updates to batch_rev to fix test_cases (#791)

* update to batch scripts to allow for custom script generation grid search w/ custom script generation functions. updated batch to run with custom functions batch update updates to JSON serializer. (batch, save, utils) -> remove legacy import grid and template modification * update template with direct mpi call * update to grid, templates and utils descriptive naming * updates to grid, template, utils, WIP * updating grid and utils, moving job * revision, grid submit now wrapper to job submit in utils * templates and utils update * updated optimization, now utilizing the same job submission as grid * from templates to jobTypes * command moved to args now args['command'] * time series and PSD plots for CSD (along with some related re-factoring) * VERSION 1.0.5 * Fixed loading point cell params from legacy models (iincl. ssue 607). Re-factored cell class detection in pop.py * extracted conditions checking code to separate method * docstring for Batch update grid and util for sge * cell inputs.py `tstop` versus `stop` * updated .rst for documentation, inputs * updated 'tstop', 'stop', integer for n_inputs * quickfix, "mpi_bulletin" update utils and save to prevent run configuration use _generate_only flag as True (for debugging purposes) update utils runJob <- two different functions (with args) exist, agg to 1 updated grid, template, utils need to use cfg.simLabel vs cfg.jobName updated test cases, utils evaluator handling 'type' updates to batch fixed test_tutorials * removed old commented code from grid.py + merge --------- Co-authored-by: James Chen <[email protected]> Co-authored-by: vvbragin <[email protected]> Co-authored-by: Valeriy Bragin <[email protected]>
suny-downstate-medical-center · Nov 3, 2023 · e8462f4 · e8462f4
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diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,20 @@
 
 **New features**
 
+**Bug fixes**
+
+- Fixed loading point cell params from legacy models (issue 607)
+
+# Version 1.0.5
+
+**New features**
+
+- Time series and PSD plots for current source density (CSD)
+
+- Added colorbar to CSD plot
+
+- Support for Sun Grid Engine HPC
+
 - Extended sim.gatherData() with more optional arguments for flexibility
 
 - Specify linear/log scale in `plotRatePSD()`
@@ -10,6 +24,10 @@
 
 - Check RxD specification for potential syntax issues
 
+- Prevent zero population size in scaled-down models
+
+- Better messages for validation errors
+
 **Bug fixes**
 
 - Fixed errors in plotting with sim.cfg.gatherOnlySimData=True
@@ -22,6 +40,8 @@
 
 - Fixed performance issue in `plotConn()` with `groupBy='pop'` (default)
 
+- Fixed `recordTraces` to not require more presicion than segment size (for stim and synMech)
+
 # Version 1.0.4.2
 
 **Bug fixes**

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.4.2'
+version = '1.0.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.4.2'
+release = '1.0.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/source/user_documentation.rst b/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)
 

diff --git a/examples/LFPrecording/src/cell/cfg.py b/examples/LFPrecording/src/cell/cfg.py
@@ -14,7 +14,5 @@
 
 cfg.analysis['plotTraces'] = {'include': [('E',0)], 'oneFigPer':'cell', 'overlay': False, 'figSize': (5,6),'saveFig': True}      # Plot recorded traces for this list of cells
 cfg.analysis['plotLFP'] = {'includeAxon': False, 'plots': ['timeSeries',  'locations'], 'figSize': (7.5,13.5), 'saveFig': True}
-#simConfig.analysis['getCSD'] = {'timeRange': [10,45],'spacing_um': 150, 'vaknin': True}
-#simConfig.analysis['plotCSD'] = {'timeRange': [10,45]}
-#sim.analysis.getCSD(...args...)
-#simConfig.analysis['plotCSD'] = {}
+# cfg.analysis['plotCSD'] = {'timeRange': [10,45],'spacing_um': 150, 'vaknin': True, 'saveFig': True}
+# cfg.analysis['plotCSDTimeSeries'] = {'saveFig': True}
diff --git a/examples/LFPrecording/src/net/cfg.py b/examples/LFPrecording/src/net/cfg.py
@@ -22,5 +22,6 @@
 cfg.analysis['plotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'timeRange': [100,1000], 'saveFig': True}  # optional: 'pop': 'E4'
 #simConfig.analysis['getCSD'] = {'spacing_um': 200, 'timeRange': [100,3000], 'vaknin': True}
 #simConfig.analysis['plotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'timeRange':[100,900], 'minFreq': 10, 'maxFreq':60, 'norm':1, 'plots': ['spectrogram'], 'showFig': True} 
-#simConfig.analysis['plotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'timeRange':[100,900], 'plots': ['spectrogram'], 'showFig': True} 
-#simConfig.analysis['plotCSD'] = True #{'timeRange':[100,200]}
+# cfg.analysis['plotCSD'] = {'saveFig': True, 'spacing_um': 150, 'overlay': 'CSD'}
+# cfg.analysis['plotCSDTimeSeries'] = {'saveFig': True}
+# cfg.analysis['plotCSDPSD'] = {'saveFig': True}
diff --git a/examples/batchSGE/src/batch.py b/examples/batchSGE/src/batch.py
@@ -19,7 +19,7 @@ def batchTauWeight():
         b.runCfg = {'type': 'hpc_sge',
                     'jobName': 'my_batch',
                     'cores': 4,
-                    'script': 'init.py',
+                    'script': 'src/init.py',
                     'skip': True}
 
         # Run batch simulations

diff --git a/examples/dipoleRecording/src/cfg_cell.py b/examples/dipoleRecording/src/cfg_cell.py
@@ -16,7 +16,4 @@
 
 cfg.analysis['plotTraces'] = {'include': [('E',0)], 'oneFigPer':'cell', 'overlay': True, 'figSize': (5,3),'saveFig': True}      # Plot recorded traces for this list of cells
 #cfg.analysis['plotLFP'] = {'includeAxon': False, 'plots': ['timeSeries',  'locations'], 'figSize': (5,9), 'saveFig': True}
-#cfg.analysis['getCSD'] = {'timeRange': [10,45],'spacing_um': 150, 'vaknin': True}
-#cfg.analysis['plotCSD'] = {'timeRange': [10,45]}
-#sim.analysis.getCSD(...args...)
-#cfg.analysis['plotCSD'] = {}
+#cfg.analysis['plotCSD'] = {'timeRange': [10,45], 'saveFig': True}
diff --git a/examples/dipoleRecording/src/init_cell.py b/examples/dipoleRecording/src/init_cell.py
@@ -1,5 +1,5 @@
 from netpyne import sim
 
-cfg, netParams = sim.loadFromIndexFile('index_cell.npjson')
+cfg, netParams = sim.loadFromIndexFile('index.npjson')
 sim.createSimulateAnalyze(netParams = netParams, simConfig = cfg)    
-#sim.analysis.plotCSD()
+#sim.analysis.plotCSD()
diff --git a/netpyne/analysis/__init__.py b/netpyne/analysis/__init__.py
@@ -81,9 +81,7 @@
     print('Warning: could not import interactive plotting functions; make sure the "bokeh" package is installed.')
 
 # Import CSD-related functions
-# from .csd import getCSD, plotCSD
 from .csd import prepareCSD
-# from .csd import prepareCSDPSD
 
 # Import dipole-related functions
 from .dipole import plotDipole, plotEEG