Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 4] (#24)

* 🎨 Update plots from pymc to arviz dependencies & replace param sd with sigma

⏪ Revert changes due to improper metadata updates

🎨 Fix divergence in last cells and outdated errors due to variou package changes

* 🔀 Prep to resolve merge conflict on GLM Linear notebook

Author: CloudChaoszero

Diff for: examples/gaussian_processes/GP-Kron.ipynb

@@ -340,7 +340,7 @@
     "    # Place a GP prior over the function f.\n",
     "    f = gp.prior(\"f\", Xs=Xs)\n",
     "\n",
-    "    y_ = pm.Normal(\"y_\", mu=f, sd=sigma, observed=y)"
+    "    y_ = pm.Normal(\"y_\", mu=f, sigma=sigma, observed=y)"
    ]
   },
   {
@@ -448,7 +448,7 @@
     }
    ],
    "source": [
-    "pm.traceplot(\n",
+    "az.plot_trace(\n",
     "    tr,\n",
     "    var_names=[\"ls1\", \"ls2\", \"eta\", \"sigma\"],\n",
     "    lines={\"ls1\": l1_true, \"ls2\": l2_true, \"eta\": eta_true, \"sigma\": sigma_true},\n",
@@ -562,9 +562,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -631,9 +629,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python (PyMC3 Dev)",
    "language": "python",
-   "name": "python3"
+   "name": "pymc3-dev"
   },
   "language_info": {
    "codemirror_mode": {
@@ -645,7 +643,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

Diff for: examples/gaussian_processes/GP-Latent.ipynb

@@ -104,6 +104,8 @@
    },
    "outputs": [],
    "source": [
+    "import warnings\n",
+    "\n",
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
@@ -129,8 +131,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import warnings\n",
-    "\n",
     "# mute future warnings from theano\n",
     "warnings.simplefilter(action=\"ignore\", category=FutureWarning)"
    ]
@@ -996,9 +996,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python (PyMC3 Dev)",
    "language": "python",
-   "name": "python3"
+   "name": "pymc3-dev"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1010,7 +1010,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

Diff for: examples/generalized_linear_models/GLM-hierarchical-binominal-model.ipynb

@@ -467,7 +467,7 @@
     }
    ],
    "source": [
-    "pm.traceplot(hierarchical_trace, var_names=[\"mu_a\", \"mu_b\", \"sigma_a\", \"sigma_b\", \"eps\"]);"
+    "az.plot_trace(hierarchical_trace, var_names=[\"mu_a\", \"mu_b\", \"sigma_a\", \"sigma_b\", \"eps\"]);"
    ]
   },
   {
@@ -500,7 +500,7 @@
     }
    ],
    "source": [
-    "pm.traceplot(hierarchical_trace, var_names=[\"a\"], coords={\"a_dim_0\": range(5)});"
+    "az.plot_trace(hierarchical_trace, var_names=[\"a\"], coords={\"a_dim_0\": range(5)});"
    ]
   },
   {
@@ -764,7 +764,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.5"
   },
   "latex_envs": {
    "bibliofile": "biblio.bib",