Merge pull request #830 from suny-downstate-medical-center/development

PR from development to master - VERSION 1.0.7

.github/workflows/tests.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

CHANGES.md

@@ -1,3 +1,43 @@
+# Version 1.0.7
+
+**New features**
+
+- Introducing `batchtools` subpackage for parameters exploration and optimization
+
+- Added progress-bar indicating network creation progress. Toggle the progress bar with cfg.progressBar
+
+- cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule
+
+- Added ability to use `sec`, `loc`, `preSec` and `preLoc` from list in connList-type connParams
+
+- Updated tests.examples.utils to allow for dynamic pathing
+
+- Dropped python2 support
+
+**Bug fixes**
+
+- Better handling of exceptions in `importCellParams()` (incl. `h.load_file()` - issue 782)
+
+- Pandas deprecated parameter fix
+
+- Fixed pointer id overflow on MPI (e.g. for gap junctions)
+
+- preSec and preLoc are no longer lost for inverse pointer connection
+
+- Fixed crash due to use of matplotlib.TextArea deprecated param (credit: Christian O'Reilly)
+
+- syncLines in rasterPlot restored
+
+- Fixed a bug in `gatherDataFromFiles()` where cellGids for node 0 were lost
+
+- Fixed generating rhythmic spiking pattern with 'uniform' option
+
+- Fixed misleading console output when cfg.recordStims is On
+
+- The colors in CSD plots are now properly aligned vertically with the CSD time-series overlays (credit: Sam Neymotin)
+
+- Update mkdir to makedirs (credit: Jacob Sprouse)
+
 # Version 1.0.6
 
 **New features**

doc/build.py

@@ -51,7 +51,7 @@
 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/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
+         See here for instructions to install or update to the latest version: https://www.netpyne.org/documentation/installation
     13b) Announce on NEURON forum:
          https://www.neuron.yale.edu/phpBB/viewtopic.php?f=45&t=3685&sid=9c380fe3a835babd47148c81ae71343e
     13c) Announce to Google group:

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.6'
+version = '1.0.7'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.6'
+release = '1.0.7'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

examples/HHTut/src/HHTut.py

@@ -70,7 +70,6 @@
 
 # Saving
 simConfig.filename = 'HHTut'  # Set file output name
-simConfig.saveFileStep = 1000 # step size in ms to save data to disk
 simConfig.savePickle = False # Whether or not to write spikes etc. to a .mat file
 simConfig.saveJson = True
 

examples/HybridTut/src/cfg.py

@@ -23,7 +23,6 @@
 
 # Saving
 cfg.filename = 'mpiHybridTut'  # Set file output name
-cfg.saveFileStep = 1000 # step size in ms to save data to disk
 cfg.savePickle = False # Whether or not to write spikes etc. to a .mat file
 cfg.saveJson = False # Whether or not to write spikes etc. to a .mat file
 cfg.saveMat = False # Whether or not to write spikes etc. to a .mat file

examples/M1/src/cfg.py

@@ -34,7 +34,6 @@
 
 # Saving
 cfg.filename = 'data/M1_ynorm_izhi'  # Set file output name
-cfg.saveFileStep = 1000 # step size in ms to save data to disk
 cfg.savePickle = False # save to pickle file
 cfg.saveJson = False # save to json file
 cfg.saveMat = False # save to mat file

examples/RL_arm/params.py

@@ -308,7 +308,6 @@
 
 # Saving
 simConfig.filename = 'simdata'  # Set file output name
-simConfig.saveFileStep = 1000 # step size in ms to save data to disk
 simConfig.savePickle = True # Whether or not to write spikes etc. to a .mat file
 simConfig.saveJson = False # Whether or not to write spikes etc. to a .mat file
 simConfig.saveMat = False # Whether or not to write spikes etc. to a .mat file

examples/netClamp/src/cfg.py

@@ -1,4 +1,3 @@
-import imp
 from netpyne import specs
 
 # Simulation options
@@ -14,4 +13,4 @@
 cfg.recordStim = True  # required for netClamp to work
 
 cfg.analysis['plotRaster'] = {'orderBy': 'y', 'orderInverse': True}      # Plot a raster
-cfg.analysis['plotTraces'] = {'include': [5]}      # Plot recorded traces for this list of cells
+cfg.analysis['plotTraces'] = {'include': [5]}      # Plot recorded traces for this list of cells

examples/rxd_buffering/src/netParams.py

@@ -1,4 +1,3 @@
-import imp
 from netpyne import specs
 
 netParams = specs.NetParams()  # object of class NetParams to store the network parameters
@@ -27,4 +26,4 @@
 netParams.rxdParams['reactions'] = {'buffering': {'reactant': '2 * ca + buf', 'product': 'cabuf', 'rate_f': kf, 'rate_b': kb}}
 
