updated py3 to development changeset 517dce6 (to test gui)

CHANGES.md

@@ -1,3 +1,26 @@
+# Version 0.8.0
+
+- Optimized implementation of raste and spikeHist plotting using Pandas
+
+- Added option for filename to saveData()
+
+- Removed pop cellModelClass when saving
+
+- Removed cell h object keys when saving
+
+- Added support for evolutionary algorithm optimization (via Inspyred) and usage example
+
+- cfg.popAvgRates now accepts a time range to calculate rates (e.g. to discard initial period)
+
+- Fixed bug initalizing batch 'mpi_bulletin' and batch tutorial example
+
+- Fixed bug: removed '\_labelid' from netParams when saving
+
+- Fixed bug: made self.scaleConnWeightModels False when not used (avoids saving weird dict in json)
+
+- Fixed bug in Pickle file encoding so works in Python3 
+
+
 # Version 0.7.9
 
 - Extended metadata structure to interact with NetPyNE-UI
@@ -34,8 +57,6 @@
 
 - Fixed bug: delete sections after import cell only if section exists
 
-- Fixed bug initalizing batch 'mpi_bulletin' and batch tutorial example
-
 
 # Version 0.7.8
 

doc/source/code/tut1.py

@@ -1,5 +1,3 @@
 import HHTut
 from netpyne import sim
 sim.createSimulateAnalyze(netParams = HHTut.netParams, simConfig = HHTut.simConfig)    
-
-# import pylab; pylab.show()  # this line is only necessary in certain systems where figures appear empty

doc/source/index.rst

@@ -8,7 +8,7 @@ Welcome to NetPyNE's documentation!
 
 NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
 
-Check out our new `NetPyNE GUI teaser video <http://www.youtube.com/watch?v=Y8Aow9zwu3E>`_! The GUI will be released July 2018, ready for our `Tutorial at CNS18 <http://www.cnsorg.org/cns-2018-tutorials#T2>`_! 
+We have also released an alpha version of the NetPyNE GUI -- `see video here <https://www.youtube.com/watch?v=Hck_bLKm7v8>`_ (open in new tab)! See a `step-by-step tutorial <http://bit.ly/netpyne-ui-tut>`_! 
 
 Join our `NetPyNE mailing list <https://groups.google.com/forum/#!forum/netpyne-mailing>`_ to receive updates on version releases and other major announcements.
 

doc/source/install.rst

@@ -3,10 +3,11 @@
 Installation
 =======================================
 
+
 Requirements
 ------------
 
-The NetPyNE package requires Python 2.7 (www.python.org).
+The NetPyNE package requires Python 2 or 3 (both are supported) (download from www.python.org).
 
 Additionally, running parallelized simulations of networks requires the NEURON simulator with python and MPI support. See NEURON's `installation instructions <http://www.neuron.yale.edu/neuron/download/>`_ and `documentation <http://www.neuron.yale.edu/neuron/static/new_doc/index.html>`_
 
@@ -20,16 +21,27 @@ Note: It is possible to use the NetPyNE package without NEURON, to convert model
 Install via pip (latest released version)
 -----------------------------------------
 
+Python 2
+^^^^^^^^^^^^
+
 To install the the package run ``pip install netpyne`` (Linux or Mac OS) or ``python -m pip install netpyne`` (Windows)
 
-To upgrade to a new version run ``pip install netpyne -U`` (Linux or Mac OS) or ``python -m pip install -U pip`` (Windows)
+To upgrade to a new version run ``pip install netpyne -U`` (Linux or Mac OS) or ``python -m pip install -U netpyne`` (Windows)
 
-If you need to install ``pip`` go to `this link <https://pip.pypa.io/en/stable/installing/>`_
+Python 3
+^^^^^^^^^^^^
 
-The NetPyNE package source files, as well as example models, are available via github at: https://github.com/Neurosim-lab/netpyne
+To install the the package run ``pip3 install netpyne_py3`` (Linux or Mac OS) or ``python -m pip3 install netpyne_py3`` (Windows)
+
+To upgrade to a new version run ``pip3 install netpyne_py3 -U`` (Linux or Mac OS) or ``python -m pip3 install -U netpyne_py3`` (Windows)
+
+
+pip
+^^^^^^^^^^
+If you need to install ``pip`` go to `this link <https://pip.pypa.io/en/stable/installing/>`_
 
 
-Install via pip (development version)
+Install via pip (development version; only for Python 2)
 --------------------------------------
 
 This will install the version in the github "development" branch -- it will include some of the latest enhancements and bug fixes, but could also include temporary bugs:
@@ -39,4 +51,13 @@ This will install the version in the github "development" branch -- it will incl
 3) git checkout development
 4) pip install -e .
 
-pip will add a symlink in the default python packages folder to the cloned netpyne folder (so you don't need to modify PYTHONPATH). If new changes are available just need to pull from cloned netpyne repo.
+pip will add a symlink in the default python packages folder to the cloned netpyne folder (so you don't need to modify PYTHONPATH). If new changes are available just need to pull from cloned netpyne repo.
+
+Install NetPyNE GUI (alpha version; only for Python 2)
+--------------------------------------
+
+You can install the tool via `pip <https://github.com/MetaCell/NetPyNE-UI/wiki/Pip-installation>`_ (requires `NEURON <https://github.com/MetaCell/NetPyNE-UI/wiki/Installing-NEURON-crxd-Version>`_ ), or using our pre-packaged `Docker <https://github.com/MetaCell/NetPyNE-UI/wiki/Docker-installation>`_ or `Virtual Machine <https://github.com/MetaCell/NetPyNE-UI/wiki/Virtual-Machine-Installation>`_.
+
+Github
+------------
+The NetPyNE package source files, as well as example models, are available via github at: https://github.com/Neurosim-lab/netpyne

examples/batchCell/batch.py

@@ -22,7 +22,7 @@ def runBatch(b, label):
 	b.batchLabel = label
 	b.saveFolder = 'data/'+b.batchLabel
 	b.method = 'grid'
-	b.runCfg = {'type': 'mpi', 
+	b.runCfg = {'type': 'mpi_bulletin', 
 				'script': 'init.py', 
 				'skip': True}
 

examples/batchCell/cells/SPI6.py

@@ -3,6 +3,8 @@
 from neuron import h
 from math import exp,log
 
+h.load_file('stdrun.hoc')
+
 Vrest       = -88.5366550238 
 h.v_init = -75.0413649414 
 h.celsius     = 34.0 # for in vitro opt