Merge pull request #23 from pythonhealthdatascience/dev

Dev

Author: amyheather

.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/*

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: >-

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>
 

docs/time_weighted_averages.ipynb

@@ -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

environment.yaml

@@ -1,6 +1,6 @@
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+        <mxCell id="ltitkqDnKHNBnyyiyaz9-4" value="&lt;font style=&quot;font-size: 18px;&quot;&gt;Param&lt;/font&gt;" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#68A9D4;" parent="1" vertex="1">
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@@ -219,13 +219,13 @@
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@@ -243,16 +243,16 @@
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@@ -262,7 +262,7 @@
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images/model_structure.drawio

@@ -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