update env

_config.yml

@@ -0,0 +1,52 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: "pyscal-rdf"
+#author: The Jupyter Book Community
+logo: docs/source/_static/logo.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: "auto"
+
+only_build_toc_files: true
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/pyscal/pyscal_rdf
+  path_to_book: book
+  branch: main
+
+notebook_interface            : "notebook"
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: false
+  use_repository_button: true
+
+parse:
+  myst_enable_extensions:
+    # don't forget to list any other extensions you want enabled,
+    # including those that are enabled by default!
+    - html_image
+    - amsmath
+    - dollarmath
+    - linkify
+    - substitution
+    - colon_fence
+
+sphinx:
+  config:
+    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+    html_theme: pydata_sphinx_theme
+    html_js_files:
+      - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    html_sidebars:
+      "**": []

_toc.yml

@@ -0,0 +1,11 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: docs/intro
+chapters:
+  - file: docs/examples.md
+    sections:
+    - file: examples/01_getting_started
+    - file: examples/02_grain_boundaries
+

docs/examples.md

@@ -0,0 +1,29 @@
+# Examples
+
+The gallery of examples below cover different ways in which pyscal-rdf can be used.
+
+::::{grid} 1 1 2 3
+:class-container: text-center
+:gutter: 3
+
+:::{grid-item-card}
+:link: ../examples/01_getting_started
+:link-type: doc
+:class-header: bg-light
+Getting started with pyscal
+^^^
+Learn the very basis, including the concepts of `System` and `Atoms`.
+:::
+
+:::{grid-item-card}
+:link: ../examples/02_grain_boundaries
+:link-type: doc
+:class-header: bg-light
+Creating structures
+^^^
+Create common atomic structures like bcc, fcc; and custom ones. Save and read from files.
+:::
+
+::::
+
+

docs/intro.ipynb

@@ -0,0 +1,49 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6f84b291-5802-4ebe-95b3-1b1ea097c466",
+   "metadata": {},
+   "source": [
+    "# pyscal-rdf"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d28592f2-8d81-4625-857c-0f3fc5c8a0b3",
+   "metadata": {},
+   "source": [
+    "`pyscal_rdf` is a python tool for ontology-based creation, manipulation, and quering of structures. `pyscal_rdf` uses the [Computational Material Sample Ontology (CMSO)](https://github.com/Materials-Data-Science-and-Informatics/cmso-ontology)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6ca98bd2-e238-4283-b29f-25eb86e72af3",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

environment.yml

@@ -16,4 +16,5 @@ dependencies:
   - pandas
   - owlready2
   - sqlalchemy <2.0.0
-  - rdflib-sqlalchemy
+  - rdflib-sqlalchemy
+  - jupyter-book