Use Jupyterbook rather than Sphinx

.ci_support/build_notebooks.sh

@@ -1,10 +1,10 @@
 # execute notebooks
 i=0;
-for notebook in $(ls notebooks/*.ipynb); do
+for notebook in $(ls *.ipynb); do
     papermill ${notebook} ${notebook%.*}-out.${notebook##*.} -k "python3" || i=$((i+1));
 done;
 
 # push error to next level
 if [ $i -gt 0 ]; then
     exit 1;
-fi;
+fi;

.ci_support/environment-docs.yml

@@ -18,3 +18,4 @@ dependencies:
 - pandas =2.2.2
 - pylammpsmpi =0.2.18
 - jinja2 =3.1.3
+- jupyter-book =1.0.0

.github/workflows/notebooks.yml

@@ -31,4 +31,5 @@ jobs:
         run: |
           pip install versioneer[toml]==0.29
           pip install . --no-deps --no-build-isolation
-          ./.ci_support/build_notebooks.sh
+          cd notebooks
+          ../.ci_support/build_notebooks.sh

.readthedocs.yml

@@ -9,10 +9,16 @@ build:
   os: "ubuntu-22.04"
   tools:
     python: "mambaforge-22.9"
+  jobs:
+    pre_build:
+      # Generate the Sphinx configuration for this Jupyter Book so it builds.
+      - "cp README.md docs"
+      - "cp notebooks/*.ipynb docs"
+      - "jupyter-book config sphinx docs/"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/source/conf.py
+  builder: html
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: []
@@ -26,3 +32,5 @@ python:
   install:
     - method: pip
       path: .
+      extra_requirements:
+        - sphinx

README.md

@@ -1,4 +1,4 @@
-# atomistics - Interfaces for atomistic simulation codes and workflows
+# atomistics
 [![Unittest](https://github.com/pyiron/atomistics/actions/workflows/unittests.yml/badge.svg)](https://github.com/pyiron/atomistics/actions/workflows/unittests.yml)
 [![Coverage Status](https://coveralls.io/repos/github/pyiron/atomistics/badge.svg?branch=main)](https://coveralls.io/github/pyiron/atomistics?branch=main)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/atomistics/HEAD)

binder/environment.yml

@@ -2,15 +2,14 @@ channels:
 - conda-forge
 dependencies:
 - ase =3.22.1
-- coverage
 - numpy =1.26.4
 - scipy =1.13.0
 - spglib =2.4.0
 - phonopy =2.22.1
 - structuretoolkit =0.0.22
 - seekpath =2.1.0
 - gpaw =24.1.0
-- lammps =2023.11.21
+- lammps =2024.02.07
 - pandas =2.2.2
 - pylammpsmpi =0.2.18
 - jinja2 =3.1.3

docs/_config.yml

@@ -0,0 +1,14 @@
+title: atomistics
+author: Jan Janssen
+logo: images/pyiron-logo.png
+
+execute:
+  execute_notebooks           : off
+
+repository:
+    url                       : https://github.com/pyiron/atomistics
+    path_to_book              : ""
+
+launch_buttons:
+  notebook_interface          : jupyterlab
+  binderhub_url               : https://mybinder.org

docs/_toc.yml

@@ -0,0 +1,12 @@
+format: jb-book
+root: README
+chapters:
+- file: installation.md
+- file: simulation_codes.ipynb
+- file: lammps_workflows.ipynb
+- file: materialproperties.md
+  sections:
+    - file: bulk_modulus_with_gpaw.ipynb
+    - file: thermal_expansion_with_lammps.ipynb
+    - file: free_energy_calculation.ipynb
+    - file: phasediagram.md

docs/materialproperties.md

@@ -0,0 +1,4 @@
+# Materials Properties
+Demonstrate the calculation of common material properties with the `atomistics` package. The examples use different 
+simulation codes, still the examples are not simulation code specific. It is one of the core features of the `atomistics`
+package that all simulation workflow to calculate a specific material property can be executed with all simulation codes.

docs/phasediagram.md

@@ -0,0 +1,3 @@
+# Phase Diagram 
+One of the goals of the `atomistics` package is to be able to calculate phase diagrams with ab-initio precision. Coming 
+soon.