Templateargs update

.github/workflows/python-app.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
         matrix:
             os: [ubuntu-latest, macOS-latest]
-            python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+            python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

.gitignore

@@ -146,3 +146,8 @@ examples/bioRxiv281717/figure_7_8/parameters
 x86_64
 arm64
 aarch64
+# ignoring downloaded model folders from GitHub for
+# examples/LFPy-example-03.ipynb and others
+examples/2488/
+# examples/LFPy-example-04.ipynb and others
+examples/139653/

LFPy/templatecell.py

@@ -39,7 +39,7 @@ class TemplateCell(Cell):
         File with cell template definition(s)
     templatename : str
         Cell template-name used for this cell object
-    templateargs : str
+    templateargs : None, str, int or list of arguments
         Parameters provided to template-definition
     v_init : float
         Initial membrane potential. Default to -65.
@@ -150,7 +150,18 @@ def __init__(self,
     def _load_geometry(self):
         """Load the morphology-file in NEURON"""
         # the python cell object we are loading the morphology into:
-        self.template = getattr(neuron.h, self.templatename)(self.templateargs)
+        # Check templateargs arguments
+        if self.templateargs is None:
+            self.template = getattr(neuron.h, self.templatename)()
+        elif isinstance(self.templateargs, (str, int)):
+            self.template = getattr(neuron.h,
+                                    self.templatename)(self.templateargs)
+        elif isinstance(self.templateargs, (list, tuple)):
+            self.template = getattr(neuron.h,
+                                    self.templatename)(*self.templateargs)
+        else:
+            msg = "templateargs must be None, int, str, list or tuple"
+            raise ValueError(msg)
 
         # perform a test if the morphology is already loaded:
         seccount = 0

LFPy/version.py

@@ -1 +1 @@
-version = "2.3.3"
+version = "2.3.4"

examples/example_EPFL_neurons.py

@@ -3,7 +3,7 @@
 """
 Test implementation using cell models of the Blue Brain Project with LFPy.
 The example assumes that the complete set of cell models available from
-https://bbpnmc.epfl.ch/nmc-portal/downloads is unzipped in this folder.
+https://bbp.epfl.ch/nmc-portal/downloads.html is unzipped in this folder.
 
 Execution:
 

examples/example_MEA.py

@@ -25,9 +25,6 @@ class LFPy.RecMEAElectrode which incorporates discontinous extracellular
 """
 import os
 from os.path import join
-from urllib.request import urlopen
-import zipfile
-import ssl
 import LFPy
 import numpy as np
 import matplotlib.pyplot as plt
@@ -188,18 +185,9 @@ def mark_subplots(axes, letters='ABCDEFGHIJKLMNOPQRSTUVWXYZ',
 
 
 # Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')):
+if not os.path.isfile(join('2488', 'cells', 'j4a.hoc')):
     # get the model files:
-    url = '{}{}'.format('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp',
-                        '?o=2488&a=23&mime=application/zip')
-    u = urlopen(url, context=ssl._create_unverified_context())
-    localFile = open('patdemo.zip', 'wb')
-    localFile.write(u.read())
-    localFile.close()
-    # unzip:
-    myzip = zipfile.ZipFile('patdemo.zip', 'r')
-    myzip.extractall('.')
-    myzip.close()
+    os.system('git clone https://github.com/ModelDBRepository/2488.git')
 
 ##########################################################################
 # Main script, set parameters and create cell, synapse and electrode objects
@@ -208,7 +196,7 @@ def mark_subplots(axes, letters='ABCDEFGHIJKLMNOPQRSTUVWXYZ',
 # Define cell parameters
 cell_parameters = {
     # from Mainen & Sejnowski, J Comput Neurosci, 1996
-    'morphology': join('cells', 'cells', 'j4a.hoc'),
+    'morphology': join('2488', 'cells', 'j4a.hoc'),
     'cm': 1.0,         # membrane capacitance
     'Ra': 150.,        # axial resistance
     'v_init': -65.,    # initial crossmembrane potential

examples/example_loadL5bPCmodelsEH.py

@@ -9,7 +9,7 @@
 this folder from ModelDB:
 http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=139653
 
-The mod-files inside /L5bPCmodelsEH/mod/ must be compiled using nrnivmodl.
+The mod-files inside /139653/mod/ must be compiled using nrnivmodl.
 
