Merge remote-tracking branch 'suny-downstate-medical-center/master' into development

jchen6727 · jchen6727 · commit 8086226bdd58 · 2025-07-22T10:59:25.000-05:00
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,4 +1,4 @@
-# Version in development
+# Version 1.1.0
 
 **New features**
 
@@ -14,6 +14,8 @@
 
 - Solve minor bug in the uniform field for extracelular stimulation (sign). Deposited the xtra.mod in support module.
 
+- Fixed batch SGE example (credit: Adam Newton)
+
 - Solved small bug when plotting colorbar in the raster plot colored by the LFP phase 
 
 - Solved conflict between diversity and segment coordinates (per population), used in LFP setups
@@ -22,6 +24,10 @@
 
 - Update of documentation (stimSourceParams and stimTargetParams) incorporating how to define extracellular stimulations
 
+- Fixed ODict in examples/batchCell (credit: Hyunsu Lee)
+
+- Fix in RxD to support NEURON 9 (credit: Adam Newton)
+
 - Fixed recording from variables of Point process
 
 - Fixed time slicing on pre-loaded data in plotCSD() (credit: Nikita Novikov)
@@ -30,6 +36,8 @@
 
 - Fixes, refactoring and fail-fast checks in multisinaptic connections
 
+- Fix verbatim function defs in mod files (credit: Ankur Sinha)
+
 # Version 1.0.7
 
 **New features**
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.7'
+version = '1.1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.7'
+release = '1.1.0'
 
 # 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
@@ -1408,9 +1408,7 @@ Example:
  
 .. code-block:: python
 
-   : $Id: MyExp2SynBB.mod,v 1.4 2010/12/13 21:27:51 samn Exp $ 
    NEURON {
-   :  THREADSAFE
      POINT_PROCESS MyExp2SynBB
      RANGE tau1, tau2, e, i, g, Vwt, gmax
      NONSPECIFIC_CURRENT i
diff --git a/examples/batchCell/src/utils.py b/examples/batchCell/src/utils.py
@@ -19,7 +19,7 @@ def readBatchData(dataFolder, batchLabel, loadAll=False, saveAll=True, vars=None
         print('\nLoading single file with all data...')
         filename = '%s/%s/%s_allData.json' % (dataFolder, batchLabel, batchLabel)
         with open(filename, 'r') as fileObj:
-            dataLoad = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            dataLoad = json.load(fileObj, object_pairs_hook=specs.ODict)
         params = dataLoad['params']
         data = dataLoad['data']
         return params, data
@@ -52,10 +52,10 @@ def readBatchData(dataFolder, batchLabel, loadAll=False, saveAll=True, vars=None
                 # read output file
                 iCombStr = ''.join([''.join('_'+str(i)) for i in iComb])
                 simLabel = b['batchLabel']+iCombStr
-                outFile = b['saveFolder']+'/'+simLabel+'.json'
+                outFile = b['saveFolder']+'/'+simLabel+'_data.json'
                 try:
                     with open(outFile, 'r') as fileObj:
-                        output = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+                        output = json.load(fileObj, object_pairs_hook=specs.ODict)
 
                     # save output file in data dict
                     data[iCombStr] = {}
@@ -87,14 +87,14 @@ def compare(source_file, target_file, source_key=None, target_key=None):
     from deepdiff import DeepDiff
     with open(source_file, 'r') as fileObj:
         if source_file.endswith('.json'):
-            source = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            source = json.load(fileObj, object_pairs_hook=specs.ODict)
         elif source_file.endswith('.pkl'):
             source = pickle.load(fileObj)
     if source_key: source = source[source_key]
 
