Merge pull request #748 from suny-downstate-medical-center/development

PR from development to master - VERSION 1.0.4

.github/workflows/tests.yml

@@ -31,6 +31,10 @@ jobs:
           pip install -r requirements.txt
           pip install -e .
 
+      - name: Info on installed package versons
+        run: |
+          pip list
+
       - name: Test with pytest
         run: |
           source tests/test.sh

.gitignore

@@ -63,3 +63,10 @@ examples/asdOptim/simple/
 *.pid
 
 examples/optunaOptim/simple/
+/examples/NeuroMLImport/test/HHTut.net.nml
+/examples/NeuroMLImport/test/HybridTut.net.nml
+/examples/NeuroMLImport/test/LEMS_HHTut.xml
+/examples/NeuroMLImport/test/LEMS_HybridTut.xml
+/examples/NeuroMLImport/test/M1.net.nml
+/examples/NeuroMLImport/test/LEMS_M1.xml
+arm64

CHANGES.md

@@ -1,6 +1,44 @@
+# Version 1.0.4
+
+**New features**
+
+- Added 'linewidth' as argument of plotting.plotSpikeHist()
+
+- More detailed validation of netParams
+
+- Save and load model in native NetPyNE format
+
+- Converted most of examples to new NetPyNE model structure
+
+- Complex stimulation ('rhythmic', 'evoked', 'poisson' and 'gauss') for VecStim created as pointCell (as a population rule)
+
+- Codebase brought into compliance with PEP8 conventions
+
+- Updates in NeuroML examples and tests
+
+**Bug fixes**
+
+- fixed handling filenames with multiple dots in `MetaFigure.saveFig()`
+
+- Fixed readCmdLimeArgs() default arguments for backward-compatibility
+
+- Cleaned up example models to drop some legacy/irrelevant params
+
+- RxD module: Parameters defined before reactions + names given by default when missing (by the key)
+
+- Analysis: try ... except call in plotDipole
+
+- Save hObj of gap junction to connParams
+
+- Removed duplicated or unused code from gridSearch()
+
+- Fixes in batch utilities to make OS-agnostic
+
 # Version 1.0.3.1
 
-- Hotfix to support new GUI functionality
+- Hotfix to support new GUI functionality (fixes in grid parameter optimization)
+
+- Removed redundant warnings
 
 # Version 1.0.3
 

doc/source/code/tut1.py

@@ -1,3 +1,4 @@
-import HHTut
 from netpyne import sim
-sim.createSimulateAnalyze(netParams = HHTut.netParams, simConfig = HHTut.simConfig)
+from netParams import netParams
+from cfg import cfg
+sim.createSimulateAnalyze(netParams = netParams, simConfig = cfg)

doc/source/code/tut6.py

@@ -11,8 +11,8 @@
 netParams.cellParams['PYR'] = {'secs': secs}                                                # add dict to list of cell params
 
 ## Population parameters
-netParams.popParams['S'] = {'cellType': 'PYR', 'numCells': 20, 'cellModel': 'HH'}
-netParams.popParams['M'] = {'cellType': 'PYR', 'numCells': 20, 'cellModel': 'HH'}
+netParams.popParams['S'] = {'cellType': 'PYR', 'numCells': 20}
+netParams.popParams['M'] = {'cellType': 'PYR', 'numCells': 20}
 
 ## Synaptic mechanism parameters
 netParams.synMechParams['exc'] = {

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.3.1'
+version = '1.0.4'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.3.1'
+release = '1.0.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/reference.rst

@@ -269,6 +269,64 @@ Example of point process artificial cell populations::
 
 	netParams.popParams['artif3'] = {'cellModel': 'VecStim', 'numCells': 100, 'spkTimes': spkTimes, 'pulses': pulses}  # VecStim with spike times
 
+When ``cellModel`` is 'VecStim', a pattern generator may be used by creating a 'spikePattern' dictionary::
+
+    netParams.popParams['artif1'] = {'cellModel': 'VecStim'
+                                     ...
+                                     'spikePattern': {'type': 'rhythmic', # can be 'rhythmic', 'evoked', 'poisson', 'gauss'
+                                                      ...                 # see netpyne/cell/inputs.py for argument entries
+                                                      }
+                                     }
+
+
+Currently, 'rhythmic', 'evoked', 'poisson' and 'gauss' spike pattern generators are available, their argument entries are:
+
+* **rhythmic** - Creates the ongoing external inputs (rhythmic)
+
+    * **start** - time of first spike. if -1, uniform distribution between startMin and startMax (ms)
+
+    * **startMin** - minimum values of uniform distribution for start time (ms)
+
+    * **startMax** - maximum values of uniform distribution for start time (ms)
+
+    * **startStd** - standard deviation of normal distrinution for start time (ms); mean is set by start param. Only used if > 0.0
+
+    * **freq** - oscillatory frequency of rhythmic pattern (Hz)
+
+    * **freqStd** - standard deviation of oscillatory frequency (Hz)
+
+    * **distribution** - distribution type fo oscillatory frequencies; either 'normal' or 'uniform'
+
+    * **eventsPerCycle** - spikes/burst per cycle; should be either 1 or 2
+
+    * **repeats** - number of times to repeat input pattern (equivalent to number of inputs)
+
+    * **stop** - maximum time for last spike of pattern (ms)
+
+* **evoked** - creates the ongoing external inputs (rhythmic)
+
+    * **start** - time of first spike. if -1, uniform distribution between startMin and startMax (ms)
+
+    * **inc** - increase in time of first spike; from cfg.inc_evinput (ms)
+
+    * **startStd** - standard deviation of start (ms)
+
+    * **numspikes** - total number of spikes to generate
+
+* **poisson** - creates external Poisson inputs
+
+    * **start** - time of first spike (ms)
+
+    * **stop** - stop time; if -1 the full duration (ms)
+
+    * **frequency** - standard deviation of start (ms)
+
+* **gauss** - Creates Gaussian inputs
+
+    * **mu** - Gaussian mean
+
+    * **sigma** - Gaussian variance
+
 Finally, it is possible to define a population composed of individually-defined cells by including the list of cells in the ``cellsList`` dictionary field. Each element of the list of cells will in turn be a dictionary containing any set of cell properties such as ``cellLabel`` or location (e.g. ``x`` or ``ynorm``). An example is shown below::
 
 	cellsList.append({'cellLabel':'gs15', 'x': 1, 'ynorm': 0.4 , 'z': 2})