resolve conflict

Merge branch 'main' of https://github.com/biodiversitydata/general-context

# Conflicts:
#	sections/slides.qmd

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# Contributing to quarto-template
+# Contributing to general-context
 
-First off, thanks for taking the time to contribute to `quarto-template`!
+First off, thanks for taking the time to contribute to `general-context`!
 
 All types of contributions are encouraged and valued. See the 
 [Table of contents](#table-of-contents) for different ways to help and details 
@@ -24,13 +24,13 @@ maintainers and smooth out the experience for all involved.
 
 ## Code of conduct
 
-This project is released with a [Contributor Code of Conduct](https://github.com/biodiversitydata/quarto-template/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to <[email protected]>.
+This project is released with a [Contributor Code of Conduct](https://github.com/biodiversitydata/general-context/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to <[email protected]>.
 
 
 
 ## Style guide
 
-We use the [Tidyverse style guide](https://style.tidyverse.org/) for writing R code. Functions are documented with the [roxygen2](https://roxygen2.r-lib.org/articles/roxygen2.html) syntax. `quarto-template` uses the `lower_snake_case`.
+We use the [Tidyverse style guide](https://style.tidyverse.org/) for writing R code. Functions are documented with the [roxygen2](https://roxygen2.r-lib.org/articles/roxygen2.html) syntax. `general-context` uses the `lower_snake_case`.
 
 
 
@@ -42,12 +42,12 @@ If you want to contribute by commiting changes, please try to use the [Conventio
 
 ## Asking questions
 
-Before you ask a question, it is best to search for existing [Issues](https://github.com/biodiversitydata/quarto-template/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue.
+Before you ask a question, it is best to search for existing [Issues](https://github.com/biodiversitydata/general-context/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue.
 
 If you then still feel the need to ask a question and need clarification, we recommend the following:
 
-- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new).
-- Use the template [other_issue.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/other_issue.md).
+- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new).
+- Use the template [other_issue.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/other_issue.md).
 - Provide as much context as you can about what you're running into.
 - Provide project and platform versions (paste the output of `sessionInfo()`).
 
@@ -63,19 +63,19 @@ We will then take care of the issue as soon as possible.
 
 A good bug report shouldn't leave others needing to chase you up for more  information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible.
 
-- Make sure that you are using the latest version of `quarto-template`.
+- Make sure that you are using the latest version of `general-context`.
 - Determine if your bug is really a bug and not an error on your side.
-- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/biodiversitydata/quarto-template/issues?q=label%3Abug).
+- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/biodiversitydata/general-context/issues?q=label%3Abug).
 
 
 
 ### How do I submit a bug report?
 
-We use [GitHub Issues](https://github.com/biodiversitydata/quarto-template/issues) to 
+We use [GitHub Issues](https://github.com/biodiversitydata/general-context/issues) to 
 track bugs and errors. If you run into an issue with the project:
 
-- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new).
-- Use the template [bug_report.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/bug_report.md).
+- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new).
+- Use the template [bug_report.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/bug_report.md).
 - Explain the behavior you would expect and the actual behavior.
 - Please provide as much context as possible and describe the 
 *reproduction steps* that someone else can follow to recreate the issue on 
@@ -91,21 +91,21 @@ We will then take care of the issue as soon as possible.
 
 ### Before requesting a feature
 
-- Make sure that you are using the latest version of `quarto-template`.
-- Read the [documentation](https://github.com/biodiversitydata/quarto-template/) and the [wiki](https://github.com/biodiversitydata/quarto-template/wiki) carefully and find out if the functionality is already covered.
-- Perform a [search](https://github.com/biodiversitydata/quarto-template/issues) to see if this enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.
+- Make sure that you are using the latest version of `general-context`.
+- Read the [documentation](https://github.com/biodiversitydata/general-context/) and the [wiki](https://github.com/biodiversitydata/general-context/wiki) carefully and find out if the functionality is already covered.
+- Perform a [search](https://github.com/biodiversitydata/general-context/issues) to see if this enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.
 