 ### rates
-netParams.rxdParams['rates'] = {'degradation': {'species': 'buf', 'rate': '-1e-3 * buf'}}
+netParams.rxdParams['rates'] = {'degradation': {'species': 'buf', 'rate': '-1e-3 * buf'}}

netpyne/__init__.py

@@ -4,7 +4,7 @@
 NetPyNE consists of a number of sub-packages and modules.
 """
 
-__version__ = '1.0.6'
+__version__ = '1.0.7'
 import os, sys
 
 display = os.getenv('DISPLAY')

netpyne/analysis/csd.py

@@ -3,15 +3,6 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
-from future import standard_library
-
-standard_library.install_aliases()
-
 try:
     basestring
 except NameError:

netpyne/analysis/dipole.py

@@ -3,24 +3,13 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
 import os
-from builtins import range
-from builtins import round
-from builtins import str
 
 try:
     basestring
 except NameError:
     basestring = str
 
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/filter.py

@@ -21,11 +21,6 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
 import warnings
 
 import numpy as np

netpyne/analysis/info.py

@@ -3,20 +3,11 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
 try:
     basestring
 except NameError:
     basestring = str
 
-from builtins import zip
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/interactive.py

@@ -3,14 +3,6 @@
 
 """
 
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 try:

netpyne/analysis/lfp.py

@@ -3,23 +3,11 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
-from builtins import range
-from builtins import round
-from builtins import str
-
 try:
     basestring
 except NameError:
     basestring = str
 
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/lfp_orig.py

@@ -3,23 +3,11 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
-from builtins import range
-from builtins import round
-from builtins import str
-
 try:
     basestring
 except NameError:
     basestring = str
 
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/network.py

@@ -3,26 +3,11 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
-from builtins import open
-from builtins import next
-from builtins import range
-from builtins import str
-
 try:
     basestring
 except NameError:
     basestring = str
-from builtins import zip
-
-from builtins import round
-from future import standard_library
 
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/rxd.py

@@ -3,19 +3,11 @@
 
 """
 
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-
 try:
     basestring
 except NameError:
     basestring = str
 
-from future import standard_library
-
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__:

netpyne/analysis/spikes.py

@@ -3,19 +3,6 @@
 
 """
 
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-
-from future import standard_library
-
-standard_library.install_aliases()
-
-from builtins import round
-from builtins import open
-from builtins import range
-
 try:
     to_unicode = unicode
 except NameError:
@@ -83,15 +70,15 @@ def prepareSpikeData(
             orderBy = 'gid'
         elif orderBy == 'pop':
             df['popInd'] = df['pop'].astype('category')
-            df['popInd'].cat.set_categories(sim.net.pops.keys(), inplace=True)
+            df['popInd'] = df['popInd'].cat.set_categories(sim.net.pops.keys())
             orderBy = 'popInd'
         elif isinstance(orderBy, basestring) and not isinstance(cells[0]['tags'][orderBy], Number):
             orderBy = 'gid'
 
         if isinstance(orderBy, list):
             if 'pop' in orderBy:
                 df['popInd'] = df['pop'].astype('category')
-                df['popInd'].cat.set_categories(sim.net.pops.keys(), inplace=True)
+                df['popInd'] = df['popInd'].cat.set_categories(sim.net.pops.keys())
                 orderBy[orderBy.index('pop')] = 'popInd'
             keep = keep + list(set(orderBy) - set(keep))
         elif orderBy not in keep:

netpyne/analysis/spikes_legacy.py

@@ -3,25 +3,11 @@
 
 """
 
-from __future__ import print_function
-from __future__ import division
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
-from builtins import dict
-from builtins import round
-from builtins import str
-
 try:
     basestring
 except NameError:
     basestring = str
-from builtins import range
-from builtins import zip
-
-from future import standard_library
 
-standard_library.install_aliases()
 from netpyne import __gui__
 
 if __gui__: