fix & clean-up for nrn embedding

ball-and-stick-1.ipynb

@@ -50,6 +50,22 @@
     "As good practice, we'll load some unit definitions:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from neuron.units import ms, mV"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We'll load the standard run library to give us high-level simulation control functions (e.g. running a simulation for a given period of time):"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1207,7 +1223,7 @@
     "        h.continuerun(25)\n",
     "        f.line(t, list(soma_v),\n",
     "               line_width=width,\n",
-    "               legend_label='amp=%g' % amp if my_cell.dend.nseg == 1 else None,\n",
+    "               legend_label='amp={:.3g}'.format(amp) if my_cell.dend.nseg == 1 else '',\n",
     "               color=color)\n",
     "        f.line(t, list(dend_v),\n",
     "               line_width=width,\n",
@@ -1277,7 +1293,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,

ball-and-stick-2.ipynb

@@ -182,7 +182,40 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you are writing a script to do this, and revising the classes as we make changes, everything should be good. If you are following along in a Jupyter notebook, you will need to rerun the definition of BallAndStick above for the changes to take effect."
+    "If you are writing a script to do this, and revising the classes as we make changes, everything should be good. If you are following along in a Jupyter notebook, you will need to rerun the definition of BallAndStick above for the changes to take effect:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run only for jupyter\n",
+    "class BallAndStick(Cell):\n",
+    "    name = 'BallAndStick'\n",
+    "    def _setup_morphology(self):\n",
+    "        self.soma = h.Section(name='soma', cell=self)\n",
+    "        self.dend = h.Section(name='dend', cell=self)\n",
+    "        self.dend.connect(self.soma)\n",
+    "        self.soma.L = self.soma.diam = 12.6157\n",
+    "        self.dend.L = 200\n",
+    "        self.dend.diam = 1\n",
+    "    def _setup_biophysics(self):\n",
+    "        for sec in self.all:\n",
+    "            sec.Ra = 100    # Axial resistance in Ohm * cm\n",
+    "            sec.cm = 1      # Membrane capacitance in micro Farads / cm^2\n",
+    "        self.soma.insert('hh')                                          \n",
+    "        for seg in self.soma:\n",
+    "            seg.hh.gnabar = 0.12  # Sodium conductance in S/cm2\n",
+    "            seg.hh.gkbar = 0.036  # Potassium conductance in S/cm2\n",
+    "            seg.hh.gl = 0.0003    # Leak conductance in S/cm2\n",
+    "            seg.hh.el = -54.3     # Reversal potential in mV\n",
+    "        # Insert passive current in the dendrite\n",
+    "        self.dend.insert('pas')                 \n",
+    "        for seg in self.dend:\n",
+    "            seg.pas.g = 0.001  # Passive conductance in S/cm2\n",
+    "            seg.pas.e = -65    # Leak reversal potential mV\n"
    ]
   },
   {
@@ -718,7 +751,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,

ball-and-stick-3.ipynb

@@ -392,7 +392,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,