Merge pull request #11 from pythonhealthdatascience/dev

v1.2.0

CHANGES.md

@@ -1,15 +1,45 @@
-# CHANGELOG
+# Changelog
 
-## v1.1.1
+All notable changes to this project will be documented in this file.
 
-* PATCH: Trauma patient treatment fixed to use correct distribution and parameters.
+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).
 
-## v1.1.0
+Consistent identifier (represents all versions, resolves to latest): [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10026326.svg)](https://doi.org/10.5281/zenodo.10026326)
 
-### Updates and new features
+## [v1.2.0]() - 2024-05-08
 
-* Upgraded internal implementation of generating non-overlapping random number streams. This is now implemented to use `np.random.SeedSequence`. See https://numpy.org/doc/stable/reference/random/parallel.html
+### Changed
 
-### Patches
+* `CHANGES.md` uses Keep a Changelog formatting, and includes release links, DOIs, and first release.
+* `CITATION.cff` includes references, new author, and spelling/grammar fixes.
+* `README.md` updated repo overview and spelling/grammar fixes
+* Full author list in `__init__`
 
-* `setup.py` now links to correct Github URL
+### Fixed
+
+* Model uses data from this repository (rather than external)
+
+### Removed
+
+* Duplicate `ed_arrivals.csv`
+
+## [v1.1.1](https://github.com/pythonhealthdatascience/stars-treat-sim/releases/tag/v1.1.1) - 2024-05-01 - [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11098944.svg)](https://doi.org/10.5281/zenodo.11098944)
+
+### Fixed
+
+* Trauma patient treatment fixed to use correct distribution and parameters.
+
+## [v1.1.0](https://github.com/pythonhealthdatascience/stars-treat-sim/releases/tag/v1.1.0) - 2024-04-06 - [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10936052.svg)](https://doi.org/10.5281/zenodo.10936052)
+
+### Changed
+
+* Upgraded internal implementation of generating non-overlapping random number streams. This is now implemented to use `np.random.SeedSequence`. See [https://numpy.org/doc/stable/reference/random/parallel.html](https://numpy.org/doc/stable/reference/random/parallel.html).
+
+### Fixed
+
+* `setup.py` now links to correct Github URL
+
+## [v1.0.0](https://github.com/pythonhealthdatascience/stars-treat-sim/releases/tag/v1.0.0) - 2023-10-20 - [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10026327.svg)](https://doi.org/10.5281/zenodo.10026327)
+
+:seedling: First release.

CITATION.cff

@@ -4,7 +4,7 @@
 cff-version: 1.2.0
 title: >-
   Towards Sharing Tools, and Artifacts, for Reusable
-  Simulation: a minimal model examplar
+  Simulation: a minimal model example
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
@@ -18,20 +18,54 @@ authors:
     family-names: Harper
     affiliation: University of Exeter
     orcid: 'https://orcid.org/0000-0001-5274-5037'
+  - given-names: Amy
+    family-names: Heather
+    affiliation: University of Exeter
+    orcid: 'https://orcid.org/0000-0002-6596-3479'
 repository-code: 'https://github.com/pythonhealthdatascience/stars-treat-sim'
+identifiers:
+  - description: Consistent identifier for archived snapshots of repository (represents all versions, resolves to latest)
+    type: doi
+    value: '10.5281/zenodo.10026326'
 abstract: >
 
