Update NBs prior to 3.9.0 release (#3955)

* Re-run and fix many notebooks...

Co-authored-by: Michael Osthege <[email protected]>

Author: AlexAndorra

docs/source/notebooks/AR.ipynb

@@ -42,12 +42,24 @@
    ],
    "source": [
     "%pylab inline\n",
+    "import arviz as az\n",
     "import pymc3 as pm\n",
-    "import theano.tensor as tt \n",
     "import scipy\n",
+    "import theano.tensor as tt\n",
+    "\n",
     "from pymc3.distributions.timeseries import EulerMaruyama"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%config InlineBackend.figure_format = 'retina'\n",
+    "az.style.use('arviz-darkgrid')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -751,6 +763,31 @@
     "plot(zs, 'r', label='$z(t)$')\n",
     "legend()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "pymc3 3.8\n",
+      "arviz 0.8.3\n",
+      "numpy 1.17.5\n",
+      "last updated: Thu Jun 11 2020 \n",
+      "\n",
+      "CPython 3.8.2\n",
+      "IPython 7.11.0\n",
+      "watermark 2.0.2\n"
+     ]
+    }
+   ],
+   "source": [
+    "%load_ext watermark\n",
+    "%watermark -n -u -v -iv -w"
+   ]
   }
  ],
  "metadata": {
@@ -770,7 +807,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.8.2"
   },
   "latex_envs": {
    "bibliofile": "biblio.bib",
@@ -1600,5 +1637,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

docs/source/notebooks/BEST.ipynb

@@ -52,13 +52,32 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
+    "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pymc3 as pm \n",
     "import pandas as pd\n",
+    "import pymc3 as pm \n",
     "import theano\n",
     "\n",
+    "print('Running on PyMC3 v{}'.format(pm.__version__))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%config InlineBackend.figure_format = 'retina'\n",
+    "az.style.use('arviz-darkgrid')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "data = pd.read_csv(pm.get_data('radon.csv'))\n",
     "data['log_radon'] = data['log_radon'].astype(theano.config.floatX)\n",
     "county_names = data.county.unique()\n",
@@ -553,6 +572,31 @@
     "### Acknowledgements\n",
     "Thanks to [Imri Sofer](http://serre-lab.clps.brown.edu/person/imri-sofer/) for feedback and teaching us about the connections to random-effects models and [Dan Dillon](http://cdasr.mclean.harvard.edu/index.php/about-us/current-lab-members/14-faculty/62-daniel-dillon) for useful comments on an earlier draft."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "pymc3 3.8\n",
+      "arviz 0.8.3\n",
+      "numpy 1.17.5\n",
+      "last updated: Thu Jun 11 2020 \n",
+      "\n",
+      "CPython 3.8.2\n",
+      "IPython 7.11.0\n",
+      "watermark 2.0.2\n"
+     ]
+    }
+   ],
+   "source": [
+    "%load_ext watermark\n",
+    "%watermark -n -u -v -iv -w"
+   ]
   }
  ],
  "metadata": {
@@ -572,7 +616,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.2"
   },
   "latex_envs": {
    "bibliofile": "biblio.bib",
@@ -583,5 +627,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }