Merge pull request #85 from mrc-ide/develop

Catching up main with updates to website

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+## Pull Request for PGEforge
+
+Thank you for your contribution to PGEforge!✨
+
+### Description of changes
+Please include a summary of the changes and the related issue, if applicable. Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+### Pull Request Checklist
+
+- [ ] I have provided a description and detailed information about the changes made
+- [ ] I have followed the [PGEforge GitHub contribution guidelines](http://mrc-ide.github.io/PGEforge/website_docs/how_to_contribute.html#contributing-guidelines-for-github) and I am merging into the `develop` branch
+- [ ] Documentation is updated, if necessary
+- [ ] Relevant issues are linked, if applicable

.github/workflows/check-quarto-render.yml

@@ -0,0 +1,28 @@
+on:
+  push:
+    branches:
+      - develop
+      - main
+      - feature/website
+  pull_request:
+    branches:
+      - develop
+      - main
+
+name: check-quarto-render
+
+jobs:
+  check-quarto-render:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v4
+
+    - name: Set up quarto
+      uses: quarto-dev/quarto-actions/setup@v2
+
+    - name: Render quarto website
+      uses: quarto-dev/quarto-actions/render@v2
+      with:
+        path: _site

.github/workflows/publish-website.yml

@@ -0,0 +1,33 @@
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: publish-quarto-website
+
+permissions:
+    contents: write
+    pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v4
+
+    - name: Set up quarto
+      uses: quarto-dev/quarto-actions/setup@v2
+      env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Publish to GitHub Pages (and render)
+      uses: quarto-dev/quarto-actions/publish@v2
+      with:
+        target: gh-pages
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -7,5 +7,5 @@
 ignore/
 .DS_Store
 /_site/
-_freeze/
 *.html
+README_files

README.md

@@ -1,2 +1,10 @@
-# PGEforge
-A place for holding tutorials related to common software tools in Plasmodium genomic epidemiology.
+# <img src="https://github.com/mrc-ide/PGEforge/blob/main/website_docs/img/PGEforge_hex.png?raw=true" width="25%" height="25%" align="left"/> PGEforge
+PGEforge is a community-driven platform designed to simplify *Plasmodium* genomic data analysis. The process of analyzing genomic data often involves various software tools with different formats, user interfaces, and levels of accessibility. These differences can create barriers, especially for those without strong computational skills.
+
+PGEforge aims to overcome these challenges by providing clear tutorials, streamlined workflows, and comprehensive resources to help researchers at all levels understand and analyze genomic data. By prioritizing the end-user, we strive to encourage better software development and foster an inclusive research community. Our goal is to make advanced genomic analysis accessible to everyone, promoting collaboration and accelerating progress in malaria research.
+
+## The PGEforge platform
+All of the resources for enhancing **P**lasmodium **G**enomic **E**pidemiology analysis are found on our open-source [website](https://mrc-ide.github.io/PGEforge/).
+
+## How to contribute
+We welcome input from all areas of the research community to continuously improve and expand our platform. Please read details on how to contribute to this community-driven resource on our [website](https://mrc-ide.github.io/PGEforge/website_docs/how_to_contribute.html). You can also [open a new issue](https://github.com/mrc-ide/PGEforge/issues).