Initial commit

.github/workflows/cff_convert.yaml

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+name: "Convert CITATION.cff"
+run-name: Convert CITATION.cff to other formats
+
+on:
+  push:
+    branches: main
+    paths: CITATION.cff
+  workflow_dispatch:
+
+jobs:
+  convert:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v4
+
+      - name: Convert CITATION.cff to Bibtex
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--infile ./CITATION.cff --format bibtex --outfile citation_bibtex.bib"
+
+      - name: Modify Bibtex entry
+        run: sed -i 's/@misc{YourReferenceHere,/@software{stars_reproduce_allen_2020,/' citation_bibtex.bib
+
+      - name: Convert CITATION.cff to APA
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--infile ./CITATION.cff --format apalike --outfile citation_apalike.apa"
+
+      - name: Commit and push the citation files
+        run: |
+          git config --global user.name 'cffconvert GitHub Action'
+          git config --global user.email '[email protected]'
+          git add citation_bibtex.bib
+          git add citation_apalike.apa
+          git commit --allow-empty -m "chore(citation): auto update .bib and .apa"
+          git push

.github/workflows/cff_validation.yaml

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+name: "Valid CITATION.cff"
+# Name of this action (else will name after the commits)
+run-name: Check if CITATION.cff is still valid
+
+# Source: https://github.com/marketplace/actions/cff-validator
+
+on:
+  push:
+    branches: main
+    paths: CITATION.cff
+  workflow_dispatch:
+
+jobs:
+  Validate-CITATION-cff:
+    runs-on: ubuntu-latest
+    name: Validate CITATION.cff
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3

.github/workflows/docker_ghr.yaml

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+name: "Publish Docker image"
+# Name of this action (else will name after the commits)
+run-name: Publish Docker image on GitHub container registry (ghcr.io)
+
+# Source: https://dev.to/github/publishing-a-docker-image-to-githubs-container-repository-4n50
+
+on:
+# TODO: Uncomment these lines once have added Dockerfile
+# (Currently, they are ensuring that action can only be triggered manually)
+#   push:
+#     branches: main
+  workflow_dispatch:
+
+jobs:
+  Publish-docker-image:
+    name: Publish docker image
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    # TODO: Remove this line once have added Dockerfile
+    # (Currently, its ensuring a triggered action will skip this job)
+    if: false
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # TODO: Update "envname" below to the correct name for your project's environment
+      - name: Build the Docker image
+        run: |
+          docker build . --file reproduction/docker/Dockerfile --tag ghcr.io/pythonhealthdatascience/envname:latest
+          docker push ghcr.io/pythonhealthdatascience/envname:latest

.github/workflows/quarto_publish.yaml

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+name: Update GitHub pages
+run-name: Render Quarto website and publish on GitHub pages
+
+# Source: https://quarto.org/docs/publishing/github-pages.html
+
+on:
+  push:
+    branches: main
+  workflow_dispatch:
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install python and dependencies
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install -r requirements.txt
+
+      - name: Render and publish to GitHub pages
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+_site/
+_freeze/
+/.quarto/
+__pycache__/
+.vscode/

CHANGELOG.md

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+# Changelog
+
+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).
+
+<!-- TODO: Delete the CHANGELOG entries for the reproduction template, but use their structure to create entries for your project, i.e.
+
+## v0.1.0
+
+**Release date:** [Date]
+
+**Contributors:** [Researcher name]
+
+[One-sentence summary of release]
+
+### Added
+
+*
+
+### Changed
+
+*
+
+### Removed
+
+*
+
+### Fixed
+
+*
+-->
+
+## v1.0.2
+
+**Release date:** 3rd July 2024
+
+**Contributors:** Amy Heather
+
+Minor improvements following the first reproducibility assessment ([Shoaib and Ramamohan 2022](https://github.com/pythonhealthdatascience/stars-reproduce-shoaib-2022)).
+
+### Added
+
+* Template page (`reflections.qmd`) for reflections on facilitators and barriers to reproduction, and for full list of troubleshooting steps
+
+### Changed
+
+* Add `.vscode/` to `.gitignore`
+* Add citation to protocol on quarto site home page
+* Order of criteria in `badges.qmd` (so it is a consistent order between the dictionary of criteria names and results, making it easier when conducting the assessment to look between the two)
+* Amended `TODO:` comments in CHANGELOG and GHCR GitHub action
+* Add missing `<!--- -->` marker in `artefacts.qmd`
+* Improved the "succesfully reproduced" template sentence in `reproduction_report.qmd`
+
+## v1.0.1
+
+**Release date:** 19th June 2024
+
+**Contributors:** Amy Heather
+
+Fix to citation file to prevent error on Zenodo.
+
+### Fixed
+
+* Completed `CITATION.cff` to reflect this repository (rather than to be a blank example), to prevent error when syncing with Zenodo
+
+## v1.0.0
+
+**Release date:** 19th June 2024
+
+**Contributors:** Amy Heather, with review of the protocol and associated artefacts (such as this template) from Tom Monks, Alison Harper and Nav Mustafee
+
+Initial release of template repository. 🌱

CITATION.cff

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+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+# TODO: Amend to 'STARS: Computational reproducibility of Author et al. Year'
+title: Template for computational reproducibility assessments on STARS
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+# TODO: Amend to list of authors involved in reproduction - first, the primary
+# researcher, followed by those providing advice/feedback on the reproduction.
+authors:
+  - given-names: Amy
+    family-names: Heather
+    email: [email protected]
+    affiliation: University of Exeter Medical School, Exeter, UK
+    orcid: 'https://orcid.org/0000-0002-6596-3479'
+  - given-names: Thomas
+    family-names: Monks
+    email: [email protected]
+    affiliation: University of Exeter Medical School, Exeter, UK
+    orcid: 'https://orcid.org/0000-0003-2631-4481'
+  - given-names: Alison
+    family-names: Harper
+    email: [email protected]
+    affiliation: University of Exeter Business School, Exeter, UK
+    orcid: 'https://orcid.org/0000-0001-5274-5037'
+  - given-names: Navonil
+    family-names: Mustafee
+    email: [email protected]
+    affiliation: University of Exeter Business School, Exeter, UK
+    orcid: 'https://orcid.org/0000-0002-2204-8924'
+  - given-names: Andrew
+    family-names: Mayne
+    email: [email protected]
+    affiliation: Taunton and Somerset NHS Foundation Trust, UK
+    orcid: 'https://orcid.org/0000-0003-1263-2286'
+# TODO: Amend to correct repository URL
+repository-code: >-
+  https://github.com/pythonhealthdatascience/stars_reproduction_template
+# TODO: Amend to short description of repo and citation for the original study
+abstract: >-
+  Template repository for assessing the computational reproducibility of discrete-event simulation studies on STARS.
+license: MIT
+# TODO: Manually update with each GitHub release (start with 0.1.0)
+version: '1.0.1'
+date-released: '2024-06-19'

CONTRIBUTING.md

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+# Contributing
+
+🎉 Thank you for checking out our project! 🎉
+
+This page contains guidelines on how to get in touch with us and potentially contribute towards this repository.
+
+## Email
+
+You can contact the researchers on this project using the provided email addresses in `CITATION.cff`.
+
+## Suggesting changes
+
+If you spot an issue, you are welcome to raise this either by:
+
+* Using **GitHub Issues**.
+* **Forking** the repository, make your changes and submit a pull request for review.

LICENSE

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+MIT License
+
+Copyright (c) 2024 STARS Project Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.