ENH: cell shouldn't take soma_props as argument

hnn_core/cell.py

@@ -74,9 +74,6 @@ class Cell:
 
     Parameters
     ----------
-    soma_props : dict
-        The properties of the soma. Must contain
-        keys 'L', 'diam'.
     pos : tuple
         The (x, y, z) coordinates.
     gid : int or None (optional)
@@ -109,9 +106,8 @@ class Cell:
         GID of the cell in a network (or None if not yet assigned)
     """
 
-    def __init__(self, soma_props, pos, gid=None):
+    def __init__(self, pos, gid=None):
         self.pos = pos
-        self.soma_props = soma_props
         # preallocate dict to store dends
         self.dends = dict()
         self.synapses = dict()
@@ -127,11 +123,7 @@ def __init__(self, soma_props, pos, gid=None):
 
     def __repr__(self):
         class_name = self.__class__.__name__
-        soma_props = self.soma_props
-        s = ('soma: L %f, diam %f, Ra %f, cm %f' %
-             (soma_props['L'], soma_props['diam'],
-              soma_props['Ra'], soma_props['cm']))
-        return '<%s | %s>' % (class_name, s)
+        return f'<{class_name} | gid={self._gid}>'
 
     @property
     def gid(self):
@@ -176,13 +168,16 @@ def create_dends(self, p_dend):
             self.dends[key].Ra = p_dend[key]['Ra']
             self.dends[key].cm = p_dend[key]['cm']
 
-    def create_soma(self):
-        """Create soma and set geometry."""
-        # make L_soma and diam_soma elements of self
-        # Used in shape_change() b/c func clobbers self.soma.L, self.soma.diam
-        soma_props = self.soma_props
+    def create_soma(self, soma_props):
+        """Create soma and set geometry.
 
-        self.soma = h.Section(cell=self, name=soma_props['name'] + '_soma')
+        Parameters
+        ----------
+        soma_props : dict
+            The properties of the soma. Must contain
+            keys 'L', 'diam', 'Ra', and 'cm'.
+        """
+        self.soma = h.Section(cell=self, name=self.name + '_soma')
         self.soma.L = soma_props['L']
         self.soma.diam = soma_props['diam']
         self.soma.Ra = soma_props['Ra']

hnn_core/cell_classes.py

@@ -42,8 +42,7 @@ def _get_soma_props(p_all, cell_type):
         'L': p_all[f'{cell_type}_soma_L'],
         'diam': p_all[f'{cell_type}_soma_diam'],
         'cm': p_all[f'{cell_type}_soma_cm'],
-        'Ra': p_all[f'{cell_type}_soma_Ra'],
-        'name': cell_type,
+        'Ra': p_all[f'{cell_type}_soma_Ra']
     }
 
 
@@ -52,8 +51,7 @@ def _get_basket_soma_props(cell_name):
         'L': 39.,
         'diam': 20.,
         'cm': 0.85,
-        'Ra': 200.,
-        'name': cell_name,
+        'Ra': 200.
     }
 
 
@@ -99,12 +97,12 @@ def basket(pos, cell_name='L2Basket', gid=None):
     cell : instance of BasketSingle
         The basket cell.
     """
-    props = _get_basket_soma_props(cell_name)
-    cell = Cell(props, pos=pos, gid=gid)
+    cell = Cell(pos=pos, gid=gid)
+    cell.name = cell_name
 
-    cell.create_soma()
+    soma_props = _get_basket_soma_props(cell_name)
+    cell.create_soma(soma_props)
     cell.sections = [cell.soma]   # XXX: needed?
-    cell.name = cell_name
     cell.secs = _secs_Basket()
 
     cell.set_geometry()
@@ -186,7 +184,7 @@ def __init__(self, pos, celltype, override_params=None, gid=None):
         # Get somatic, dendritic, and synapse properties
         soma_props = _get_soma_props(p_all, self.name)
 
-        Cell.__init__(self, soma_props, pos=pos, gid=gid)
+        Cell.__init__(self, pos=pos, gid=gid)
 
         level2_keys = ['L', 'diam', 'Ra', 'cm']
         p_dend = _flat_to_nested(p_all, cell_type=self.name,
@@ -196,7 +194,7 @@ def __init__(self, pos, celltype, override_params=None, gid=None):
 
         # Geometry
         # dend Cm and dend Ra set using soma Cm and soma Ra
-        self.create_soma()
+        self.create_soma(soma_props)
         self.create_dends(p_dend)  # just creates the sections
         self.sections = [self.soma] + list(self.dends.values())
 

hnn_core/tests/test_cell.py

@@ -10,20 +10,17 @@
 
 def test_cell():
     """Test cells object."""
-    # test that ExpSyn always takes nrn.Segment, not float
-    soma_props = {"L": 22.1, "diam": 23.4, "cm": 0.6195, "Ra": 200.0,
-                  'name': 'test_cell'}
     pos = (0., 0., 0.)
 
     # GID is assigned exactly once for each cell, either at initialisation...
-    cell = Cell(soma_props=soma_props, pos=pos, gid=42)
+    cell = Cell(pos=pos, gid=42)
     assert cell.gid == 42
     with pytest.raises(RuntimeError,
                        match='Global ID for this cell already assigned!'):
         cell.gid += 1
     # ... or later
     # cells can exist fine without gid
-    cell = Cell(soma_props=soma_props, pos=pos)
+    cell = Cell(pos=pos)
     assert cell.gid is None  # check that it's initialised to None
     with pytest.raises(ValueError,
                        match='gid must be an integer'):
@@ -33,8 +30,9 @@ def test_cell():
     with pytest.raises(ValueError,
                        match='gid must be an integer'):
         # test init checks gid
-        cell = Cell(soma_props=soma_props, pos=pos, gid='one')
+        cell = Cell(pos=pos, gid='one')
 
+    # test that ExpSyn always takes nrn.Segment, not float
     with pytest.raises(TypeError, match='secloc must be instance of'):
         cell.syn_create(0.5, e=0., tau1=0.5, tau2=5.)