original file line numberDiff line numberDiff line change
@@ -236,7 +236,7 @@ extern void _cvode_abstol( Symbol**, double*, int);
236236
pnt_receive[_mechtype] = _net_receive;
237237
pnt_receive_size[_mechtype] = 1;
238238
hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
239-
ivoc_help("help ?1 Izhi2007b /home/adrian/code/geppetto/NEURON-UI/neuron_ui/tests/tut4/x86_64/izhi2007b.mod\n");
239+
ivoc_help("help ?1 Izhi2007b /home/adrian/code/geppetto/NetPyNE-UI/netpyne_ui/tests/tut4/x86_64/izhi2007b.mod\n");
240240
hoc_register_limits(_mechtype, _hoc_parm_limits);
241241
hoc_register_units(_mechtype, _hoc_parm_units);
242242
}

‎netpyne_ui/tests/tut4/x86_64/special

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,4 +10,4 @@ if test "" = "yes" ; then
1010
else
1111
NRNIV="${NRNBIN}nrniv"
1212
fi
13-
"${NRNIV}" -dll "/home/adrian/code/geppetto/NEURON-UI/neuron_ui/tests/tut4/x86_64/.libs/libnrnmech.so" "$@"
13+
"${NRNIV}" -dll "/home/adrian/code/geppetto/NetPyNE-UI/netpyne_ui/tests/tut4/x86_64/.libs/libnrnmech.so" "$@"

‎setup.py

+5-5
Original file line numberDiff line numberDiff line change
@@ -1,19 +1,19 @@
11
from setuptools import setup, find_packages
22

33
setup(
4-
name="neuron_ui",
5-
version="0.0.1",
6-
url="https://github.com/MetaCell/NEURON-UI",
4+
name="netpyne_ui",
5+
version="0.1",
6+
url="https://github.com/MetaCell/NetPyNE-UI",
77
author="MetaCell",
88
author_email="info@metacell.us",
9-
description="User interface for NEURON based on web technologies and Jupyter",
9+
description="NetPyNE User interface",
1010
license="MIT",
1111
long_description=open('README.rst').read(),
1212
packages=find_packages(),
1313
package_data={
1414
'': ['*.hoc']
1515
},
16-
scripts=['NEURON-UI'],
16+
scripts=['NetPyNE-UI'],
1717
classifiers=[
1818
'Development Status :: 3 - Alpha',
1919
'Intended Audience :: Science/Research',

‎utilities/gitall.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#!/usr/bin/python
22

33
#
4-
# Utility script for mass git operatiosn on NEURON-UI
4+
# Utility script for mass git operatiosn on NetPyNE-UI
55
# Usage:
66
# gitall branches: print current branch of each repo
77
#
@@ -24,9 +24,9 @@
2424

2525
"repos": [
2626
{
27-
"name": "NEURON_UI",
27+
"name": "NetPyNE_UI",
2828
"path": "..",
29-
"url": "https://github.com/MetaCell/NEURON-UI"
29+
"url": "https://github.com/MetaCell/NetPyNE-UI"
3030
},
3131
{
3232
"name": "org.geppetto.frontend.jupyter",

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