pythonhealthdatascience · amyheather · Feb 3, 2025 · Jan 30, 2025 · Jan 30, 2025 · Jan 30, 2025
diff --git a/.gitignore b/.gitignore
@@ -3,7 +3,9 @@ __pycache__
 .pytest_cache
 .pytype
 
+# Log messages, except the example one generated by logs.ipynb
 *.log
+!log_example.log
 
 # vscode
 .vscode/*

diff --git a/CITATION.cff b/CITATION.cff
@@ -14,6 +14,11 @@ authors:
     email: a.heather2@exeter.ac.uk
     affiliation: University of Exeter
     orcid: 'https://orcid.org/0000-0002-6596-3479'
+  - given-names: Thomas
+    family-names: Monks
+    email: t.m.w.monks@exeter.ac.uk
+    affiliation: University of Exeter
+    orcid: 'https://orcid.org/0000-0003-2631-4481'
 repository-code: >-
   https://github.com/pythonhealthdatascience/rap_template_python_des
 abstract: >-

diff --git a/README.md b/README.md
@@ -193,7 +193,7 @@ This section describes the purposes of each class in the simulation.
 
 **Model Run Process:**
 
-1. **Set Parameters:** Create a `Defaults` instance and modify it with desired model parameters.
+1. **Set Parameters:** Create a `Param` instance with desired model parameters.
 2. **Initialise Model:** Instantiate `Model` using the parameters. During setup, `Model` creates `Exponential` instances for each distribution.
 3. **Run Simulation:** Call `model.run()` to execute the simulation within the SimPy environment, running two processes:
 
@@ -260,17 +260,18 @@ These times were obtained on an Intel Core i7-12700H with 32GB RAM running Ubunt
 
 If you use this template, please cite the archived repository:
 
-> Heather, A. (2025). Simple Reproducible Python Discrete-Event Simulation (DES) Template. Zenodo. https://doi.org/10.5281/zenodo.14622466
+> Heather, A. Monks, T. (2025). Python DES RAP Template. Zenodo. https://doi.org/10.5281/zenodo.14622466
 
 You can also cite the GitHub repository:
 
-> Heather, A. (2025). Simple Reproducible Python Discrete-Event Simulation (DES) Template. GitHub. https://github.com/pythonhealthdatascience/rap_template_python_des.
+> Heather, A. Monks, T. (2025). Python DES RAP Template. GitHub. https://github.com/pythonhealthdatascience/rap_template_python_des.
 
 Researcher details:
 
-| Contributor | ORCID | GitHub |
-| --- | --- | --- |
-| Amy Heather | [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) | https://github.com/amyheather |
+| Contributor | Role | ORCID | GitHub |
+| --- | --- | --- | --- |
+| Amy Heather | Author | [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) | https://github.com/amyheather |
+| Tom Monks | Code review | [![ORCID: Monks](https://img.shields.io/badge/ORCID-0000--0003--2631--4481-brightgreen)](https://orcid.org/0000-0003-2631-4481) | https://github.com/TomMonks |
 
 <br>
 

diff --git a/docs/time_weighted_averages.ipynb b/docs/time_weighted_averages.ipynb
diff --git a/environment.yaml b/environment.yaml
@@ -15,6 +15,7 @@ dependencies:
   - pytest=8.3.4
   - pytest-xdist=3.6.1
   - python=3.13.1
+  - rich=13.9.4
   - simpy=4.1.1
   - pip:
     - kaleido==0.2.1

diff --git a/images/model_structure.drawio b/images/model_structure.drawio
@@ -1,6 +1,6 @@
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@@ -243,16 +243,16 @@
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diff --git a/images/model_structure.png b/images/model_structure.png
diff --git a/lint.sh b/lint.sh
@@ -7,7 +7,4 @@ echo "Linting tests..."
 pylint ./tests
 
 echo "Linting notebooks..."
-nbqa pylint ./notebooks
-
-echo "Linting time-weighted averages notebook..."
-nbqa pylint ./docs/time_weighted_averages.ipynb
+nbqa pylint ./notebooks
diff --git a/notebooks/analysis.ipynb b/notebooks/analysis.ipynb
diff --git a/notebooks/choosing_parameters.ipynb b/notebooks/choosing_parameters.ipynb
diff --git a/notebooks/generate_exp_results.ipynb b/notebooks/generate_exp_results.ipynb
@@ -53,7 +53,7 @@
     "import time\n",
     "from IPython.display import display\n",
     "\n",
-    "from simulation.model import Defaults, Runner"
+    "from simulation.model import Param, Runner"
    ]
   },
   {
@@ -104,16 +104,17 @@
    "outputs": [],
    "source": [
     "# Define model parameters\n",
-    "param = Defaults()\n",
-    "param.patient_inter = 4\n",
-    "param.mean_n_consult_time = 10\n",
-    "param.number_of_nurses = 4\n",
-    "param.warm_up_period = 500\n",
-    "param.data_collection_period = 1500\n",
-    "param.number_of_runs = 5\n",
-    "param.audit_interval = 50\n",
-    "param.scenario_name = 0\n",
-    "param.cores = 1\n",
+    "param = Param(\n",
+    "    patient_inter=4,\n",
+    "    mean_n_consult_time = 10,\n",
+    "    number_of_nurses = 4,\n",
+    "    warm_up_period = 500,\n",
+    "    data_collection_period = 1500,\n",
+    "    number_of_runs=5,\n",
+    "    audit_interval = 50,\n",
+    "    scenario_name = 0,\n",
+    "    cores = 1\n",
+    ")\n",
     "\n",
     "# Run the replications\n",
     "experiment = Runner(param)\n",