Merge branch 'master' into guidelines-authors

Author: astamm

blog/2025-07-31-computo-workflow/index.qmd

@@ -0,0 +1,40 @@
+---
+title: Computo's publication workflow
+date: '2025-07-31'
+description: Diagram summarizing the publication workflow
+categories:
+  - authors
+  - reproducibility
+format:
+  html:
+    toc: true
+page-layout: article
+---
+
+The Computo workflows provide a streamlined publishing pipeline for authors to submit and render Quarto articles directly on GitHub Pages without requiring technical expertise.
+
+### Workflow Summary
+
+![Computo Workflow Structure](/assets/img/2025-03-20-revised-github-process/workflow.svg){#fig-workflow width="100%"}
+
+As illustrated in @fig-workflow, the publication process consists of two main phases:
+
+1.  **Environment Setup and Caching** (`global-env.yml`)
+    -   Detects and installs required dependencies (Python, R)
+    -   Caches the environment for faster subsequent runs
+    -   Customizable via `setup-env-ci.sh`
+2.  **Rendering and Deployment** (`publish-render.yml`)
+    -   Renders Quarto documents to HTML
+    -   Publish the output to GitHub Pages
+    -   Customizable via `setup-render-ci.sh`
+
+Authors only need to reference the main workflow file (`build.yml`) in their repository, which orchestrates these processes.
+
+### Key Benefits
+
+-   **Simplified Process**: Authors need minimal GitHub Actions knowledge
+-   **Optimized Performance**: Environment caching for faster builds
+-   **Customization Points**: Two script entry points for custom configurations
+-   **Automated Deployment**: Direct publishing to GitHub Pages
+
+Authors simply use the `build.yml` workflow in their repository to trigger the complete process from environment setup to final publication.

blog/2025-07-31-reproduce-paper/index.qmd

@@ -0,0 +1,21 @@
+---
+title: Reproducing an existing paper published in Computo
+date: '2025-07-31'
+description: How to reproduce a published paper?
+categories:
+  - authors
+  - reproducibility
+format:
+  html:
+    toc: true
+page-layout: article
+---
+
+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:
+
+```bash
+git clone https://github.com/computorg/published-202412-giorgi-efficient.git
+cd published-202412-giorgi-efficient
+quarto add computorg/computo-quarto-extension
+quarto render
+```

blog/3021-04-23-submission-process/index.qmd

@@ -36,13 +36,11 @@ Now you can write your contribution, using all the packages you need. Install th
 renv::install("ggplot2") # or equivalently install.packages("ggplot2")
 ```
 
-Non-CRAN packages (*e.g.* Github packages) can be used. To install such packages, you need to first install the **remotes** package. Then, if you want to install the development version of *e.g.* the **gt** package hosted by `rstudio` GitHub account (useful for nicely and easily formatting tables btw), you would do:
+Non-CRAN packages (*e.g.* Github packages) can be used. For instance, if you want to install the development version of *e.g.* the **gt** package hosted by `rstudio` GitHub account, you would do
 
 ```r
-install.packages("remotes")
-remotes::install_github("rstudio/gt")
+renv::install("rstudio/gt")
 ```
-
 Once you are done, you need to freeze the environment and package versions that are going to be used to run the calculations within your paper. This is achieved via:
 
 ```r
@@ -51,7 +49,11 @@ renv::snapshot()
 ```
 
 ::: {.callout-warning title="The `renv.lock` file"}
-The `renv.lock` should be versioned with git. Other files that `renv::snapshot()` might produce should be listed under `.gitignore` and therefore not put under versioning.
+The `renv.lock` should be versioned with git. Other files that `renv::snapshot()` might produce should be listed under `.gitignore` and therefore not put under versioning (which is done in the default template version of `.gitignore`).
+:::
+
+::: {.callout-tip title="R version"}
+A seamless workflow has been reported with `renv` when using `R` version `>= 4.5.1`. We recommand to update your system to this version or later.
 :::
 
 More details for using **renv** can be found:

site/_handle_dependencies_R.qmd

@@ -51,4 +51,4 @@ Currently and differently from what we provide for R users, we do not have imple
 
 ::: {.callout-tip title="`requirements.txt`"}
 If your work exclusively depends on packages installed from `pip` and you are used to listing dependencies in a `requirements.txt` file, you can ship this file instead of the `environment.yml` file and our CI/CD scripts should run smoothly.
-:::
+:::