diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index bbae1bd..d42c695 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,6 @@ -# Contributing to quarto-template +# Contributing to software-paper -First off, thanks for taking the time to contribute to `quarto-template`! +First off, thanks for taking the time to contribute to `software-paper`! 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 . +This project is released with a [Contributor Code of Conduct](https://github.com/biodiversitydata/software-paper/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to . ## 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. `software-paper` 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/software-paper/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/software-paper/issues/new). +- Use the template [other_issue.md](https://github.com/biodiversitydata/software-paper/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 `software-paper`. - 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/software-paper/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/software-paper/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/software-paper/issues/new). +- Use the template [bug_report.md](https://github.com/biodiversitydata/software-paper/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 `software-paper`. +- Read the [documentation](https://github.com/biodiversitydata/software-paper/) and the [wiki](https://github.com/biodiversitydata/software-paper/wiki) carefully and find out if the functionality is already covered. +- Perform a [search](https://github.com/biodiversitydata/software-paper/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/software-paper/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/software-paper/issues/new). +- Use the template [feature_request.md](https://github.com/biodiversitydata/software-paper/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 `software-paper` 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/software-paper/compare). We will then review the PR as soon as possible. diff --git a/README.md b/README.md index 37bcf16..34fca75 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,9 @@
Logo
- Quarto template + Software paper
- HTML presentation w/ RevealJS + Promoting the tool you developed to access your data
@@ -15,7 +15,7 @@

- View presentation + View presentation


@@ -37,13 +37,13 @@
- - GHA render + + GHA render - - GHA deploy + + GHA deploy

@@ -52,57 +52,46 @@

Overview • - Features • Usage • Citation • Contributing • Acknowledgments

-![](images/readme/title-slide-screenshot.png) -
## 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 [Writing a software paper](https://biodiversitydata.github.io/software-paper) 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_. . +Casajus N (2024) Writing a software paper. Online presentation available at . ## 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/software-paper/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 `software-paper` 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). diff --git a/index.qmd b/index.qmd index 2a5a4a2..ab7fc6f 100644 --- a/index.qmd +++ b/index.qmd @@ -3,7 +3,7 @@ from: markdown+emoji format: revealjs: logo: images/logo-affiliation.png - footer: "{{< fa brands github >}}  " + footer: "{{< fa brands github >}}  " smaller: true auto-stretch: false chalkboard: true @@ -21,14 +21,15 @@ engine: knitr + ```{r} -#| child: "sections/quarto-basics.qmd" +#| child: "sections/main.qmd" ``` diff --git a/sections/main.qmd b/sections/main.qmd new file mode 100644 index 0000000..24ca404 --- /dev/null +++ b/sections/main.qmd @@ -0,0 +1,3 @@ +# Introduction + +Coming soon... diff --git a/sections/quarto-basics.qmd b/sections/quarto-basics.qmd deleted file mode 100644 index b57034a..0000000 --- a/sections/quarto-basics.qmd +++ /dev/null @@ -1,111 +0,0 @@ -# Section 1 - - - -## Slide title - -Neque porro quisquam est qui dolorem ipsum quia dolor sit amet, consectetur, adipisci velit[^1]... - -
- -:::: {.columns} - -::: {.column width=50%} -**Left column** - -Neque porro quisquam est qui dolorem ipsum. - -![](images/logo-title-slide.png){width=25%} -::: - -::: {.column .center width=50%} -**Right column (content centered)** - -Neque porro quisquam est qui dolorem ipsum. - -![](images/logo-title-slide.png){width=50%} -::: - -:::: - -Neque porro quisquam est qui dolorem ipsum quia dolor sit amet, consectetur, adipisci velit... - - -[^1]: This is a footnote. - - - -# Section 2 - - - -## Slide title - - -:::: {.columns} - -::: {.column width=30%} -**Left column** - -Neque porro quisquam est. - -![](images/logo-title-slide.png){width=55%} -::: - -::: {.column width=70%} -**Right column** - -Neque porro quisquam est qui dolorem ipsum. - -| Header 1 | Header 2 | Header 3 | Header 4 | Header 5 | Header 6 | -|:------------|:-----------:|------------:|------------:|------------:|------------:| -| Row 1 Col 1 | Row 1 Col 2 | Row 1 Col 3 | Row 1 Col 4 | Row 1 Col 5 | Row 1 Col 6 | -| Row 2 Col 1 | Row 2 Col 2 | Row 2 Col 3 | Row 2 Col 4 | Row 2 Col 5 | Row 2 Col 6 | -| Row 3 Col 1 | Row 3 Col 2 | Row 3 Col 3 | Row 3 Col 4 | Row 3 Col 5 | Row 3 Col 6 | -| Row 4 Col 1 | Row 4 Col 2 | Row 4 Col 3 | Row 4 Col 4 | Row 4 Col 5 | Row 4 Col 6 | - -: Table 1: Table caption -::: - -:::: - -
- -Insert icons with [Font Awesome](https://fontawesome.com/search) {{< fa brands github >}} or [Academicons](https://jpswalsh.github.io/academicons/) {{< ai sci-hub >}} - - -
- -:::: {.columns} - -::: {.column width=50%} -::: - -::: {.column width=50%} -```{r} -#| echo: true -#| eval: true - -# Block code with unicode symbol ---- -x <- "I \u2665 Quarto" -print(x) -``` -::: - -:::: - - - -# Resources - - - -## Resources - -- [Quarto guide](https://quarto.org/docs/guide/) -- [Markdown syntax](https://quarto.org/docs/authoring/markdown-basics.html) -- [RevealJS guide](https://quarto.org/docs/presentations/revealjs/) - -
- -To use this template, visit the [**Wiki**](https://github.com/biodiversitydata/quarto-template/wiki). diff --git a/sections/title-slide.qmd b/sections/title-slide.qmd index 2bfaad9..ccab409 100644 --- a/sections/title-slide.qmd +++ b/sections/title-slide.qmd @@ -11,11 +11,11 @@ ::: {.column .information width="68%"} ::: {.title} -Quarto template +Software paper ::: ::: {.subtitle} -HTML presentation w/ RevealJS framework +Promoting the tool you developed to access your data ::: ::: {.date} diff --git a/styles/main.scss b/styles/main.scss index 8185beb..dd0d9c9 100644 --- a/styles/main.scss +++ b/styles/main.scss @@ -142,3 +142,35 @@ aside { text-align: center; } + +.callout-title p { + font-size: 1.8em; +} + +.callout-content p { + font-size: 1.8em; +} + +blockquote { + border: 0 !important; + margin: 0.5em 0 !important; + margin-bottom: 2em !important; + padding: 0 !important; + margin-left: 2% !important; + margin-right: 2% !important; +} + + +blockquote p { + font-style: normal; + padding: 0.5em 1em; + border-left: 5px solid #cccccc; +} + +/* +blockquote p::before { + content: "\27A4"; + font-style: normal; + padding-right: 10px; +} +*/