a few docs fixes (#284)

we don't need to turn off verbosity or I/O for Pyro() runs
anymore

Author: zingale

docs/source/compressible-convergence.ipynb

@@ -69,31 +69,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "cc7c0964-e0cf-43f4-8ca8-3ea6ed11c9fd",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[1mpyro ...\u001b[0m\n",
-      "\u001b[1minitializing the acoustic pulse problem...\u001b[0m\n",
-      "\u001b[1mpyro ...\u001b[0m\n",
-      "\u001b[1minitializing the acoustic pulse problem...\u001b[0m\n",
-      "\u001b[1mpyro ...\u001b[0m\n",
-      "\u001b[1minitializing the acoustic pulse problem...\u001b[0m\n",
-      "\u001b[1mpyro ...\u001b[0m\n",
-      "\u001b[1minitializing the acoustic pulse problem...\u001b[0m\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "sims = []\n",
     "\n",
     "for N in [32, 64, 128, 256]:\n",
     "    dt = timestep(N)\n",
-    "    params = {\"driver.fix_dt\": dt, \"mesh.nx\": N, \"mesh.ny\": N, \"driver.verbose\": 0}\n",
+    "    params = {\"driver.fix_dt\": dt, \"mesh.nx\": N, \"mesh.ny\": N}\n",
     "    p = Pyro(\"compressible\")\n",
     "    p.initialize_problem(problem_name=\"acoustic_pulse\", inputs_dict=params)\n",
     "    p.run_sim()\n",
@@ -111,7 +96,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "9705ab17-81c6-4b8a-becd-6a9af75371e1",
    "metadata": {},
    "outputs": [],
@@ -122,10 +107,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "97d051b5-563a-40ea-a838-9b4f7832380f",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " 64 ->  32 : 0.0002674195946900653\n",
+      "128 ->  64 : 5.7696409241208797e-05\n",
+      "256 -> 128 : 1.3860268814816614e-05\n"
+     ]
+    }
+   ],
    "source": [
     "for coarse, fine in pairwise(sims):\n",
     "    cvar = coarse.get_var(var)\n",
@@ -161,7 +156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "dd7a64cb-992e-4e0f-96f7-c8c03c0ca3eb",
    "metadata": {},
    "outputs": [],
@@ -170,7 +165,7 @@
     "\n",
     "for N in [32, 64, 128, 256]:\n",
     "    dt = timestep(N)\n",
-    "    params = {\"driver.fix_dt\": dt, \"mesh.nx\": N, \"mesh.ny\": N, \"driver.verbose\": 0}\n",
+    "    params = {\"driver.fix_dt\": dt, \"mesh.nx\": N, \"mesh.ny\": N}\n",
     "    p = Pyro(\"compressible_fv4\")\n",
     "    p.initialize_problem(problem_name=\"acoustic_pulse\", inputs_dict=params)\n",
     "    p.run_sim()\n",
@@ -179,10 +174,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "f03120c8-bc1d-4f0d-b79f-e498c64076a3",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " 64 ->  32 : 6.519131423273572e-05\n",
+      "128 ->  64 : 4.825569192556014e-06\n",
+      "256 -> 128 : 3.0769222917915304e-07\n"
+     ]
+    }
+   ],
    "source": [
     "for coarse, fine in pairwise(sims):\n",
     "    cvar = coarse.get_var(var)\n",

docs/source/compressible-rt-compare.ipynb

@@ -52,8 +52,7 @@ Pyro class
 ----------
 
 Alternatively, pyro can be run using the :func:`Pyro <pyro.pyro_sim.Pyro>` class. This provides
-an interface that enables simulations to be set up and run in a Jupyter notebook -- see
-``examples/examples.ipynb`` for an example notebook. A simulation can be set up and run
+an interface that enables simulations to be set up and run in a Jupyter notebook. A simulation can be set up and run
 by carrying out the following steps:
 
 * create a :func:`Pyro <pyro.pyro_sim.Pyro>` object, initializing it with a specific solver
@@ -67,7 +66,7 @@ Kelvin-Helmholtz problem ``kh``, we would do the following:
 
     from pyro import Pyro
     p = Pyro("compressible")
-    p.initialize_problem(problem_name="kh")
+    p.initialize_problem("kh")
     p.run_sim()
 
 This will use the default set of parameters for the problem specified
@@ -99,8 +98,7 @@ verbosity for the previous example, we would do:
 .. code-block:: python
 
     parameters = {"driver.verbose": 1}
-    p.initialize_problem(problem_name="kh",
-                         inputs_dict=parameters)
+    p.initialize_problem("kh", inputs_dict=parameters)
 
 It's possible to evolve the simulation forward timestep by timestep manually using
 the :func:`single_step <pyro.pyro_sim.Pyro.single_step>` function (rather than allowing