Merge pull request #806 from suny-downstate-medical-center/development

PR from development to master - VERSION 1.0.6

.github/workflows/tests.yml

@@ -8,14 +8,15 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         #python-version: [2.7, 3.7]
-        python-version: [3.7]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+      fail-fast: false
 
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

CHANGES.md

@@ -1,3 +1,39 @@
+# Version 1.0.6
+
+**New features**
+
+- Raster plot colored by phase
+
+- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster
+
+- API for loading .mod files selectively
+
+- Ability to specify custom executor to run batch with (defaults to `sh`)
+
+**Bug fixes**
+
+- Fixed loading point cell params from legacy models (issue 607)
+
+- Fix voltage movie tutorial
+
+- Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'
+
+- Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)
+
+- Fix of `plotRaster` pops coloring if ordered not by gid
+
+- Made cells diversity work with popParams based on `cellsList` and `gridSpacing`
+
+- Fixed handling of output of `sim.create()` - was wrong order (credit: Kate Doxey)
+
+- Fixed undeclared var `dpi` in `plotShape()`
+
+- Fixes in batch utils
+
+- Added some missing math functions to use with 'Functions as string' functionality
+
+- Switch file copying method to shutil to be compatible over all operating systems (credit: Henrik Podeus)
+
 # Version 1.0.5
 
 **New features**

doc/build.py

@@ -11,11 +11,7 @@
 5) Twine packager: https://twine.readthedocs.io/en/latest/
 
 Which can be installed with:
-python3 -m pip install -U sphinx
-python3 -m pip install -U sphinx_rtd_theme
-python3 -m pip install -U autodocsumm
-python3 -m pip install -U wheel
-python3 -m pip install -U twine
+python3 -m pip install -U sphinx sphinx_rtd_theme autodocsumm wheel twine
 
 Here are the steps to release a new version of NetPyNE
 (step 10 is completed by executing this file):
@@ -54,7 +50,7 @@
          Username: salvadord
 13) Announce the new release
     13a) New release announcement text:
-         NetPyNE v#.#.# is now available. For a complete list of changes and bug fixes see: https://github.com/Neurosim-lab/netpyne/releases/tag/v#.#.#
+         NetPyNE v#.#.# is now available. For a complete list of changes and bug fixes see: https://github.com/suny-downstate-medical-center/netpyne/releases/tag/v#.#.#
          See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html
     13b) Announce on NEURON forum:
          https://www.neuron.yale.edu/phpBB/viewtopic.php?f=45&t=3685&sid=9c380fe3a835babd47148c81ae71343e

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.5'
+version = '1.0.6'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.5'
+release = '1.0.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/user_documentation.rst

@@ -305,7 +305,7 @@ Currently, 'rhythmic', 'evoked', 'poisson' and 'gauss' spike pattern generators
 
 * **evoked** - creates the ongoing external inputs (rhythmic)
 
-    * **start** - time of first spike. if -1, uniform distribution between startMin and startMax (ms)
+    * **start** - time of first spike
 
     * **inc** - increase in time of first spike; from cfg.inc_evinput (ms)
 

examples/CA3model_RasterColoredbyPhase/index.npjson

@@ -0,0 +1,6 @@
+{
+    "mod_folder": "mod",
+    "simConfig": "src/cfg.py",
+    "python_run": "src/init.py",
+    "netParams": "src/netParams.py"
+}

examples/CA3model_RasterColoredbyPhase/mod/CA1ih.mod

@@ -0,0 +1,64 @@
+: $Id: CA1ih.mod,v 1.4 2010/12/13 21:35:47 samn Exp $ 
+TITLE Ih CA3
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX hcurrent
+  NONSPECIFIC_CURRENT ih
+  RANGE g, e, v50, htau, hinf
+  RANGE gfactor
+}
+
+PARAMETER {
+  celsius	(degC)
+  g= 0.0001	(mho/cm2)
+  e= -30	(mV)
+  v50=-82	(mV)
+  gfactor = 1
+}
+
+STATE {
+  h
+}
+
+ASSIGNED {
+  ih	  (mA/cm2) 
+  hinf
+  htau    (ms)
+  v	  (mV)
+}
+
+PROCEDURE iassign () { ih=g*h*(v-e)*gfactor }
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  h'= (hinf- h)/ htau
+}
+
+INITIAL { 
+  rates(v)
+  h = hinf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  UNITSOFF
+  : HCN1
+  :hinf = 1/(1+exp(0.151*(v-v50)))
+  :htau = exp((0.033*(v+75)))/(0.011*(1+exp(0.083*(v+75))))
+
+  : HCN2
+  hinf = 1/(1+exp((v-v50)/10.5))
+  htau = (1/(exp(-14.59-0.086*v)+exp(-1.87+0.0701*v))) 
+  UNITSON
+}
+

examples/CA3model_RasterColoredbyPhase/mod/CA1ika.mod

@@ -0,0 +1,85 @@
+: $Id: CA1ika.mod,v 1.2 2010/12/01 05:06:07 samn Exp $ 
+TITLE Ika CA1
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX kacurrent
+  NONSPECIFIC_CURRENT ika, ikad
+  RANGE g, gd, e, ninf, ntau, ndinf, ndtau, linf, ltau
+}
+
+PARAMETER {
+  celsius	(degC)
+  g= 0.048	(mho/cm2)
+  gd= 0		(mho/cm2)
+  e= -90	(mV)
+}
+
+STATE {
+  n
+  nd : distal
+  l
+}
+
+ASSIGNED {
+  v	(mV)
+  ika	(mA/cm2) 
+  ikad	(mA/cm2)
+  ninf
+  ntau  (ms)
+  ndinf
+  ndtau (ms)
+  linf
+  ltau	(ms)
+}
+
+PROCEDURE iassign () {
+  ika=g*n*l*(v-e)
+  ikad=gd*nd*l*(v-e)
+}
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  n'= (ninf- n)/ ntau
+  l'= (linf- l)/ ltau
+  nd'= (ndinf-nd)/ndtau
+}
+
+INITIAL { 
+  rates(v)
+  n = ninf
+  l = linf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  LOCAL  a, b
+  UNITSOFF
+  a = exp(-0.038*(1.5+1/(1+exp(v+40)/5))*(v-11))
+  b =	exp(-0.038*(0.825+1/(1+exp(v+40)/5))*(v-11))
+  ntau=4*b/(1+a)
+  if (ntau<0.1) {ntau=0.1}
+  ninf=1/(1+a)
+
+  a=exp(-0.038*(1.8+1/(1+exp(v+40)/5))*(v+1))
+  b=exp(-0.038*(0.7+1/(1+exp(v+40)/5))*(v+1))
+  ndtau=2*b/(1+a)
+  if (ndtau<0.1) {ndtau=0.1}
+  ndinf=1/(1+a)
+
+  a = exp(0.11*(v+56))
+  ltau=0.26*(v+50)
+  if (ltau<2) {ltau=2}
+  linf=1/(1+a)
+  UNITSON
+}
+

examples/CA3model_RasterColoredbyPhase/mod/CA1ikdr.mod

@@ -0,0 +1,60 @@
+: $Id: CA1ikdr.mod,v 1.2 2010/12/01 05:10:52 samn Exp $ 
+TITLE IKDR CA1
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX kdrcurrent
+  NONSPECIFIC_CURRENT ik
+  RANGE g, e, ninf, ntau
+}
+
+PARAMETER {
+  celsius	(degC)
+  g = 0.010	(mho/cm2)
+  e = -90	(mV)
+}
+
+STATE {
+  n 
+}
+
+ASSIGNED {
+  v	  (mV)
+  ik	  (mA/cm2) 
+  ninf
+  ntau    (ms)
+}
+
+PROCEDURE iassign () { ik=g*n*(v-e) }
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  n'= (ninf- n)/ ntau
+}
+
+INITIAL { 
+  rates(v)
+  n = ninf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  LOCAL  a, b
+  UNITSOFF
+  a = exp(-0.11*(v-13))
+  b = exp(-0.08*(v-13)) 	
+  ntau=50*b/(1+a)
+  if (ntau<2) {ntau=2}
+  ninf=1/(1+a)
+  UNITSON
+}
+