From 8c6a9ccdca9045ed05c8dc903648a0a359b6a83c Mon Sep 17 00:00:00 2001 From: amyheather Date: Tue, 25 Mar 2025 10:37:50 +0000 Subject: [PATCH 1/6] docs(README/app): removed nav from author list, and correct deployment description --- Home.py | 6 +++--- README.md | 14 +++++++------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/Home.py b/Home.py index feca052..d9e64ea 100644 --- a/Home.py +++ b/Home.py @@ -12,14 +12,14 @@ """ This application is complementary to: -> Thomas Monks, Alison Harper, Amy Heather, and Navonil Mustafee. **Using Large +> Thomas Monks, Alison Harper, and Amy Heather. **Using Large Language Models to support researchers reproduce and reuse unpublished health care discrete-event simulation computer models: a feasibility and pilot study in Python**. https://github.com/pythonhealthdatascience/llm_simpy. It deploys the streamlit applications generated using Perplexity as a single -app on Streamlit Community Cloud. - +app via stlite and GitHub pages. + Use the sidebar to navigate to each app. """ ) diff --git a/README.md b/README.md index 1cbace7..060a1af 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ This repository is complementary to: -> Thomas Monks, Alison Harper, Amy Heather, and Navonil Mustafee. **Using Large Language Models to support researchers reproduce and reuse unpublished health care discrete-event simulation computer models: a feasibility and pilot study in Python**. https://github.com/pythonhealthdatascience/llm_simpy. +> Thomas Monks, Alison Harper, and Amy Heather. **Using Large Language Models to support researchers reproduce and reuse unpublished health care discrete-event simulation computer models: a feasibility and pilot study in Python**. https://github.com/pythonhealthdatascience/llm_simpy. It contains the final formatted code from each of the SimPy discrete-event simulation models that were generated by Perplexity as part of that project. @@ -32,8 +32,6 @@ For a full record of the generation of these models, please refer to: https://gi * Amy Heather    [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) -* Navonil Mustafee    [![ORCID: Mustafee](https://img.shields.io/badge/ORCID-0000--0002--2204--8924-brightgreen)](https://orcid.org/0000-0002-2204-8924) - ## 🌐 Creating the environment The project uses `conda` to manage dependencies. Navigate your terminal to the directory containing the code and run: @@ -72,13 +70,15 @@ python3 -m http.server ## 📝 Citation -Please cite this repository as: +Please cite the archived repository: -> Thomas Monks, Alison Harper, Amy Heather, and Navonil Mustafee. **Complementary repository: Final discrete-event simulation models and streamlit applications from Large Language Models**. . +> Thomas Monks, Alison Harper, and Amy Heather. **Complementary repository: Final discrete-event simulation models and streamlit applications from Large Language Models**. . -A `CITATION.cff` file is also provided. +You can also cite this GitHub repository as: - +> Thomas Monks, Alison Harper, and Amy Heather. **Complementary repository: Final discrete-event simulation models and streamlit applications from Large Language Models**. . + +A `CITATION.cff` file is also provided. ## 💰 Funding From e786d1b08c2518c9c4d59cbf02788a79f992540c Mon Sep 17 00:00:00 2001 From: amyheather Date: Tue, 25 Mar 2025 10:40:26 +0000 Subject: [PATCH 2/6] chore(release): update changelog and citation.cff for v1.0.1 --- CHANGELOG.md | 9 +++++++++ CITATION.cff | 7 +------ 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 12fc7a8..bb324ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,15 @@ 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). +## v1.0.1 - 2025-03-25 + +Update author list and correct app home page. + +### Changed + +* Removed Nav from `README.md`, `CITATION.cff` and `Home.py`. +* Correct `Home.py` (to describe deployment as stlite and GitHub pages, and not Streamlit Community Cloud). + ## v1.0.0 - 2025-03-25 🌱 First release. Functioning streamlit app containing each of the LLM-generated apps as pages. Deployed using stlite and GitHub pages. \ No newline at end of file diff --git a/CITATION.cff b/CITATION.cff index d4bdbf0..767c6a7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -25,14 +25,9 @@ authors: email: a.heather2@exeter.ac.uk affiliation: University of Exeter orcid: 'https://orcid.org/0000-0002-6596-3479' - - given-names: Navonil - family-names: Mustafee - orcid: 'https://orcid.org/0000-0002-2204-8924' - affiliation: University of Exeter - email: n.mustafee@exeter.ac.uk repository-code: 'https://github.com/pythonhealthdatascience/llm_simpy_models' abstract: >- The SimPy models and apps generated by LLMs, deployed as a single app. license: MIT -version: '1.0.0' +version: '1.0.1' date-released: '2025-03-25' \ No newline at end of file From af4cbb8c11e079e94d1b5accbecffef9b72c8403 Mon Sep 17 00:00:00 2001 From: Amy Heather <92166537+amyheather@users.noreply.github.com> Date: Tue, 25 Mar 2025 10:42:17 +0000 Subject: [PATCH 3/6] chore(release): add mention of DOI for v1.0.1 --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb324ed..998deb8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.0.1 - 2025-03-25 -Update author list and correct app home page. +Update author list, add DOI, and correct app home page. ### Changed * Removed Nav from `README.md`, `CITATION.cff` and `Home.py`. * Correct `Home.py` (to describe deployment as stlite and GitHub pages, and not Streamlit Community Cloud). +* Add DOI to `README.md`. ## v1.0.0 - 2025-03-25 -🌱 First release. Functioning streamlit app containing each of the LLM-generated apps as pages. Deployed using stlite and GitHub pages. \ No newline at end of file +🌱 First release. Functioning streamlit app containing each of the LLM-generated apps as pages. Deployed using stlite and GitHub pages. From 3a2c5ecd781b320aa98ffa440c5c2ebeae1ed47c Mon Sep 17 00:00:00 2001 From: amyheather Date: Tue, 25 Mar 2025 14:15:01 +0000 Subject: [PATCH 4/6] feat(home): add info box explaining st.spinner() absence with stlite --- Home.