 
 
 ### How do I submit a feature request?
 
-Feature requests are tracked as [GitHub Issues](https://github.com/biodiversitydata/quarto-template/issues).
+Feature requests are tracked as [GitHub Issues](https://github.com/biodiversitydata/general-context/issues).
 
-- Open a new [Issue](https://github.com/biodiversitydata/quarto-template/issues/new).
-- Use the template [feature_request.md](https://github.com/biodiversitydata/quarto-template/blob/main/.github/ISSUE_TEMPLATE/feature_request.md).
+- Open a new [Issue](https://github.com/biodiversitydata/general-context/issues/new).
+- Use the template [feature_request.md](https://github.com/biodiversitydata/general-context/blob/main/.github/ISSUE_TEMPLATE/feature_request.md).
 - Provide a clear and descriptive title for the issue to identify the suggestion.
 - Provide a step-by-step description of the suggested enhancement in as many details as possible.
-- Explain why this enhancement would be useful to most `quarto-template` users.
+- Explain why this enhancement would be useful to most `general-context` users.
 
 We will then take care of the issue as soon as possible.
 
@@ -122,7 +122,7 @@ We use the [GitHub flow](https://docs.github.com/en/get-started/quickstart/githu
 1. Make your contribution.
 1. Stage (`git add`) and commit (`git commit`) your changes as often as necessary
 1. Push your changes to GitHub w/ `git push origin branch-name`.
-3. Submit a [Pull Request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) on the [original repo](https://github.com/biodiversitydata/quarto-template/compare).
+3. Submit a [Pull Request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) on the [original repo](https://github.com/biodiversitydata/general-context/compare).
 
 We will then review the PR as soon as possible.
 

README.md

@@ -4,9 +4,9 @@
   <br>
   <img src="images/readme/logo-readme.png" alt="Logo" width="200">
   <br>
-  Quarto template
+  Biodiversity data: General context
   <br>
-  HTML presentation w/ RevealJS
+  Open science, complex landscape & reproducibility
   <br>
 </h1>
 
@@ -15,7 +15,7 @@
 
 <br>
 <p align="center">
-  <a href="https://biodiversitydata.github.io/quarto-template" target="_blank"><b>View presentation</b></a>
+  <a href="https://biodiversitydata.github.io/general-context" target="_blank"><b>View presentation</b></a>
 </p>
 <br>
 
@@ -37,13 +37,13 @@
   <br/>
 
   <!-- Quarto render -->
-  <a href="https://github.com/biodiversitydata/quarto-template/actions/workflows/quarto-render.yml">
-    <img src="https://github.com/biodiversitydata/quarto-template/actions/workflows/quarto-render.yml/badge.svg" alt="GHA render">
+  <a href="https://github.com/biodiversitydata/general-context/actions/workflows/quarto-render.yml">
+    <img src="https://github.com/biodiversitydata/general-context/actions/workflows/quarto-render.yml/badge.svg" alt="GHA render">
   </a>
 
   <!-- GitHub deployment -->
-  <a href="https://github.com/biodiversitydata/quarto-template/actions/workflows/pages/pages-build-deployment">
-    <img src="https://github.com/biodiversitydata/quarto-template/actions/workflows/pages/pages-build-deployment/badge.svg" alt="GHA deploy">
+  <a href="https://github.com/biodiversitydata/general-context/actions/workflows/pages/pages-build-deployment">
+    <img src="https://github.com/biodiversitydata/general-context/actions/workflows/pages/pages-build-deployment/badge.svg" alt="GHA deploy">
   </a>
 </p>
 
@@ -52,57 +52,46 @@
 
 <p align="center">
   <a href="#overview">Overview</a> •
-  <a href="#features">Features</a> •
   <a href="#usage">Usage</a> •
   <a href="#citation">Citation</a> •
   <a href="#contributing">Contributing</a> •
   <a href="#acknowledgments">Acknowledgments</a>
 </p>
 
