No github style codeblocks in notebook markdown

Author: tjduigna

docs/source/notebooks/03_orbitals.ipynb

@@ -28,25 +28,26 @@
     "- First you parse the output \n",
     "     - must contain full basis set specification and a matrix of basis function coefficients\n",
     "     \n",
-    "```python\n",
+    "```\n",
     "ed = exatomic.myqmcode.Output('/path/to/my/output')\n",
     "```\n",
+    "\n",
     "- Inspect the parsed data. Does it look correct?\n",
     "\n",
-    "```python\n",
+    "```\n",
     "ed.basis_set         # houses primitive exponents, coefficients\n",
     "ed.momatrix          # contains the basis function coefficients\n",
     "ed.basis_set_order   # indices specifying full basis set order\n",
     "```\n",
     "- `ed` is an Editor, an object that makes parsing files fun!\n",
     "    - `ed` must be converted to a universe for the magic to happen\n",
     "\n",
-    "```python\n",
+    "```\n",
     "uni = ed.to_universe()\n",
     "```\n",
     "- A Universe has an add_molecular_orbitals method\n",
     "\n",
-    "```python\n",
+    "```\n",
     "uni.add_molecular_orbitals?   # to see all keyword arguments\n",
     "uni.add_molecular_orbitals()  # tries to guess smart defaults\n",
     "```\n",
@@ -65,6 +66,7 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {
+    "collapsed": true,
     "scrolled": true
    },
    "outputs": [],
@@ -426,7 +428,9 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from exatomic import molcas\n",
@@ -494,7 +498,9 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from exatomic import nwchem\n",