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README.md

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@@ -7,74 +7,5 @@ Documentation and sample of a simple `R`-based submission for the [Computo journ
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It shows how to automatically setup and build the HTML and PDF outputs, ready to submit to our peer-review platform.
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:warning: **All important information about writing and preparing an article to be submitted to Computo, and related technicalities** are detailed [in the template manuscript](https://computo.sfds.asso.fr/template-computo-R). :warning:
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:warning: **All important information about writing and preparing an article to be submitted to Computo, and related technicalities** are detailed [in the guidelines for authors](https://computo-journal.org/site/guidelines-authors.html). :warning:
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More information about submission and **guidelines for authors** can be found on the [dedicated page](https://computo.sfds.asso.fr/submit/).
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## Process overview
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Submissions to [Computo](https://computorg.github.io) require both scientific content (typically equations, codes and figures, data) and a proof that this content is reproducible. This is achieved by means of i) a notebook system, ii) a virtual environment fixing the dependencies and iii) continuous integration (plus, if needed, an external website to store large data files such a [Zenodo](https://zenodo.org/) or [OSF](https://osf.io/) ).
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A Computo submission is thus a git(hub) repository like this one containing
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- the source files of the notebook (a quarto `.qmd` file + a BibTeX `.bib` file + some statics files, _e.g._ figures or small `.csv` data tables)
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- configuration files to set up the dependencies in a virtual environment
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- configuration files to set up the continuous integration rendering the final documents
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In this template, we focus on `R` users and detail a solution based on
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- The `knitr` kernel of Quarto for rendering the document,
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- The `renv` package for setting the virtual environment,
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- Github actions for handling the continuous integration.
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## Step-by-step procedure
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### Step 0: setup a git repository
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Use this repository as a template via the **"use this template"** button on the top of this page.
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**Note**: _You can use Gitlab for submitting for Computo. We hope giving more support in the future._
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### Step 1. setup Quarto and Computo extension on your system
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You need [quarto](https://quarto.org/) installed on your computer, as well as the [Computo extension](https://github.com/computorg/computo-quarto-extension) to prepare your document.
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The latter can be installed as follows:
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```.bash
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quarto add computorg/computo-quarto-extension
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```
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### Step 2. write your contribution
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Write your notebook as usual, [as demonstrated in the `template-computo-R.qmd` sample](https://computorg.github.io/template-computo-R/).
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**Note**: _Make sure that you are able to build your manuscript as a standard notebook on your system before proceeding to the next step._
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To build your document (both in PDF and HTML by default), you can run the command `quarto render`, e.g. for the template:
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```.bash
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quarto render template-computo-R.qmd # will render both to html and PDF
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```
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### Step 3: setup dependencies with `renv`
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Use the [`renv` package manager](https://rstudio.github.io/renv/articles/renv.html) to setup a reproducible environment handling your `R` dependencies.
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See [this page](https://computo.sfds.asso.fr/template-computo-R/#handle-r-dependencies-with-renv) for more details about `R` dependency setup.
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### Step 4: proof reproducibility
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Put everything together and check that your work is indeed reproducible. To this end, you need to rely on a github action, whose default is pre-configured and found here: [.github/workflows/build.yml](https://github.com/computorg/template-computo-R/blob/main/.github/workflows/build.yml)
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This action will
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1. Check out repository on the ubuntu-latest machine
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2. Install quarto and dependencies, including the Computo extension for Quarto
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3. Install R and dependencies with `renv`, using your `renv.lock` file
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4. Render your .qmd file and Publish the results on a gh-page (both HTML and PDF)
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**Note**: _Gitlab CI can be used to obtained similar results._
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### Step 5. submit
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Once step 4 is successful, you should end up with an HTML version published as a gh-page, as well as a PDF version (see "Other format" at the end of the table of content of the rendered HTML). This PDF version can be submitted to the [OpenReview platform](https://openreview.net/group?id=Computo).

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