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/Home.py b/Home.py index d9e64ea..5ee78a7 100644 --- a/Home.py +++ b/Home.py @@ -24,6 +24,16 @@ """ ) +st.divider() +st.info(""" +The apps use `st.spinner()` to show a spinning icon when the model is running, +but this does not work with `stlite`. Hence, it may appear like nothing is +happening, when the model is actually running behind the scenes (once you +click "simulate"). This is mainly relevant to the stroke model which takes a +little longer to run, but you can speed it up by reducing the number of +replications. +""", icon="ℹī¸") + st.divider() st.markdown( """ From 4567fcdc6d4a39d1b9fc95e8a1e5167ad49f70df Mon Sep 17 00:00:00 2001 From: amyheather Date: Tue, 25 Mar 2025 14:16:26 +0000 Subject: [PATCH 5/6] chore(release): update changelog and citation.cff for v1.0.2 --- CHANGELOG.md | 8 ++++++++ CITATION.cff | 2 +- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 998deb8..927dbc9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,14 @@ 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). +## v1.0.2 - 2025-03-25 + +Add note about `st.spinner()` to the home page. + +### Changed + +* Explained that `st.spinner()` won't work on stlite in an info box in `Home.py`. + ## v1.0.1 - 2025-03-25 Update author list, add DOI, and correct app home page. diff --git a/CITATION.cff b/CITATION.cff index 767c6a7..a8bc246 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -29,5 +29,5 @@ repository-code: 'https://github.com/pythonhealthdatascience/llm_simpy_models' abstract: >- The SimPy models and apps generated by LLMs, deployed as a single app. license: MIT -version: '1.0.1' +version: '1.0.2' date-released: '2025-03-25' \ No newline at end of file From 2ea6799465f632d9967224f3047f2e42d9288a8e Mon Sep 17 00:00:00 2001 From: amyheather Date: Tue, 25 Mar 2025 15:30:37 +0000 Subject: [PATCH 6/6] docs(llm_simpy): update title of llm_simpy repository (+ add line breaks and DOI badge to README) --- Home.py | 7 +++---- README.md | 13 ++++++++++++- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/Home.py b/Home.py index 5ee78a7..e6aede7 100644 --- a/Home.py +++ b/Home.py @@ -12,10 +12,9 @@ """ This application is complementary to: -> Thomas Monks, Alison Harper, and Amy Heather. **Using Large -Language Models to support researchers reproduce and reuse unpublished health -care discrete-event simulation computer models: a feasibility and pilot study -in Python**. https://github.com/pythonhealthdatascience/llm_simpy. +> Thomas Monks, Alison Harper, and Amy Heather. **Research Compendium: +Replicating Simulations in Python using Generative AI**. +https://github.com/pythonhealthdatascience/llm_simpy. It deploys the streamlit applications generated using Perplexity as a single app via stlite and GitHub pages. diff --git a/README.md b/README.md index 060a1af..657fdcb 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,12 @@ [![Licence: MIT](https://img.shields.io/badge/Licence-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Python 3.10+](https://img.shields.io/badge/-Python_â‰Ĩ_3.10-306998?logo=python&logoColor=white)](https://www.python.org/downloads/release/python-360+/) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15082494.svg)](https://doi.org/10.5281/zenodo.15082494) # Complementary repository: Final discrete-event simulation models and streamlit applications from Large Language Models This repository is complementary to: -> Thomas Monks, Alison Harper, and Amy Heather. **Using Large Language Models to support researchers reproduce and reuse unpublished health care discrete-event simulation computer models: a feasibility and pilot study in Python**. https://github.com/pythonhealthdatascience/llm_simpy. +> Thomas Monks, Alison Harper, and Amy Heather. **Research Compendium: Replicating Simulations in Python using Generative AI**. https://github.com/pythonhealthdatascience/llm_simpy. It contains the final formatted code from each of the SimPy discrete-event simulation models that were generated by Perplexity as part of that project. @@ -24,6 +25,8 @@ The stroke `.py` files combine the seperate model and app .py files from the [ll For a full record of the generation of these models, please refer to: https://github.com/pythonhealthdatascience/llm_simpy. +
+ ## đŸ‘Ĩ Authors * Thomas Monks    [![ORCID: Monks](https://img.shields.io/badge/ORCID-0000--0003--2631--4481-brightgreen)](https://orcid.org/0000-0003-2631-4481) @@ -32,6 +35,8 @@ For a full record of the generation of these models, please refer to: https://gi * Amy Heather    [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) +
+ ## 🌐 Creating the environment The project uses `conda` to manage dependencies. Navigate your terminal to the directory containing the code and run: @@ -48,6 +53,8 @@ conda activate gen_simpy_apps This environment is a simplified version of that from the [llm_simpy](https://github.com/pythonhealthdatascience/llm_simpy) repository, containing only the dependencies required for running the apps. +
+ ## đŸ–Ĩī¸ Viewing the apps locally For deployment, we have brought the LLM-generated apps together into a single app, which can be deployed by running: @@ -68,6 +75,8 @@ To test the stlite app locally, run the following command, and then open + ## 📝 Citation Please cite the archived repository: @@ -80,6 +89,8 @@ You can also cite this GitHub repository as: A `CITATION.cff` file is also provided. +
+ ## 💰 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)]. \ No newline at end of file pFad - Phonifier reborn

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