chore(lint): lint, and re-run notebooks

Author: amyheather

README.md

@@ -142,13 +142,13 @@ To generate the figures and tables from the paper (`mock_paper.md`), execute:
 
 Run times from our analyses (on Intel Core i7-12700H, 32GB RAM, Ubuntu 24.04.1):
 
-* `analysis.ipynb` - 23s
-* `choosing_cores.ipynb` - 19s
-* `choosing_replications.ipynb` - 33s
-* `choosing_warmup.ipynb` - 4s
-* `generate_exp_results.ipynb` - 7s
+* `analysis.ipynb` - 35s
+* `choosing_cores.ipynb` - 34s
+* `choosing_replications.ipynb` - 46s
+* `choosing_warmup.ipynb` - 38s
+* `generate_exp_results.ipynb` - 1s
 * `logs.ipynb` - 0s
-* `time_weighted_averages.ipynb` - 1s
+* `time_weighted_averages.ipynb` - 2s
 
 </details>
 

notebooks/analysis.ipynb

@@ -56,8 +56,6 @@
     "import time\n",
     "from IPython.display import display\n",
     "\n",
-    "import pandas as pd\n",
-    "\n",
     "from simulation import Param, Runner, run_scenarios"
    ]
   },
@@ -652,19 +650,19 @@
      "text": [
       "There are 4 scenarios. Running:\n",
       "{'patient_inter': 3, 'number_of_nurses': 6}\n",
-      "Scenario parameters: {'_initialising': False, 'patient_inter': 3, 'mean_n_consult_time': 10, 'number_of_nurses': 6, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 0, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x753e4b2c3b60>}\n",
+      "Scenario parameters: {'_initialising': False, 'patient_inter': 3, 'mean_n_consult_time': 10, 'number_of_nurses': 6, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 0, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x771e484ffb60>}\n",
       "{'patient_inter': 3, 'number_of_nurses': 7}\n",
-      "Scenario parameters: {'_initialising': False, 'patient_inter': 3, 'mean_n_consult_time': 10, 'number_of_nurses': 7, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 1, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x753e4b2c3b60>}\n",
-      "{'patient_inter': 4, 'number_of_nurses': 6}\n",
-      "Scenario parameters: {'_initialising': False, 'patient_inter': 4, 'mean_n_consult_time': 10, 'number_of_nurses': 6, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 2, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x753e4b2c3b60>}\n"
+      "Scenario parameters: {'_initialising': False, 'patient_inter': 3, 'mean_n_consult_time': 10, 'number_of_nurses': 7, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 1, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x771e484ffb60>}\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "{'patient_inter': 4, 'number_of_nurses': 6}\n",
+      "Scenario parameters: {'_initialising': False, 'patient_inter': 4, 'mean_n_consult_time': 10, 'number_of_nurses': 6, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 2, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x771e484ffb60>}\n",
       "{'patient_inter': 4, 'number_of_nurses': 7}\n",
-      "Scenario parameters: {'_initialising': False, 'patient_inter': 4, 'mean_n_consult_time': 10, 'number_of_nurses': 7, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 3, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x753e4b2c3b60>}\n"
+      "Scenario parameters: {'_initialising': False, 'patient_inter': 4, 'mean_n_consult_time': 10, 'number_of_nurses': 7, 'warm_up_period': 2000, 'data_collection_period': 6000, 'number_of_runs': 3, 'scenario_name': 3, 'cores': 1, 'seed_offset': 0, 'logger': <simulation.simlogger.SimLogger object at 0x771e484ffb60>}\n"
      ]
     },
     {
@@ -868,7 +866,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Notebook run time: 0m 0s\n"
+      "Notebook run time: 0m 1s\n"
      ]
     }
    ],

notebooks/choosing_cores.ipynb

@@ -5,6 +5,7 @@
 from .runner import Runner
 
 
+# pylint: disable=too-few-public-methods
 class SimulationAdapter:
     """
     Adapter for running model replications compatible with