Merge pull request #5 from scientificcomputing/dokken/restructure

Restructure repos

Author: jorgensd

.github/workflows/build_docs.yml

@@ -3,15 +3,31 @@ 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
     container:
       image: finsberg/fenics-gmsh:latest
+
     env:
       # Directory that will be published on github pages
-      PUBLISH_DIR: ./docs/_build/html
+      PUBLISH_DIR: ./_build/html
 
     steps:
       - uses: actions/checkout@v3
@@ -20,13 +36,30 @@ jobs:
         run: python3 -m pip install -r requirements.txt
 
       - name: Build docs
-        run: jupyter book build docs
-
-      - name: Copy Dockerfile into gh-pages
-        run: cp Dockerfile ${PUBLISH_DIR}/
+        run: jupyter book build .
 
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ${{ env.PUBLISH_DIR }}
+          path: ${{ env.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 }}
+
+    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

@@ -81,7 +81,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+_build/
 
 # PyBuilder
 .pybuilder/

Dockerfile

@@ -1,5 +1,5 @@
 # Use github pages for docker image
-FROM ghcr.io/scientificcomputing/example-paper-fenics:latest
+FROM ghcr.io/scientificcomputing/example-paper-fenics:v0.1.5
 
 # Create user with a home directory
 ARG NB_USER
@@ -17,6 +17,4 @@ RUN chown -R ${NB_UID} ${HOME}
 
 USER ${NB_USER}
 
-ENV PYTHONPATH /repo/example-paper-fenics/code:${PYTHONPATH}
-
 ENTRYPOINT []

docs/_config.yml renamed to _config.yml

@@ -3,7 +3,7 @@
 
 title: Example FEniCS paper
 author: Henrik Finsberg
-logo: "logo.png"
+logo: "docs/logo.png"
 copyright: "2022"
 
 # Force re-execution of notebooks on each build.
@@ -14,9 +14,7 @@ execute:
 # Information about where the book exists on the web
 repository:
   url: https://github.com/scientificcomputing/example-paper-fenics # 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)
-
+ 
 launch_buttons:
   notebook_interface: "jupyterlab" # The interface interactive links will activate ["classic", "jupyterlab"]
   binderhub_url: "https://mybinder.org"
@@ -34,7 +32,7 @@ parse:
 
 sphinx:
   config:
-    bibtex_bibfiles: ["refs.bib"]
+    bibtex_bibfiles: ["docs/refs.bib"]
     suppress_warnings: ["bibtex.duplicate_citation"] # If the same paper is cited in multiple files
 
   extra_extensions:

_toc.yml

@@ -0,0 +1,9 @@
+format: jb-book
+root: index
+
+chapters:
+  - file: docs/abstract
+  - file: docs/reproducing
+  - file: docs/docker
+  - file: code/demo
+  - file: docs/citation