Merge pull request #140 from kaeldai/cleanup/0.8_release

fixing tutorials

Author: kaeldai

.travis.yml

@@ -2,7 +2,6 @@ language: python
 
 matrix:
   include:
-    - python: 2.7
     - python: 3.6
 
 before_install:

bmtk/analyzer/spike_trains.py

@@ -71,6 +71,7 @@ def _find_spikes(spikes_file=None, config_file=None, population=None):
                 spikes_f))
 
         spikes_obj = SpikeTrains.load(spikes_f)
+
         if len(spikes_obj.populations) > 1:
             raise ValueError('Spikes file {} contains more than one node population.'.format(spikes_f))
         else:
@@ -208,5 +209,7 @@ def calc_stats(r):
 
 
 def to_dataframe(config_file, spikes_file=None, population=None):
-    _, spike_trains = _find_spikes(config_file=config_file, spikes_file=spikes_file, population=population)
+    # _, spike_trains = _find_spikes(config_file=config_file, spikes_file=spikes_file, population=population)
+    pop, spike_trains = _find_spikes(config_file=config_file, spikes_file=spikes_file, population=population)
+
     return spike_trains.to_dataframe()

bmtk/simulator/bionet/biocell.py

@@ -69,8 +69,8 @@ class BioCell(Cell):
     """Implemntation of a morphologically and biophysically detailed type cell.
 
     """
-    def __init__(self, node, bionetwork):
-        super(BioCell, self).__init__(node)
+    def __init__(self, node, population_name, bionetwork):
+        super(BioCell, self).__init__(node=node, population_name=population_name, network=bionetwork)
 
         # Set up netcon object that can be used to detect and communicate cell spikes.
         self.set_spike_detector(bionetwork.spike_threshold)

bmtk/simulator/bionet/bionetwork.py

@@ -123,9 +123,9 @@ def get_virtual_cells(self, population, node_id, spike_trains):
             self._virtual_nodes[population][node_id] = virt_cell
             return virt_cell
 
-    def _build_cell(self, bionode):
+    def _build_cell(self, bionode, population_name):
         if bionode.model_type in self._model_type_map:
-            cell = self._model_type_map[bionode.model_type](bionode, self)
+            cell = self._model_type_map[bionode.model_type](bionode, population_name=population_name, bionetwork=self)
             self._rank_nodes_by_model[bionode.model_type][cell.gid] = cell
             return cell
         else:
@@ -142,7 +142,7 @@ def build_nodes(self):
             node_ids_map = {}
             if node_pop.internal_nodes_only:
                 for node in node_pop[MPI_rank::MPI_size]:
-                    cell = self._build_cell(node)
+                    cell = self._build_cell(bionode=node, population_name=node_pop.name)
                     node_ids_map[node.node_id] = cell
                     self._rank_node_gids[cell.gid] = cell
 
@@ -154,8 +154,10 @@ def build_nodes(self):
                     if node.model_type == 'virtual':
                         continue
                     else:
-                        cell = self._build_cell(node)
+                        cell = self._build_cell(bionode=node, population_name=node_pop.name)
                         node_ids_map[node.node_id] = cell
+
+
                         self._rank_node_gids[cell.gid] = cell
 
             elif node_pop.virtual_nodes_only:

bmtk/simulator/bionet/cell.py

@@ -35,9 +35,10 @@ class Cell(object):
     a Cell object directly. Cell classes act as wrapper around HOC cell object with extra functionality for setting
     positions, synapses, and other parameters depending on the desired cell class.
     """
-    def __init__(self, node):
+    def __init__(self, node, population_name, network=None):
         self._node = node
-        self._gid = node.gid
+
+        self._gid = network.gid_pool.get_gid(name=population_name, node_id=node.node_id)
         self._node_id = node.node_id
         self._props = node
         self._netcons = []  # list of NEURON network connection object attached to this cell

bmtk/simulator/bionet/config.py

@@ -42,6 +42,8 @@ def load_nrn_modules(self):
         nrn.load_neuron_modules(self.mechanisms_dir, self.templates_dir)
 
     def build_env(self):
+        self.io = io
+        self._set_logging()
         self.create_output_dir()
         self.copy_to_output()
         if io.mpi_size > 1:

bmtk/simulator/bionet/gids.py

@@ -23,7 +23,7 @@ def add_pool(self, name, n_nodes):
         self._accumulated_offset += n_nodes
 
     def get_gid(self, name, node_id):
-        return self._pool_offsets[name] + node_id
+        return int(self._pool_offsets[name] + node_id)
 
     def get_pool_id(self, gid):
         offset_indx = np.searchsorted(self._offsets, gid, 'right')

bmtk/simulator/bionet/pointprocesscell.py

@@ -54,8 +54,8 @@ def syn_weight(self, val):
 
 class PointProcessCell(Cell):
     """Implimentation of a Leaky Integrate-and-file neuron type cell."""
-    def __init__(self, node, bionetwork):
-        super(PointProcessCell, self).__init__(node)
+    def __init__(self, node, population_name, bionetwork):
+        super(PointProcessCell, self).__init__(node, population_name=population_name, network=bionetwork)
         self.set_spike_detector()
         self._src_gids = []
         self._src_nets = []

bmtk/simulator/core/node_sets.py

@@ -39,7 +39,7 @@ def gids(self):
         else:
             for pop in self._populations:
                 for node in pop.filter(self._filter):
-                    yield node.node_id
+                    yield self._network.gid_pool.get_gid(name=pop.name, node_id=node.node_id)
 
     def nodes(self):
         return None

bmtk/simulator/pointnet/gids.py

@@ -24,8 +24,7 @@ def add(self, name, node_id, gid):
         raise NotImplementedError()
 
     def get_gid(self, name, node_id):
-        # return self._popid2gid[name][node_id]
-        raise NotImplementedError()
+        return self.get_nestids(name=name, node_ids=[node_id])[0]
 
     def get_pool_id(self, gid):
         return self._gid2pop_id[gid]