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guidelines simplification and hopefully, enhancement
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site/guidelines-authors.qmd

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number-sections: true
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fig-align: "center"
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page-layout: article
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bibliography: ../publications/published.bib
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lightbox: true
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listing:
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- id: examples
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template: publications.ejs
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contents: mock-papers.yml
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sort: date desc
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type: table
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---
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## Introduction
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![Deploy your website with GitHub Actions](/assets/img/2025-03-20-revised-github-process/depoy-github.png){#fig-deploy width="100%"}
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Authors can find more details about Computo's workflow in @sec-workflow.
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Authors can find more details about Computo's workflow [in the corresponding FAQ entry](../blog/2025-07-31-computo-workflow/index.html).
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::: {.callout-note title="Compatibility with old reproducibility system"}
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You can safely delete the `gh-pages` branch if you have one, as we don't need anymore to push the HTML files to the site.
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![The ownership transfer page.](/assets/img/transfer-ownership.003.png){#fig-transfer-ownership-3 width="100%" fig-align="center"}
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## Example papers {#sec-examples}
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## Advanced examples {#sec-examples}
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In addition to the template repositories that can serve as example papers [see @sec-templates], we provide more in-depth illustrations of the expected content and available features through mock contributions consisting of a complete reworking of the famous t-SNE article.
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### Mock contributions
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::: {.grid}
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::: {.g-col-6}
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::: {.callout-note icon="false"}
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### R
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In addition to the template repositories that can serve as example papers (see @sec-templates), we provide more in-depth illustrations of the expected content and available features through mock contributions consisting of a complete reworking of the famous t-SNE article.
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[![](/assets/img/published-paper-tsne.png)](https://computo-journal.org/published-paper-tsne/)
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<https://computo-journal.org/published-paper-tsne/>
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:::
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::: {#examples}
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:::
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::: {.g-col-6}
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::: {.callout-tip icon="false"}
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### Python
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[![](/assets/img/published-paper-tsne.png)](https://computo-journal.org/published-paper-tsne-R/)
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<https://computo-journal.org/published-paper-tsne-R/>
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:::
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:::
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### Previously published papers
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::: {.callout-tip title="Reproducing a paper"}
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For other advanced examples, do not hesitate to explore the source code of any [paper already published in Computo](https://computo-journal.org/site/publications.html) to see how the template is used in practice. In particular, reproducing an existing paper published in Computo can be easily done [as detailed in the FAQ](../blog/2025-07-31-reproduce-paper/index.html).
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:::
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:::{.callout-tip}
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## Accessing paper source
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For other advanced examples, do not hesitate to explore the source code of any [paper already published in Computo](https://computo-journal.org/site/publications.html) to see how the template is used in practice. You can also access the source code of the example papers mentioned above by clicking on the `</> Source` button in the upper-right corner of the page as illustrated in @fig-template-source.
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## Accessing source code
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You can also access the source code of the example papers mentioned above by clicking on the `</> Source` button in the upper-right corner of the page as illustrated in @fig-template-source.
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:::
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![Accessing sources of the rendered example papers.](/assets/img/computo-template-r-source.png){#fig-template-source width="100%"}
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![Copying the sources of the rendered example papers.](/assets/img/computo-template-r-source-display.png){#fig-template-source-display width="100%"}
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## Computo's publication workflow {#sec-workflow}
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The Computo workflows provide a streamlined publishing pipeline for authors to submit and render Quarto articles directly on GitHub Pages without requiring technical expertise.
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### Workflow Summary
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![Computo Workflow Structure](/assets/img/2025-03-20-revised-github-process/workflow.svg){#fig-workflow width="100%"}
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As illustrated in @fig-workflow, the publication process consists of two main phases:
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1. **Environment Setup and Caching** (`global-env.yml`)
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- Detects and installs required dependencies (Python, R)
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- Caches the environment for faster subsequent runs
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- Customizable via `setup-env-ci.sh`
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2. **Rendering and Deployment** (`publish-render.yml`)
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- Renders Quarto documents to HTML
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- Publish the output to GitHub Pages
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- Customizable via `setup-render-ci.sh`
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Authors only need to reference the main workflow file (`build.yml`) in their repository, which orchestrates these processes.
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### Key Benefits
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- **Simplified Process**: Authors need minimal GitHub Actions knowledge
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- **Optimized Performance**: Environment caching for faster builds
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- **Customization Points**: Two script entry points for custom configurations
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- **Automated Deployment**: Direct publishing to GitHub Pages
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Authors simply use the `build.yml` workflow in their repository to trigger the complete process from environment setup to final publication.
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### Reproducing an existing paper published in Computo
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Our publication workflow makes it very easy for anyone to reproduce a given paper. Consider for instance the paper <https://doi.org/10.57750/sfxn-1t05> associated with the Github repository [published-202412-giorgi-efficient][https://github.com/computorg/published-202412-giorgi-efficient]. You first need to clone the repository. Then you need to install Quarto and the Computo Quarto extension in the `published-202412-giorgi-efficient` folder that the cloning step made. Finally, you can render the document. In summary, you do that with the following commands:
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```bash
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git clone https://github.com/computorg/published-202412-giorgi-efficient.git
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cd published-202412-giorgi-efficient
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quarto add computorg/computo-quarto-extension
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quarto render
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```
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## Computo's code of ethics {#sec-ethics}
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