 Note that LFPy can only deal with one cell at the time, creating several
 cell objects will slow everything down, but each cell *should* get the correct
@@ -37,44 +37,29 @@
 import matplotlib.pyplot as plt
 import os
 import sys
-if sys.version < '3':
-    from urllib2 import urlopen
-else:
-    from urllib.request import urlopen
-import zipfile
-import ssl
 from warnings import warn
 
 
 # Fetch Hay et al. 2011 model files
-if not os.path.isfile('L5bPCmodelsEH/morphologies/cell1.asc'):
+if not os.path.isfile('139653/morphologies/cell1.asc'):
     # get the model files:
-    url = '{}{}'.format('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp',
-                        '?o=139653&a=23&mime=application/zip')
-    u = urlopen(url, context=ssl._create_unverified_context())
-    localFile = open('L5bPCmodelsEH.zip', 'wb')
-    localFile.write(u.read())
-    localFile.close()
-    # unzip:
-    myzip = zipfile.ZipFile('L5bPCmodelsEH.zip', 'r')
-    myzip.extractall('.')
-    myzip.close()
+    os.system('git clone https://github.com/ModelDBRepository/139653.git')
 
 # compile mod files every time, because of incompatibility with Mainen96 files:
 if "win32" in sys.platform:
-    pth = "L5bPCmodelsEH/mod/"
+    pth = "139653/mod/"
     warn("no autompile of NMODL (.mod) files on Windows."
          + "Run mknrndll from NEURON bash in the folder "
-         + "L5bPCmodelsEH/mod and rerun example script")
+         + "139653/mod and rerun example script")
     if pth not in neuron.nrn_dll_loaded:
         neuron.h.nrn_load_dll(pth + "nrnmech.dll")
     neuron.nrn_dll_loaded.append(pth)
 else:
     os.system('''
-              cd L5bPCmodelsEH/mod/
+              cd 139653/mod/
               nrnivmodl
               ''')
-    neuron.load_mechanisms('L5bPCmodelsEH/mod/')
+    neuron.load_mechanisms('139653/mod/')
 
 # remove cells from previous script executions
 neuron.h('forall delete_section()')
@@ -84,11 +69,11 @@
 # 'templateargs'!
 # Reason is LFPy looks for a default rotation .rot-file.
 cellParams = {
-    'morphology': 'L5bPCmodelsEH/morphologies/cell1.asc',
-    'templatefile': ['L5bPCmodelsEH/models/L5PCbiophys3.hoc',
-                     'L5bPCmodelsEH/models/L5PCtemplate.hoc'],
+    'morphology': '139653/morphologies/cell1.asc',
+    'templatefile': ['139653/models/L5PCbiophys3.hoc',
+                     '139653/models/L5PCtemplate.hoc'],
     'templatename': 'L5PCtemplate',
-    'templateargs': 'L5bPCmodelsEH/morphologies/cell1.asc',
+    'templateargs': '139653/morphologies/cell1.asc',
     'nsegs_method': None,
     'v_init': -80,
     'tstart': 0,

examples/example_mpi.py

@@ -39,12 +39,6 @@
 from LFPy.inputgenerators import get_activation_times_from_distribution
 import neuron
 import sys
-if sys.version < '3':
-    from urllib2 import urlopen
-else:
-    from urllib.request import urlopen
-import zipfile
-import ssl
 from warnings import warn
 from mpi4py import MPI
 
@@ -54,37 +48,27 @@
 RANK = COMM.Get_rank()
 
 # Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')) and RANK == 0:
-
+if not os.path.isfile(join('2488', 'cells', 'j4a.hoc')) and RANK == 0:
     # get the model files:
-    url = '{}{}'.format('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp',
-                        '?o=2488&a=23&mime=application/zip')
-    u = urlopen(url, context=ssl._create_unverified_context())
-    localFile = open('patdemo.zip', 'w')
-    localFile.write(u.read())
-    localFile.close()
-    # unzip:
-    myzip = zipfile.ZipFile('patdemo.zip', 'r')
-    myzip.extractall('.')
-    myzip.close()
+    os.system('git clone https://github.com/ModelDBRepository/2488.git')
 
 # compile mod files every time, because of incompatibility with Hay2011 files:
 if "win32" in sys.platform:
-    pth = "cells"
+    pth = "2488"  # path to folder
     warn("no autompile of NMODL (.mod) files on Windows. "
-         + "Run mknrndll from NEURON bash in the folder cells and "
+         + "Run mknrndll from NEURON bash in the folder 2488 and "
          + "rerun example script")
     if pth not in neuron.nrn_dll_loaded:
         neuron.h.nrn_load_dll(pth + "/nrnmech.dll")
     neuron.nrn_dll_loaded.append(pth)
 else:
     if RANK == 0:
         os.system('''
-                  cd cells
+                  cd 2488
                   nrnivmodl
                   ''')
     COMM.Barrier()
-    neuron.load_mechanisms('cells')
+    neuron.load_mechanisms('2488')
 
 
 # set one global seed, ensure all randomizations are set on RANK 0 in script!
@@ -199,7 +183,8 @@ def drawRandCellPositions(self):
         return COMM.bcast(cellPositions, root=0)
 
     def drawRandCellRotations(self):
-        '''draw and distribute random cell rotations for all cells in population
+        '''draw and distribute random cell rotations
+        for all cells in population
         '''
         if RANK == 0:
             cellRotations = np.random.rand(self.POPULATION_SIZE) * np.pi * 2

examples/example_mpi_2.py

@@ -29,13 +29,6 @@
 from matplotlib.collections import LineCollection
 import os
 from os.path import join
-import sys
-if sys.version < '3':
-    from urllib2 import urlopen
-else:
-    from urllib.request import urlopen
-import zipfile
-import ssl
 import LFPy
 from mpi4py import MPI
 
@@ -67,25 +60,16 @@ def stationary_poisson(nsyn, lambd, tstart, tstop):
 
 
 # Fetch Mainen&Sejnowski 1996 model files
-if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')) and RANK == 0:
+if not os.path.isfile(join('2488', 'cells', 'j4a.hoc')) and RANK == 0:
     # get the model files:
-    url = '{}{}'.format('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp',
-                        '?o=2488&a=23&mime=application/zip')
-    u = urlopen(url, context=ssl._create_unverified_context())
-    localFile = open('patdemo.zip', 'w')
-    localFile.write(u.read())
-    localFile.close()
-    # unzip:
-    myzip = zipfile.ZipFile('patdemo.zip', 'r')
-    myzip.extractall('.')
-    myzip.close()
+    os.system('git clone https://github.com/ModelDBRepository/2488.git')
 
 # resync MPI threads
 COMM.Barrier()
 
 # Define cell parameters
 cell_parameters = {          # various cell parameters,
-    'morphology': join('cells', 'cells', 'j4a.hoc'),  # Mainen&Sejnowski, 1996
+    'morphology': join('2488', 'cells', 'j4a.hoc'),  # Mainen&Sejnowski, 1996
     'cm': 1.0,         # membrane capacitance
     'Ra': 150,         # axial resistance
     'v_init': -65.,    # initial crossmembrane potential
@@ -229,7 +213,7 @@ def stationary_poisson(nsyn, lambd, tstart, tstop):
     plt.axis('off')
 
     for i_cell in range(n_cells):
-        cell = LFPy.Cell(join('cells', 'cells', 'j4a.hoc'),
+        cell = LFPy.Cell(join('2488', 'cells', 'j4a.hoc'),
                          nsegs_method='lambda_f',
                          lambda_f=5)
         cell.set_rotation(z=z_rotation[i_cell], **xy_rotations)