Dev

CHANGELOG.md

@@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). Dates formatted as YYYY-MM-DD as per [ISO standard](https://www.iso.org/iso-8601-date-and-time-format.html).
 
+## v0.2.0 - 2025-11-06
+
+This release has some small additions (e.g., data dictionary, coverage), alongside lots of refactoring and changes (e.g., parameters in JSON, using `DistributionRegistry`, renaming repository, using updated version of `sim-tools`).
+
+### Added
+
+* Data dictionary.
+* Add coverage badge (requiring `pytest-cov` and `genbadge` to be add to environment).
+* Add option to choose between operating system and coverage when run tests via GitHub actions.
+* Add tests for `LockedDict`.
+
+### Changed
+
+* Refactored to used `parameters.json` and `sim-tools.DistributionRegistry()`, and fixed analysis and tests etc. to work with this new set-up.
+* Renamed (`stroke_rap_python` -> `pydesrap_stroke`, `rap_template_python_des` -> `pydesrap_mms`).
+* README - add DOI, contributors, licence, funding, and generally improved.
+* STRESS-DES - rewrote/improved answers.
+* Environment - renamed environment, and upgraded kaleido and sim-tools.
+* Removed `tia_esd` from parameters and csv (as upgraded sim-tools no longer allows it).
+* Updated `Discrete` to `DiscreteEmpiricial` (as updated sim-tools name)
+* Updated pyproject.toml (non-dynamic description, author list).
+* Other minor corrections/changes (e.g. moving `RestrictAttributes`, docstring corrections).
+
+### Fixed
+
+* Fixed `run_notebooks.sh`.
+* Blocked dot notation for `LockedDict`.
+
 ## v0.1.0 - 2025-06-02
 
 🌱 First release of the repository. Contains implementation of the DES model from Monks et al. 2016, with reproduction of all tables and figures with results from the article and supplementary material. Also includes some tests, and a demonstration of logging, and of how parameters could be stored in a `.csv`.

CITATION.cff

@@ -25,5 +25,5 @@ abstract: >-
   Reproducible analytical pipeline (RAP) for python discrete-event simulation
   (DES) implementing the Stroke Capacity Planning Model from Monks et al. 2016.
 license: MIT
-version: '0.1.0'
-date-released: '2025-06-02'
+version: '0.2.0'
+date-released: '2025-11-06'

README.md

@@ -11,6 +11,14 @@
 
 </div>
 
+<br>
+
+This repository is an example accompanying the [**DES RAP Book**](https://github.com/pythonhealthdatascience/des_rap_book) — an open educational resource on reproducible discrete-event simulation (DES) in Python and R. The book demonstrates best practices for building, validating, and sharing DES models within a reproducible analytical pipeline (RAP). The `pydesrap_stroke` model illustrates how these principles can be applied to a real-world healthcare capacity planning problem.
+
+<br>
+
+## Repository overview
+
 This repository provides a reproducible analytical pipeline (RAP) that implements a real-life stroke service capacity planning model in python. It serves as a practical example, fully reproducible and aligned with RAP principles, based on the following study:
 
 > Monks T, Worthington D, Allen M, Pitt M, Stein K, James MA. A modelling tool for capacity planning in acute and community stroke services. BMC Health Serv Res. 2016 Sep 29;16(1):530. doi: [10.1186/s12913-016-1789-4](https://doi.org/10.1186/s12913-016-1789-4). PMID: 27688152; PMCID: PMC5043535.
@@ -21,7 +29,9 @@ Model diagram:
 
 <br>
 
-## Installation
+## Usage and reproduction instructions
+
+<details><summary><b>Installation</b></summary>
 
 Clone the repository locally:
 
@@ -39,9 +49,11 @@ conda activate
 
 There is also a `requirements.txt` file which can be used to set up the environment with `virtualenv`, but this won't fetch a specific version of Python - so please note the version listed in `environment.yaml`.
 
+</details>
+
 <br>
 
-## How to run
+<details><summary><b>How to run</b></summary>
 
 The simulation code is provided as a **package** within `simulation/`. There are notebooks executing the model and analysing the results in `notebooks/`.
 
@@ -68,7 +80,11 @@ runner = Runner(param=param)
 rep_results = runner.run_reps()
 ```
 
-### Generating the results from the article
+</details>
+
+<br>
+
+<details><summary><b>Generating the results from the article</b></summary>
 
 The original study used Simul8. Each of the outputs from that article have been replicated in this repository using Python:
 
@@ -103,23 +119,23 @@ From this repository:
 
 ![](outputs/figure3_asu.png)
 
+</details>
+
 <br>
 
-## Run time and machine specification
+<details><summary><b>Run time and machine specification</b></summary>
 
 The run time for this analysis (`notebooks/analysis.ipynb`) is 10 seconds. This was on an Intel Core i7-12700H, 32GB RAM, Ubuntu 24.04.1.
 
 The other notebooks generate results for tests and illustrate other functionality (e.g. importing parameters from csv, running with logs), and these just take a second or two.
 
-<br>
-
-## Community
-
-Curious about contributing? Check out the [contributing guidelines](CONTRIBUTING.md) to learn how you can help.
+</details>
 
 <br>
 
-## Citation
+## Project details and credits
+
+### How to cite the repository
 
 For this applied example, please cite either:
 
@@ -129,7 +145,7 @@ For this applied example, please cite either:
 
 A `CITATION.cff` file is also provided.
 
-**Contributors:**
+### Contributors
 
 **Amy Heather** - developed the repository.
 
@@ -141,14 +157,14 @@ A `CITATION.cff` file is also provided.
 * [![ORCID](https://img.shields.io/badge/ORCID-0000--0003--2631--4481-A6CE39?style=for-the-badge&logo=orcid&logoColor=white)](https://orcid.org/0000-0003-2631-4481)
 * [![GitHub](https://img.shields.io/badge/GitHub-TomMonks-181717?style=for-the-badge&logo=github&logoColor=white)](https://github.com/TomMonks)
 
-<br>
-
-## Licence
+### Licence
 
 MIT Licence. See `LICENSE` for details.
 
-<br>
+### Community
+
+Curious about contributing? Check out the [contributing guidelines](CONTRIBUTING.md) to learn how you can help.
 
-## Funding
+### Funding
 
 This project was developed as part of the project STARS: Sharing Tools and Artefacts for Reproducible Simulations. It is supported by the Medical Research Council [grant number [MR/Z503915/1](https://gtr.ukri.org/projects?ref=MR%2FZ503915%2F1)].