   The materials and methods in this repository support work
   towards developing the S.T.A.R.S healthcare framework
-  (Sharing Tools and Artifacts for Reuable Simulations in
+  (Sharing Tools and Artifacts for Reusable Simulations in
   healthcare).  The code and written materials re
   demonstrate the application of S.T.A.R.S' version 1 to
-  sharing a `simpy` discrete-event simulation model and
+  sharing a `SimPy` discrete-event simulation model and
   associated research artifacts.  
 keywords:
   - Free and Open Source Software
   - Model Reuse
   - Discrete-event simulation
   - Open Science
-  - Simpy
+  - SimPy
 license: MIT
+references:
+  - type: article
+    title: 'Towards sharing tools and artefacts for reusable simulations in healthcare'
+    authors:
+      - given-names: Thomas
+        family-names: Monks
+      - given-names: Alison
+        family-names: Harper
+      - given-names: Navonil
+        family-names: Mustafee
+    doi: 10.1080/17477778.2024.2347882
+    journal: 'Journal of Simulation'
+    publisher:
+      name: 'Taylor & Francis'
+    month: 5
+    year: 2024
+  - type: book
+    title: 'Foundations and Methods of Stochastic Simulation'
+    authors:
+      - given-names: Barry L.
+        family-names: Nelson
+    publisher:
+      name: 'Springer New York'
+    year: 2013
+    doi: 10.1007/978-1-4614-6160-9
+    edition: '1st edition'

README.md

@@ -1,7 +1,7 @@
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pythonhealthdatascience/stars-treat-sim/HEAD)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/release/python-360+/)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10026327.svg)](https://doi.org/10.5281/zenodo.10026327)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/release/python-380+/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10026326.svg)](https://doi.org/10.5281/zenodo.10026326)
 [![PyPI version fury.io](https://badge.fury.io/py/treat-sim.svg)](https://pypi.org/project/treat-sim/)
 
 [<img src="https://img.shields.io/static/v1?label=dockerhub&message=images&color=important?style=for-the-badge&logo=docker">](https://hub.docker.com/r/tommonks01/treat_sim)
@@ -11,14 +11,14 @@
 
 ## Overview
 
-The materials and methods in this repository support work towards developing the S.T.A.R.S healthcare framework (**S**haring **T**ools and **A**rtifacts for **R**euable **S**imulations in healthcare).  The code and written materials here demonstrate the application of S.T.A.R.S' version 1 to sharing a `simpy` discrete-event simuilation model and associated research artifacts.  
+The materials and methods in this repository support work towards developing the S.T.A.R.S healthcare framework (**S**haring **T**ools and **A**rtifacts for **R**eusable **S**imulations in healthcare).  The code and written materials here demonstrate the application of S.T.A.R.S' version 1 to sharing a `SimPy` discrete-event simulation model and associated research artifacts.  
 
 * All artifacts in this repository are linked to study researchers via ORCIDs;
 * Model code is made available under an MIT license;
-* Python dependencies are managed through `conda`;`
+* Python dependencies are managed through `conda`;
 * Documentation of the model is enhanced using a Jupyter notebook.
 * The python code itself can be viewed and executed in Jupyter notebooks via [Binder](https://mybinder.org); 
-* The materials are deposited and made citatable using Zenodo;
+* The materials are deposited and made citable using Zenodo;
 * The model is sharable with other researchers and the NHS without the need to install software.
 
 ## Author ORCIDs
@@ -36,7 +36,7 @@ This code is part of independent research supported by the National Institute fo
 
 The python code for the model has been setup to run online in Jupyter notebooks via binder [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pythonhealthdatascience/stars-treat-sim/HEAD)
 
-> mybinder.org is a free tier service.  If it has not been used in a while Binder will need to re-containerise the code repository, and push to binderhub. This will take several minutes. After that the online environment will be quick to load.
+> mybinder.org is a free tier service.  If it has not been used in a while Binder will need to re-containerise the code repository, and push to BinderHub. This will take several minutes. After that the online environment will be quick to load.
 
