From d856bec8ee7d7a1f075a4874696e561a8dc51f9e Mon Sep 17 00:00:00 2001 From: Aymeric Stamm Date: Tue, 5 Aug 2025 18:43:35 +0200 Subject: [PATCH 1/3] Add pointer to nice book for git newbies. --- site/guidelines-authors.qmd | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/site/guidelines-authors.qmd b/site/guidelines-authors.qmd index 2b3370e..0f503c6 100644 --- a/site/guidelines-authors.qmd +++ b/site/guidelines-authors.qmd @@ -63,6 +63,12 @@ These templates provide a starting point for authors to format their contributio ### Setup a git repository {#sec-git} +::: {.callout-note title="Git and GitHub"} +Git is a versioning tool and GitHub is an online platform owned by Microsoft which provides the service of hosting repositories with all the capabilities of versioning offered by Git. + +Computo requires authors to submit their contribution as a GitHub repository. Hence, authors are expected to have basic knowledge of Git. We refer authors to the following online book which is particularly well written: . +::: + Create a new GitHub repository by navigating to the [R](https://github.com/computorg/template-computo-R), [Python](https://github.com/computorg/template-computo-python), or [Julia](https://github.com/computorg/template-computo-julia) template repository and clicking the **"Use this template"** button at the top of the page, as shown in @fig-template. ![Screenshot of the R Computo template GitHub page.](/assets/img/computo-template-screenshot.png){#fig-template width="100%"} @@ -71,7 +77,7 @@ Create a new GitHub repository by navigating to the [R](https://github.com/compu When you fork a GitHub repository – whether it is a classic repository or a template – GitHub will ask if you want to include all branches (there is a box labeled *Include all branches*). You only need to fork the main branch, so you do not need to check that box. ::: -::: {.callout-caution title="Public repository"} +::: {.callout-caution title="Public/private repository"} The paper will be automatically published online using GitHub pages. This is possible only with public repositories (which is the default behavior when you initialize your repository from this template). It is fine to keep your repository private during the writing phase. However, we ask you to set it public at the submission stage; so that the paper can be rendered and published online for the reviewers. ::: From ccf384583a8d4b513935242bad6601f7bc50180d Mon Sep 17 00:00:00 2001 From: Aymeric Stamm Date: Thu, 7 Aug 2025 08:47:46 +0200 Subject: [PATCH 2/3] Add multiple language support. --- site/guidelines-authors.qmd | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/site/guidelines-authors.qmd b/site/guidelines-authors.qmd index 0f503c6..db988c2 100644 --- a/site/guidelines-authors.qmd +++ b/site/guidelines-authors.qmd @@ -121,7 +121,13 @@ There are mainly two files you are expected to modify in your repository for wri The main body of your paper (starting with the *Introduction* section) should be written in the `template-computo-LANG.qmd` following the formatting suggestions therein. -::: {.callout-note title="Local compilation"} +::: {.callout-tip title="Multiple languages"} +Quarto relies on a specific engine to compile your document. By default, that engine detects code blocks, executes them and paste the result below the code block in the rendered document. + +It is possible to use multiple languages within the same document (e.g. R and Python or Python and Julia, etc.) provided that you use the **knitr** engine. Indeed, [**knitr**](https://yihui.org/knitr/) is an R package that is able to parse code blocks from many languages. This can be achieved by specifying `engine: knitr` in your document metadata. The default engine binding that Quarto uses is detailed here: . +::: + +::: {.callout-caution title="Local compilation"} Make sure that you are able to build your manuscript as a standard notebook on your system before proceeding to the next step. ::: From 291717480ac10bae501496f39a784cbb59c8789c Mon Sep 17 00:00:00 2001 From: Aymeric Stamm Date: Thu, 7 Aug 2025 08:51:04 +0200 Subject: [PATCH 3/3] Remove content of build.yml. --- site/guidelines-authors.qmd | 27 +-------------------------- 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/site/guidelines-authors.qmd b/site/guidelines-authors.qmd index db988c2..2914507 100644 --- a/site/guidelines-authors.qmd +++ b/site/guidelines-authors.qmd @@ -217,32 +217,7 @@ Now that you have written your contribution in the correct template and set up i #### Use Computo's built-in GitHub Action workflow -Computo has a built-in workflow for just that purpose which comes in the form of a YAML file describing a GitHub Action. It should have been automatically added to your repository when you cloned one of our templates. It is located under `.github/workflows/build.yml` and its content should exactly match the following: - -```yml -name: Main Workflows - -on: - push: - branches: ["main","master"] - repository_dispatch: - types: [custom-event] - workflow_dispatch: - pull_request: - branches: ["main","master"] - - -jobs: - call_env_workflow: - uses: computorg/workflows/.github/workflows/global-env.yml@main - call_quartopublish_workflow: - permissions: - id-token: write - contents: write - pages: write - uses: computorg/workflows/.github/workflows/publish-render.yml@main - needs: call_env_workflow -``` +Computo has a built-in workflow for just that purpose which comes in the form of a YAML file describing a GitHub Action. It should have been automatically added to your repository when you cloned one of our templates. It is located under `.github/workflows/build.yml`. ::: {.callout-important title="Content of `build.yml`"} Authors should **under no circumstances** modify this file. If you encounter a problem (such as the CI not completing successfully), please get in touch with us at .