Restructure code

.github/workflows/build_docs.yml

@@ -3,13 +3,29 @@ name: Github Pages
 on:
   push:
     branches:
-      - main
+      - "**"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+
 jobs:
-  deploy:
+  build:
     runs-on: ubuntu-22.04
     env:
       # Directory that will be published on github pages
-      PUBLISH_DIR: ./docs/_build/html
+      PUBLISH_DIR: ./_build/html
 
     steps:
       - uses: actions/checkout@v3
@@ -23,19 +39,30 @@ jobs:
         run: python3 -m pip install -r requirements-docs.txt
 
       - name: Build docs
-        run: jupyter book build docs
+        run: jupyter book build .
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: ${{ env.PUBLISH_DIR }}
 
-      - name: Copy requirements.txt into gh-pages
-        run: cp requirements.txt ${PUBLISH_DIR}/
 
-      - name: Copy code and data into gh-pages
-        run: |
-          cp -r code ${PUBLISH_DIR}/
-          cp -r data ${PUBLISH_DIR}/
-          cp runtime.txt ${PUBLISH_DIR}/
+    # Single deploy job since we're just deploying
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
 
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ${{ env.PUBLISH_DIR }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v2
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.gitignore

@@ -76,7 +76,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+_build/
 
 # PyBuilder
 .pybuilder/

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2022 Simula Reaseach Laboratory
+Copyright 2022 Simula Research Laboratory
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

README.md

@@ -1,5 +1,5 @@
 # Supplementary code for the paper: Title of paper
-
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/scientificcomputing/example-paper/HEAD)
 
 This repository contains supplementary code for the paper
 > Finsberg, H., Dokken, J. 2022.

docs/_config.yml → _config.yml

@@ -3,7 +3,7 @@
 
 title: Example paper
 author: Henrik Finsberg
-logo: "logo.png"
+logo: "docs/logo.png"
 copyright: "2022"
 
 # Force re-execution of notebooks on each build.
@@ -14,8 +14,7 @@ execute:
 # Information about where the book exists on the web
 repository:
   url: https://github.com/scientificcomputing/example-paper # Online location of your book
-  path_to_book: _sources # Optional path to your book, relative to the repository root
-  branch: gh-pages  # Which branch of the repository should be used when creating links (optional)
+  branch: main  # Which branch of the repository should be used when creating links (optional)
 
 launch_buttons:
   notebook_interface: "jupyterlab" # The interface interactive links will activate ["classic", "jupyterlab"]
@@ -33,7 +32,7 @@ parse:
 
 sphinx:
   config:
-    bibtex_bibfiles: ["refs.bib"]
+    bibtex_bibfiles: ["docs/refs.bib"]
 
   extra_extensions:
   - 'sphinx.ext.autodoc'

_toc.yml

@@ -0,0 +1,8 @@
+format: jb-book
+root: index
+
+chapters:
+  - file: docs/abstract
+  - file: docs/reproducing
+  - file: code/demo
+  - file: docs/citation

docker/Dockerfile

@@ -14,7 +14,7 @@ ARG REPO_BRANCH="main"
 
 WORKDIR /repo
 
-# Copy pyproject.toml first so that we done need to reinstall in case anoter file
-# is changing ater rebuiding docker image
+# Copy pyproject.toml first so that we done need to reinstall in case another file
+# is changing after rebuiding docker image
 RUN git clone --branch ${REPO_BRANCH} --single-branch https://github.com/scientificcomputing/example-paper.git
-RUN cd example-paper && python3 -m pip install pip --upgrade && python3 -m pip install --no-cache-dir -r requirements.txt && rm -rf /tmp
+RUN cd example-paper && python3 -m pip install --no-cache-dir -r requirements.txt && rm -rf /tmp