 ### To download code and run locally
 
@@ -50,24 +50,23 @@ git clone https://github.com/pythonhealthdatascience/stars-treat-sim
 
 #### Installing dependencies
 
-[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/release/python-390/)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/release/python-380/)
 
 All dependencies can be found in [`binder/environment.yml`]() and are pulled from conda-forge.  To run the code locally, we recommend install [mini-conda](https://docs.conda.io/en/latest/miniconda.html); navigating your terminal (or cmd prompt) to the directory containing the repo and issuing the following command:
 
 ```
 conda env create -f binder/environment.yml
 ```
 
-Activate the conda environment using the following command
+Activate the conda environment using the following command:
 
 ```
 conda activate stars_treat_sim
 ```
 
 #### Running the model
 
-To run 50 multiple replications of across a number of example experiments use the following code
-
+To run 50 multiple replications across a number of example experiments, use the following code:
 
 ```python
 from treat_sim.model import (get_scenarios, run_scenario_analysis,
@@ -85,7 +84,7 @@ if __name__ == '__main__':
 
 ```
 
-Alternative you can design and execute individual experiments by creating a `Scenario` object
+Alternative you can design and execute individual experiments by creating a `Scenario` object:
 
 ```python
 from treat_sim.model import Scenario, multiple_replications
@@ -100,13 +99,14 @@ if __name__ == '__main__':
 
 ```
 
-
 ## Repo overview
 
 ```
 .
 ├── binder
 │   └── environment.yml
+├── CHANGES.md
+├── CITATION.cff
 ├── LICENSE
 ├── MANIFEST.in
 ├── notebooks
@@ -122,30 +122,39 @@ if __name__ == '__main__':
     └── model.py
 ```
 
-* `binder` - contains the environment.yml file (sim) and all dependencies managed via conda
-* `data` - directory containing data files used by analysis notebooks. 
+* `binder/` - contains the environment.yml file (sim) and all dependencies managed via conda, used to set-up the notebooks on Binder.
+* `CHANGES.md` - changelog with record of notable changes to project between versions.
+* `CITATION.cff` - citation information for the package.
 * `LICENSE` - details of the MIT permissive license of this work.
-* `notebooks` - contains a notebook to run the model and provides basic enhanced model documentation.
-* `main.py` - an example simpy model to use to test the virtual environment 
-* `README` - what you are reading now!
-* `treat_sim` - contains a packaged version of the model.
-
+* `MANIFEST.in` - files to include in the package.
+* `notebooks/` - contains a notebook to run the model and provides basic enhanced model documentation.
+* `README.md` - what you are reading now!
+* `requirements.txt` - list of packages and minimum versions required.
+* `setup.py` - used to build and distribute package.
+* `treat_sim/` - contains packaged version of the model.
+    * `data/` - directory containing data file used by package.
+    * `distributions.py` - distribution classes.
+    * `__init__.py` - required as part of package - contains author and version.
+    * `model.py` - example SimPy model.
 
 ## Citation
 
 If you use the materials within this repository we would appreciate a citation.
 
+```
+Monks, T., Harper, A., & Heather, A. (2024). Towards Sharing Tools, and Artifacts, for Reusable Simulation: a minimal model example (v1.2.0). Zenodo. https://doi.org/10.5281//zenodo.10026326
+```
+
 ```bibtex
-@software{monks_2023_10026327,
-  author       = {Monks, Thomas and
-                  Harper, Alison},
+@software{stars_treat_sim,
+  author       = {Thomas Monks, Alison Harper and Amy Heather},
   title        = {{Towards Sharing Tools, and Artifacts, for Reusable 
-                   Simulation: a minimal model examplar}},
-  month        = oct,
-  year         = 2023,
+                   Simulation: a minimal model example}},
+  month        = May,
+  year         = 2024,
   publisher    = {Zenodo},
-  version      = {v1.0.0},
-  url 	       = {https://zenodo.org/records/10026327}
+  version      = {v1.2.0},
+  doi          = {10.5281//zenodo.10026326.},
+  url          = {https://doi.org/10.5281//zenodo.10026326}
 }
 ```
-

treat_sim/__init__.py

@@ -1,2 +1,2 @@
-__author__ = 'T.Monks'
-__version__ = '1.1.1'
+__author__ = 'Thomas Monks, Alison Harper and Amy Heather'
+__version__ = '1.2.0'