     with open(target_file, 'r') as fileObj:
         if target_file.endswith('.json'):
-            target = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            target = json.load(fileObj, object_pairs_hook=specs.ODict)
         elif source_file.endswith('.pkl'):
             target = pickle.load(fileObj)
     if target_key: target = target[target_key]
diff --git a/examples/batchCellMapping/src/utils.py b/examples/batchCellMapping/src/utils.py
@@ -19,7 +19,7 @@ def readBatchData(dataFolder, batchLabel, loadAll=False, saveAll=True, vars=None
         print('\nLoading single file with all data...')
         filename = '%s/%s/%s_allData.json' % (dataFolder, batchLabel, batchLabel)
         with open(filename, 'r') as fileObj:
-            dataLoad = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            dataLoad = json.load(fileObj, object_pairs_hook=specs.ODict)
         params = dataLoad['params']
         data = dataLoad['data']
         return params, data
@@ -52,10 +52,10 @@ def readBatchData(dataFolder, batchLabel, loadAll=False, saveAll=True, vars=None
                 # read output file
                 iCombStr = ''.join([''.join('_'+str(i)) for i in iComb])
                 simLabel = b['batchLabel']+iCombStr
-                outFile = b['saveFolder']+'/'+simLabel+'.json'
+                outFile = b['saveFolder']+'/'+simLabel+'_data.json'
                 try:
                     with open(outFile, 'r') as fileObj:
-                        output = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+                        output = json.load(fileObj, object_pairs_hook=specs.ODict)
 
                     # save output file in data dict
                     data[iCombStr] = {}
@@ -87,14 +87,14 @@ def compare(source_file, target_file, source_key=None, target_key=None):
     from deepdiff import DeepDiff
     with open(source_file, 'r') as fileObj:
         if source_file.endswith('.json'):
-            source = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            source = json.load(fileObj, object_pairs_hook=specs.ODict)
         elif source_file.endswith('.pkl'):
             source = pickle.load(fileObj)
     if source_key: source = source[source_key]
 
