Initial commit

Author: lauraporta

.github/workflows/render_and_deploy.yml

@@ -0,0 +1,54 @@
+name: Render presentation and publish to GitHub Pages
+
+# Render presentation with Quarto on all merges to main, all pull requests, 
+# or by manual workflow dispatch. The build job can be used as a CI check 
+# that the presentation still renders successfully.
+# The deploy step only runs when a release tag is pushed to the main branch 
+# and actually pushes the generated html to the gh-pages branch 
+# (which triggers a GitHub pages deployment).
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: render and publish
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Render Quarto Project
+        run: |
+          quarto render index.qmd --to revealjs
+
+      - name: Move outputs to build folder
+        if: github.event_name == 'push' && github.ref_type == 'tag'
+        run: |
+          mkdir build
+          mv index.html build/
+          mv index_files build/
+          touch build/.nojekyll
+          cp -r img build/
+
+      - name: Deploy
+        if: github.event_name == 'push' && github.ref_type == 'tag'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: build
+  

.gitignore

@@ -0,0 +1,4 @@
+index.html
+index_files/
+build/
+.DS_Store

LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, SWC/GCNU Neuroinformatics Unit
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -0,0 +1,43 @@
+# quarto-presentation-template
+
+## Prerequisites
+
+You only need to do these once locally. 
+* Install [Quarto](https://quarto.org/docs/get-started/)
+* Install the [VS Code Quarto extension](https://quarto.org/docs/get-started/hello/vscode.html)
+
+## Create a new presentation
+
+* Click on "Use this template" -> "Create a new repository"
+* Choose a repository name that starts with `slides-` (this should help us spot quarto presentation repositories at a glance, especially important if they proliferate)
+* Clone the newly created repository and navigate to its root folder
+* Create a conda environment with `conda create -n quarto python=3.11`
+* Activate the environment with `conda activate quarto`
+* `pip install -r requirements.txt`
+* If you have additional requirements for your execution environment (e.g. your Python package) add them to `requirements.txt`
+* Edit the `index.qmd` file to your liking, using the example slides as a guide.
+
+## Build the presentation locally
+
+You can either:
+* Use the VS Code extension's GUI ("Render" button)
+* Use the command line:
+  * `quarto render index.qmd --to revealjs` for reveal.js slides
+  * `quarto render index.qmd --to html` for a standalone HTML page with embedded resources.
+
+## Deploy the presentation on GitHub Pages
+For the first deployment:
+* Create an empty `gh-pages` branch:
+  ```sh
+  git checkout --orphan gh-pages
+  git reset --hard
+  git commit --allow-empty -m "fresh and empty gh-pages branch"
+  git push origin gh-pages
+  ```
+* Review the repository Settings/Pages to ensure that deployment is enabled from the `gh-pages` branch.
+* Make the first release on GitHub, tagged with a version number (see below for versioning schemes).
+
+For all subsequent deployments:
+* Simply make a new release tagged with the appropriate version number. For presentations, we prefer a date-based versioning scheme, e.g. `YY.MM` or `YY.MM.DD`. You are encouraged to include some additional information on location, event, etc. in the release notes. If the release is a work-in-progress, append `dev` to the version tag (`YY.MM.dev`) and tick the "Set as a pre-release" checkbox.
+* GitHub actions will take care of the rest (see example deployment [here](https://neuroinformatics-unit.github.io/quarto-presentation-template/#/title-slide))
+* Deployed presentations can be found at `https://{USER}.github.io/{REPOSITORY-NAME}/#/title-slide`. For repositories of the neuroinformatics-unit organisation, this redirects to `https://neuroinformatics.dev/{REPOSITORY-NAME}/#/title-slide`

img/bg_logo_wide.png

@@ -0,0 +1,111 @@
+---
+title: A template presentation
+subtitle: so much fun
+author: SWC Neuroinformatics Unit
+execute: 
+  enabled: true
+format:
+    revealjs:
+        theme: [default, niu-dark.scss]
+        logo: img/logo_niu_dark.png
+        footer: "Edit this footer | 2023-07-26"
+        slide-number: c
+        menu:
+            numbers: true
+        chalkboard: true
+        scrollable: true
+        preview-links: false
+        view-distance: 10
+        mobile-view-distance: 10
+        auto-animate: true
+        auto-play-media: true
+        code-overflow: wrap
+        highlight-style: atom-one
+        mermaid: 
+          theme: neutral
+          fontFamily: arial
+          curve: linear
+    html:
+        theme: [default, niu-dark.scss]
+        logo: img/logo_niu_dark.png
+        date: "2023-07-05"
+        toc: true
+        code-overflow: scroll
+        highlight-style: atom-one
+        mermaid: 
+          theme: neutral
+          fontFamily: arial
+          curve: linear
+          margin-left: 0
+        embed-resources: true
+        page-layout: full
+my-custom-stuff:
+   my-reuseable-variable: "I can use this wherever I want in the markdown, and change it in only once place :)"
+---
+
+## Contents
+
+Some example slides - [also look at example RevealJS slides in the Quarto docs](https://quarto.org/docs/presentations/revealjs/)
+
+* Non-executable and executable code-blocks
+* bullet points with highlighting 
+* two-column slides 
+* how to include a slide from a separate MD file
+* preview and link to a webpage
+
+## Just a code block, nothing gets executed...
+
+... but there is some fancy highlighting
+
+```{.python code-line-numbers="1|3|4-9"}
+from pathlib import Path
+
+home_path = Path.home()
+if home_path.exists():
+  data_path = home_path / "data"
+else:
+  pass
+  # raise some error maybe?
+```
+
+## A code block that's actually executed at render-time
+
+```{python}
+#| echo: true
+#| code-fold: true
+
+from pathlib import Path
+
+print("Hello world")
+```
+
+## You can execute code without showing that you have by using #|echo: false
+```{python}
+#| echo: false
+
+from pathlib import Path
+
+print("Hello world")
+```
+
+{{< include slides/extra_slide.qmd >}}
+
+## An example image
+
+Include an image:
+
+![](img/bg_logo_wide.png){width=900 fig-align=center}
+
+
+## Link and a preview a webpage:
+
+::: {style="text-align: center; margin-top: 1em"}
+[interoperable Python-based tools for computational neuroanatomy](https://brainglobe.info/index.html){preview-link="true" style="text-align: center"}
+:::
+
+## Use a variable several times
+
+Variables defined in the metadata is re-useable anywhere
+
+* {{< meta my-custom-stuff.my-reuseable-variable >}}
+* {{< meta my-custom-stuff.my-reuseable-variable >}}

img/logo_niu_dark.png

@@ -0,0 +1,8 @@
+/*-- scss:defaults --*/
+
+$body-bg: #1E1E1E !default;
+$body-color: #fff !default;
+$link-color: #04B46D !default;
+$font-family-sans-serif: arial, "open sans", "helvetica neue", helvetica, sans-serif !default;
+$mermaid-font-family: arial;
+/*-- scss:rules --*/

img/logo_niu_light.png

@@ -0,0 +1,8 @@
+/*-- scss:defaults --*/
+
+$body-bg: #fff !default;
+$body-color: #1E1E1E !default;
+$link-color: #03A062 !default;
+$font-family-sans-serif: arial, "open sans", "helvetica neue", helvetica, sans-serif !default;
+$mermaid-font-family: arial;
+/*-- scss:rules --*/

index.qmd

@@ -0,0 +1,2 @@
+jupyter
+jupyter-cache

niu-dark.scss

@@ -0,0 +1,3 @@
+## A slide imported from outside the qmd
+
+This will become an example about how to use a common slide deck for the group.