-![](images/readme/title-slide-screenshot.png)
-
 <br>
 
 
 ## Overview
 
-This repository contains files and folders required to setup a minimal [Quarto HTML Presentation](https://quarto.org/docs/presentations/) based on the [RevealJS](https://quarto.org/docs/presentations/revealjs/) framework with a custom CSS theme.
-This is a [Template Repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) and you can generate a new repository from this template with the same directory structure, branches, and files.
-
+This repository contains files used to generate the online presentation [Biodiversity data: General context](https://biodiversitydata.github.io/general-context) based on [Quarto](https://quarto.org/) and the [RevealJS](https://quarto.org/docs/presentations/revealjs/) framework.
 
 
-## Features
+## Usage
 
-- Basics of Quarto presentation (title slide, two column slides, code block, images and tables)
-- Custom CSS style
-- Emoji support
-- [Fontawesome](https://github.com/quarto-ext/fontawesome) & [Academicons](https://github.com/schochastics/academicons) extensions
-- Complete repository structure
-- GitHub Action to automatically render `index.qmd`
-- Website deployment on `gh-pages` branch
+If you want to render the slides locally, you need to install the following tools:
 
+- [`R`](https://cran.r-project.org/) and [`RStudio Desktop`](https://posit.co/download/rstudio-desktop/)
+- [`Quarto CLI`](https://quarto.org/docs/get-started/)
 
-## Usage
+[Fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) this repository and [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) your copy.
 
-A dedicated Wiki is available [**here**](https://github.com/biodiversitydata/quarto-template/wiki/).
+Then, open the `index.qmd` in RStudio and click on the button **Render**. This will create an `index.html` containing your presentation. Open this `index.html` in your favorite web browser to access slides.
 
-- Read the [Installation](https://github.com/biodiversitydata/quarto-template/wiki/Installation) page to learn how to use this template.
-- Read the [Content](https://github.com/biodiversitydata/quarto-template/wiki/Content) page to discover the role of each file.
-- Read the [Usage](https://github.com/biodiversitydata/quarto-template/wiki/Usage) page to start writing your own presentation.
+To understand the file organisation of this repository, please read this [Wiki](https://github.com/biodiversitydata/quarto-template/wiki).
 
 
 ## Citation
 
-Casajus N (2024) _A Quarto template for HTML presentation with RevealJS framework_. <https://github.com/biodiversitydata/quarto-template/>.
+Norvez O, Pamerlon S & Casajus N (2024) Biodiversity data: General context. Online presentation available at <https://github.com/biodiversitydata/general-context/>.
 
 
 ## Contributing
 
-All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/biodiversitydata/quarto-template/blob/main/CONTRIBUTING.md).
+All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/biodiversitydata/general-context/blob/main/CONTRIBUTING.md).
 
-Please note that the `quarto-template` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the `general-context` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
 
 ## Acknowledgments
 
-This project has been developed for the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) training courses [program](https://frbcesab.github.io/content/courses.html).
+This project has been developed for the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) training courses [program](https://frbcesab.github.io/content/courses.html) and it's part of the training course [Biodiversity data management](https://biodiversitydata.github.io).

_quarto.yml

@@ -1,2 +1,4 @@
 project:
-  title: "index"
+  title: "General context"
+
+pagetitle: "General context"

index.qmd

@@ -3,12 +3,15 @@ from: markdown+emoji
 format:
   revealjs:
     logo: images/logo-affiliation.png
-    footer: "{{< fa brands github >}} &nbsp;<https://biodiversitydata.github.io/course-data-context>"
+    footer: "{{< fa brands github >}} &nbsp;[`biodiversitydata/general-context`](https://github.com/biodiversitydata/general-context) &nbsp; &bull; &nbsp; {{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}} &nbsp;[`cc-by-4.0`](https://creativecommons.org/licenses/by/4.0/deed.en)"
     smaller: true
     auto-stretch: false
     chalkboard: true
     toc-depth: 1
     theme: [default, "styles/main.scss"]
+knitr:
+  opts_chunk: 
+    comment: "##" 
 engine: knitr
 ---