Restrucuture source files

Author: finsberg

.github/workflows/main.yml

@@ -5,9 +5,6 @@ on:
   push:
     branches:
       - source
-  pull_request:
-    branches:
-      - source
 
 # This job installs dependencies, build the book, and pushes it to `gh-pages`
 jobs:
@@ -17,29 +14,23 @@ jobs:
       - uses: actions/checkout@v2
 
       # Install dependencies
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python 3
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: "3.10"
 
-      # Set up Miniconda with environment
-      - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.1.2
-        with:
-          environment-file: environment.yml
-          activate-environment: comphy-site
-          python-version: 3.7
-          auto-activate-base: false
+      - name: Install requirements
+        run: python -m pip install -r requirements.txt
 
       # Build the book
       - name: Build the book
         shell: bash -l {0}
-        run: |
-          make docs
+        run: jupyter-book build docs
+
       # Push the book's HTML to github-pages
       - name: GitHub Pages action
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html
-          publish_branch: master # deploying branch
+          publish_branch: main # deploying branch

Makefile

@@ -1,31 +1,34 @@
-#######################################################################################
 # Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
 title: Computational Physiology
 author: Henrik Finsberg
-logo: "_static/simula_main_rgb.png"
+logo: "_static/logo.png"
+copyright: "2022"
+-description: The Computational Physiology (ComPhy) department at Simula Research Laboratory is an integrated team of researchers working to develop cutting edge biological simulation tools.
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: cache
 
 # Information about where the book exists on the web
-description: >-
-  The Computational Physiology (ComPhy) department at Simula Research Laboratory is an integrated team of researchers working to develop cutting edge biological simulation tools.
+repository:
+  url: https://github.com/ComputationalPhysiology/computationalphysiology.github.io # Online location of your book
 
-#######################################################################################
-# HTML-specific settings
 html:
-  home_page_in_navbar: true
-  use_issues_button: false
+  use_issues_button: true
+  use_repository_button: true
   extra_navbar: See more at <a href="https://www.simula.no/research/projects/department-computational-physiology">simula.no</a>
 
-# #######################################################################################
-# Interact link settings
-notebook_interface: "notebook"
-
-#######################################################################################
-# Launch button settings
-repository:
-  url: https://github.com/ComputationalPhysiology/computationalphysiology.github.io
-  path_to_book: "."
+parse:
+  myst_enable_extensions:
+    - amsmath
+    - dollarmath
+    - linkify
 
-latex:
-  latex_engine: "xelatex"
-  latex_documents:
-    targetname: book.tex
+sphinx:
+  extra_extensions:
+    - "sphinx.ext.autodoc"
+    - "sphinx.ext.napoleon"
+    - "sphinx.ext.viewcode"

docs/_config.yml

@@ -1,4 +1,8 @@
-- file: content/about.md
-- file: content/contributing.md
-- file: content/projects.md
-- file: content/publications.md
+format: jb-book
+root: index
+
+chapters:
+  - file: about.md
+  - file: reproducibility
+  - file: projects.md
+  - file: publications.md

docs/_static/logo.png

@@ -1,4 +1,4 @@
-# Computational Physiology at Simula Research Laboratory
+# About
 
 In recent years, modeling and simulation of biophysical phenomena has matured in both scope and methodology, such that it can contribute significantly to the present understanding of physiology and disease. The Computational Physiology (ComPhy) department at Simula is an integrated team of researchers working to develop cutting edge biological simulation tools. The group collaborates closely with both experimentalists and clinicians around the world to drive basic research and promote innovation.
 
@@ -20,6 +20,6 @@ Some other sites that are of relevance:
 
 We also have our own channel at [anaconda](https://anaconda.org/ComPhy)
 
-## Where are we located
+## More info
 
-We are located just outside Oslo, the capital of Norway at a place called Fornebu, but we plan to move to downtown Oslo in the near future.
+For more info about Simula, please checkout the [simula web page](https://www.simula.no)

docs/_static/simula_main_rgb.png

@@ -0,0 +1,7 @@
+# Computational Physiology at Simula Research Laboratory
+
+This page contains information about the Computational Physiology department at Simula Research Laboratory
+
+## Contents
+```{tableofcontents}
+```