Use jupyter book for documentation

pyiron · May 1, 2024 · fd305a8 · fd305a8
1 parent 9ac77bd
commit fd305a8
Show file tree

Hide file tree

Showing 17 changed files with 42 additions and 206 deletions.
diff --git a/.readthedocs.yml b/.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
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
-# pysqa - a simple queue adapter for python
+# pysqa
 
 [![Python package](https://github.com/pyiron/pysqa/workflows/Python%20package/badge.svg)](https://github.com/pyiron/pysqa/actions)
 [![Documentation Status](https://readthedocs.org/projects/pysqa/badge/?version=latest)](https://pysqa.readthedocs.io/en/latest/?badge=latest)
 [![Coverage Status](https://coveralls.io/repos/github/pyiron/pysqa/badge.svg?branch=main)](https://coveralls.io/github/pyiron/pysqa?branch=main)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/pysqa/HEAD?labpath=notebooks%2Fexample.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyiron/pysqa/HEAD?labpath=example.ipynb)
 
 High-performance computing (HPC) does not have to be hard. In this context the aim of `pysqa` is to simplify the submission of calculation to an HPC cluster as easy as starting another subprocess locally. This is achieved based on the assumption that even though modern HPC queuing systems offer a wide range of different configuration options, most users submit the majority of their jobs with very similar parameters. 
 

diff --git a/binder/postBuild b/binder/postBuild
@@ -3,4 +3,11 @@ mkdir -p /home/jovyan/.local/share/jupyter/kernels/flux
 cp binder/kernel.json /home/jovyan/.local/share/jupyter/kernels/flux
 
 # install pympipool
-pip install . --no-deps --no-build-isolation
+pip install . --no-deps --no-build-isolation
+
+# copy notebooks
+mv notebooks/*.ipynb .
+rm -rf notebooks
+
+# clean up
+rm -rf .ci_support .github binder docs notebooks pysqa pysqa.egg-info tests .coveralls.yml .gitignore .readthedocs.yml CODE_OF_CONDUCT.md LICENSE MANIFEST.in README.md pyproject.toml setup.py build
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -0,0 +1,14 @@
+title: pysqa
+author: Jan Janssen
+logo: images/pyiron-logo.png
+
+execute:
+  execute_notebooks           : off
+
+repository:
+    url                       : https://github.com/pyiron/pysqa
+    path_to_book              : ""
+
+launch_buttons:
+  notebook_interface          : jupyterlab
+  binderhub_url               : https://mybinder.org
diff --git a/docs/_static/pyiron_logo.ico b/docs/_static/pyiron_logo.ico
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -0,0 +1,9 @@
+format: jb-book
+root: README
+chapters:
+- file: installation.md
+- file: queue.md
+- file: example.ipynb
+- file: command.md
+- file: advanced.md
+- file: debug.md
diff --git a/docs/source/advanced.md → docs/advanced.md b/docs/source/advanced.md → docs/advanced.md
diff --git a/docs/source/command.md → docs/command.md b/docs/source/command.md → docs/command.md
diff --git a/docs/source/debug.md → docs/debug.md b/docs/source/debug.md → docs/debug.md
diff --git a/docs/_static/pyiron-logo.png → docs/images/pyiron-logo.png b/docs/_static/pyiron-logo.png → docs/images/pyiron-logo.png
diff --git a/docs/source/installation.md → docs/installation.md b/docs/source/installation.md → docs/installation.md
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/source/queue.md → docs/queue.md b/docs/source/queue.md → docs/queue.md
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/docs/source/python.md b/docs/source/python.md