style(lint): linting

Author: amyheather

notebooks/analysis.ipynb

@@ -20,9 +20,12 @@
     "\n",
     "# pylint: disable=wrong-import-position\n",
     "import os\n",
+    "\n",
+    "from IPython.display import display\n",
     "import plotly.express as px\n",
     "\n",
     "from simulation.parameters import Param\n",
+    "from simulation.model import Model\n",
     "from simulation.runner import Runner"
    ]
   },
@@ -47,6 +50,32 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'time': 1095, 'asu_occupancy': 7, 'rehab_occupancy': 12},\n",
+       " {'time': 1096, 'asu_occupancy': 5, 'rehab_occupancy': 11},\n",
+       " {'time': 1097, 'asu_occupancy': 5, 'rehab_occupancy': 10},\n",
+       " {'time': 1098, 'asu_occupancy': 4, 'rehab_occupancy': 10},\n",
+       " {'time': 1099, 'asu_occupancy': 5, 'rehab_occupancy': 10}]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# View the raw model run and output\n",
+    "model = Model(Param(), run_number=0)\n",
+    "model.run()\n",
+    "display(model.audit_list[0:5])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Set up runner\n",
@@ -55,7 +84,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -140,7 +169,7 @@
        "4     5   134  0.073425  0.143562    0.511450"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -153,7 +182,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +201,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,7 +262,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -1964,7 +1993,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -2049,7 +2078,7 @@
        "4     5   134  0.073425  0.143562    0.511450"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2093,7 +2122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2148,7 +2177,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {

notebooks/generate_exp_results.ipynb

@@ -22,6 +22,8 @@
     "\n",
     "# pylint: disable=wrong-import-position\n",
     "import os\n",
+    "\n",
+    "from IPython.display import display\n",
     "import pandas as pd\n",
     "\n",
     "from simulation.parameters import Param\n",

tests/test_backtest.py

@@ -21,7 +21,7 @@ def test_model():
     Notes
     -----
     This is adapted from `test_reproduction` in
-    pythonhealthdatascience/rap_template_python_des.
+    github.com/pythonhealthdatascience/rap_template_python_des.
     """
     # Run model and get audit list as a dataframe
     model = Model(param=Param(), run_number=0)
@@ -49,7 +49,7 @@ def test_runner(unit):
     Notes
     -----
     This is adapted from `test_reproduction` in
-    pythonhealthdatascience/rap_template_python_des.
+    github.com/pythonhealthdatascience/rap_template_python_des.
     """
     # Run model and get occupancy dataframe
     runner = Runner(param=Param())

tests/test_functionaltest.py

@@ -120,8 +120,6 @@ def test_long_los(stroke_no_esd_mean):
         assert len(model.patients) > total_occupancy
 
 
-# TODO: test_ev_5/6/7/8 - requires patient counts by unit and patient type
-
 def test_warmup_only():
     """
     Check that results are as expected if model is run with no data collection

tests/test_unittest.py

@@ -53,6 +53,7 @@ def test_param_valid():
     """
     try:
         Param().check_param_validity()
+    # pylint: disable=broad-exception-caught
     except Exception as exc:
         pytest.fail(
             f"check_param_validity() raised an unexpected exception: {exc}")