     with open(target_file, 'r') as fileObj:
         if target_file.endswith('.json'):
-            target = json.load(fileObj, object_pairs_hook=specs.OrderedDict)
+            target = json.load(fileObj, object_pairs_hook=specs.ODict)
         elif source_file.endswith('.pkl'):
             target = pickle.load(fileObj)
     if target_key: target = target[target_key]
diff --git a/examples/batchSGE/README.md b/examples/batchSGE/README.md
@@ -35,7 +35,7 @@ simulation logs are generated in ~/qsub/
     b.runCfg = {'type': 'hpc_sge',
                 'jobName': 'my_batch',
                 'cores': 4,
-                'script': 'init.py',
+                'script': 'src/init.py',
                 'skip': True} 
 ```
 
diff --git a/examples/batchSGE/src/batch.py b/examples/batchSGE/src/batch.py
@@ -19,12 +19,12 @@ def batchTauWeight():
         b.runCfg = {'type': 'hpc_sge',
                     'jobName': 'my_batch',
                     'cores': 4,
-                    'script': 'init.py',
+                    'script': 'src/init.py',
                     'skip': True}
 
         # Run batch simulations
         b.run()
 
 # Main code
 if __name__ == '__main__':
-        batchTauWeight()
+        batchTauWeight()
diff --git a/netpyne/__init__.py b/netpyne/__init__.py
@@ -4,7 +4,7 @@
 NetPyNE consists of a number of sub-packages and modules.
 """
 
-__version__ = '1.0.7'
+__version__ = '1.1.0'
 import os, sys
 
 display = os.getenv('DISPLAY')
diff --git a/netpyne/batch/grid.py b/netpyne/batch/grid.py
@@ -326,7 +326,8 @@ def gridSubmit(batch, pc, netParamsSavePath, jobName, simLabel, processes, proce
             'vmem': '32G',
             'queueName': 'cpu.q',
             'cores': 2,
-            'pre': '', 'post': '',
+            'pre': 'source ~/.bashrc',
+            'post': '',
             'mpiCommand': 'mpiexec',
             #'log': "~/qsub/{}".format(jobName)
             'log': "{}/{}".format(os.getcwd(), jobName)
@@ -335,8 +336,9 @@ def gridSubmit(batch, pc, netParamsSavePath, jobName, simLabel, processes, proce
         sge_args.update(batch.runCfg)
 
         #(batch, pc, netParamsSavePath, jobName, simLabel, processes, processFiles):
-        sge_args['command'] = '%s -n $NSLOTS -hosts $(hostname) nrniv -python -mpi %s simConfig=%s netParams=%s' % (
+        sge_args['command'] = '%s -n %i nrniv -python -mpi %s simConfig=%s netParams=%s' % (
             sge_args['mpiCommand'],
+            sge_args['cores'],
             script,
             cfgSavePath,
             netParamsSavePath,
diff --git a/netpyne/batch/utils.py b/netpyne/batch/utils.py
@@ -107,7 +107,6 @@ def jobStringHPCSGE(jobName, walltime, vmem, queueName, cores, pre, command, pos
 #$ -o {log}.run
 #$ -e {log}.err
 {pre}
-source ~/.bashrc
 {command}
 {post}
         """
diff --git a/netpyne/batchtools/search.py b/netpyne/batchtools/search.py
@@ -363,14 +363,14 @@ def generate_constructors(job_type, comm_type, **kwargs):
 
 def generate_parameters(params, algorithm, **kwargs):
     """
-    returns a dictionary of parameters for ray_search based on the input dictionary
-    from NOTES Salvador:
-    params = {'synMechTau2': [3.0, 5.0, 7.0], # assumes list of values by default if grid search-like algo
-		  #'synMechTau2': [3.0, 7.0], # assumes lower/upper bounds by default if evol-like algo
-          'connWeight' : paramtypes.sample_from(lambda _: numpy.random.uniform(0.005, 0.15))} # can optionally pass any of the paramtypes (= ray.tune data types)
-
-    #TODO: check coverage of conditional statements (looks okay?)
+    Returns a dictionary of parameters for ray_search based on the input dictionary from:
+    params = {
+    'synMechTau2': [3.0, 5.0, 7.0], # assumes list of values by default if grid search-like algo
+    #'synMechTau2': [3.0, 7.0], # assumes lower/upper bounds by default if evol-like algo
+    'connWeight' : paramtypes.sample_from(lambda _: numpy.random.uniform(0.005, 0.15))
+    } # can optionally pass any of the paramtypes (= ray.tune data types)
     """
+    #TODO: check coverage of conditional statements (looks okay?)
     ray_params = {}
     _expected_trials_per_sample = 1
     for param, space in params.items():
diff --git a/netpyne/sim/setup.py b/netpyne/sim/setup.py
@@ -91,14 +91,16 @@ def initialize(netParams=None, simConfig=None, net=None):
 
     if hasattr(sim.cfg, 'validateNetParams') and sim.cfg.validateNetParams:  # whether to validate the input parameters
         try:
-            print('Validating NetParams ...')
+            print('\nValidating NetParams ...')
             sim.timing('start', 'validationTime')
             valid, failed = validator.validateNetParams(netParams)
             sim.timing('stop', 'validationTime')
             if failed:
                 failedComps = [err.component for err in failed] # get failed component name
                 failedComps = list(set(failedComps)) # keep unique elements only
-                print(f"\n✋ NetParams validation identified some potential issues in {', '.join(failedComps)}. See above for details.")
+                BOLD = "\033[1m"
+                RESET = "\033[0m"
+                print(f"\n✋ NetParams validation identified some potential issues in {BOLD}{', '.join(failedComps)}{RESET}. See above for details.")
             else:
                 print("\n✅ NetParams validation successful.")
         except Exception as e:
diff --git a/netpyne/sim/validator.py b/netpyne/sim/validator.py
@@ -47,7 +47,6 @@
 MECH_PARAM_TYPE_ERROR = "Parameter '{0}' of '{1}' must be a number, a list of numbers (per segment), or a function as string."
 POINTP_PARAM_ERROR = "Parameter '{0}' is not valid for point process '{1}'."
 POINTP_PARAM_TYPE_ERROR = "Parameter '{0}' of '{1}' must be a number, boolean, or function as string."
-RXD_DIMENSION_ERROR = 'Dimension must be 1, 2, or 3.'
 COND_PARAM_ERROR = 'Condition value must be a string, a list of strings, or a list of two numbers (from, to).'
 INVALID_VALUE_ERROR = 'Invalid value.'
 NUMBER_OR_3NUMS_ERROR = 'Expected a number or a list of three numbers.'
@@ -823,7 +822,7 @@ def rxd_specs():
                         ),
                         None,
                     ),
-                    Optional('dimension'): Or(lambda s: s in [1, 2, 3], None, error=RXD_DIMENSION_ERROR),
+                    Optional('dimension'): object, # no longer used. Kept here for backward compatibility
                     Optional('dx'): numberOrNone,
                 },
             )
