notebooks: update to work with flakes

Author: wd15

_data/python-pfhub/notebooks/test.ipynb

@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 7,
    "id": "occupied-accuracy",
    "metadata": {},
    "outputs": [
@@ -38,7 +38,12 @@
    "source": [
     "from pfhub.main import line_plot, levelset_plot, get_table_data_style, plot_order_of_accuracy, get_result_data\n",
     "from itables import init_notebook_mode\n",
-    "init_notebook_mode(all_interactive=True);"
+    "init_notebook_mode(all_interactive=True);\n",
+    "\n",
+    "from pathlib import Path\n",
+    "\n",
+    "cwd = Path().resolve()\n",
+    "benchmark_path = f'{cwd}/../../simulation_list.yaml'"
    ]
   },
   {
@@ -7072,7 +7077,8 @@
     "        x='time (s)',\n",
     "        y='Free Energy',\n",
     "        title=\"Free Energy, <i>r</i><sub>0</sub>=0.99<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -14078,7 +14084,8 @@
     "        x='time (s)',\n",
     "        y='Solid Fraction',\n",
     "        title=\"Solid Fraction, <i>r</i><sub>0</sub>=0.99<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -21084,7 +21091,8 @@
     "        x='time (s)',\n",
     "        y='Free Energy',\n",
     "        title=\"Free Energy, <i>r</i><sub>0</sub>=<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -28090,7 +28098,8 @@
     "        x='time (s)',\n",
     "        y='Solid Fraction',\n",
     "        title=\"Solid Fraction, <i>r</i><sub>0</sub>=<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -35096,7 +35105,8 @@
     "        x='time (s)',\n",
     "        y='Free Energy',\n",
     "        title=\"Free Energy, <i>r</i><sub>0</sub>=1.01<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -42102,7 +42112,8 @@
     "        x='time (s)',\n",
     "        y='Solid Fraction',\n",
     "        title=\"Solid Fraction, <i>r</i><sub>0</sub>=1.01<i>r</i><sup>*</sup>\"\n",
-    "    )\n",
+    "    ),\n",
+    "    benchmark_path=benchmark_path\n",
     ")"
    ]
   },
@@ -48558,7 +48569,7 @@
    "source": [
     "#PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "\n",
-    "data = get_result_data(['phase_field_1'], ['8a.1'], ['x', 'y', 'z'])\n",
+    "data = get_result_data(['phase_field_1'], ['8a.1'], ['x', 'y', 'z'], benchmark_path=benchmark_path)\n",
     "\n",
     "levelset_plot(\n",
     "    data,\n",
@@ -55022,7 +55033,7 @@
     }
    ],
    "source": [
-    "data = get_result_data(['phase_field_2'], ['8a.1'], ['x', 'y', 'z'])\n",
+    "data = get_result_data(['phase_field_2'], ['8a.1'], ['x', 'y', 'z'], benchmark_path=benchmark_path)\n",
     "\n",
     "levelset_plot(\n",
     "    data,\n",
@@ -78333,7 +78344,7 @@
     }
    ],
    "source": [
-    "data = get_result_data(['phase_field_3'], ['8a.1'], ['x', 'y', 'z'])\n",
+    "data = get_result_data(['phase_field_3'], ['8a.1'], ['x', 'y', 'z'], benchmark_path=benchmark_path)\n",
     "\n",
     "levelset_plot(\n",
     "    data,\n",
@@ -79354,7 +79365,7 @@
     "keys = ['x', 'y', 'z']\n",
     "\n",
     "data_names = ['phase_field_3', 'phase_field_4', 'phase_field_5']\n",
-    "df = get_result_data(data_names, ['8a.1'], keys=keys)\n",
+    "df = get_result_data(data_names, ['8a.1'], keys=keys, benchmark_path=benchmark_path)\n",
     "\n",
     "plot_order_of_accuracy(\n",
     "    df,\n",
@@ -79455,7 +79466,7 @@
     "#PYTEST_VALIDATE_IGNORE_OUTPUT\n",
     "\n",
     "init_notebook_mode(False)\n",
-    "get_table_data_style('8a.1')"
+    "get_table_data_style('8a.1', benchmark_path=benchmark_path)"
    ]
   },
   {