Fix docs redirect

Fix mkdocs redirect

Update URLs to org repo

Fix issue with mike redirects

Fix missing pipe

Set default versions with mike

Fix broken doc links

Update pre-alpha disclaimer

.github/workflows/develop_docs.yml

@@ -25,4 +25,6 @@ jobs:
           git config --global user.name "Docs Deploy"
           git config --global user.email "docs.deploy@example.co.uk"
       - name: Build Docs Website
-        run: mike deploy --push develop
+        run:  |
+          mike deploy develop
+          mike set-default --push latest

.github/workflows/release_docs.yml

@@ -26,4 +26,6 @@ jobs:
           git config --global user.name "Docs Deploy"
           git config --global user.email "docs.deploy@example.co.uk"
       - name: Build Docs Website
-        run: mike deploy --push --update-aliases ${{ github.event.release.tag_name }} latest
+        run: |
+          mike deploy --update-aliases ${{ github.event.release.tag_name }} latest
+          mike set-default --push --allow-empty latest

.gitignore

@@ -14,3 +14,4 @@ MnO_Magnon.py
 VBT.vasp
 VBTS_mdm.h5
 hcp_He_lsm.h5
+venv/**

README.md

@@ -2,8 +2,8 @@
 [![Develop Docs](https://img.shields.io/badge/status-pre--alpha-red)](https://oashour.github.io/DarkMAGIC/develop/)
 ![Tests](https://github.com/oashour/DarkMAGIC/actions/workflows/run_tests.yaml/badge.svg)
 [![License](https://img.shields.io/badge/License-MIT-blue)](#license "Go to license section")
-[![Stable Docs](https://img.shields.io/badge/docs-stable-blue)](https://oashour.github.io/DarkMAGIC/latest/)
-[![Develop Docs](https://img.shields.io/badge/docs-develop-purple)](https://oashour.github.io/DarkMAGIC/develop/)
+[![Stable Docs](https://img.shields.io/badge/docs-stable-blue)](https://Griffin-Group.github.io/DarkMAGIC/latest/)
+[![Develop Docs](https://img.shields.io/badge/docs-develop-purple)](https://Griffin-Group.github.io/DarkMAGIC/develop/)
 <!--![GitHub Release](https://img.shields.io/github/v/release/oashour/DarkMAGIC?include_prereleases)-->
 
 The **D**ark **M**atter ***A****b* *initio* phonon/ma**G**non **I**nteraction **C**alculator (**DarkMAGIC**) is a python package for calculating dark matter interaction rates with phonons and magnons in real materials, based on properties calculated from first principles (mainly, density functional theory). It is based on [the effective field theory developed by Trickle, Zhang and Zurek](https://arxiv.org/abs/2009.13534), and takes inspiration from the code they released with that paper, [PhonoDark](https://github.com/tanner-trickle/PhonoDark). 
@@ -35,4 +35,4 @@ DarkMAGIC will soon be made available on pip. For now, please install it as
 
 ```shell
 pip install git+https://github.com/oashour/DarkMAGIC
-```
+```

docs/formalism.md

@@ -0,0 +1,3 @@
+# Formalism
+
+Coming soon! For now refer to [this paper](https://arxiv.org/abs/2009.13534).

docs/index.md

@@ -2,7 +2,7 @@
 
 The **D**ark **M**atter ***A****b* *initio* phonon/ma**G**non **I**nteraction **C**alculator (DarkMAGIC) is a python package for calculating dark matter interaction rates with phonons and magnons in real materials, based on properties calculated from first principles (mainly, density functional theory). It is based on [the effective field theory developed by Trickle, Zhang and Zurek](https://arxiv.org/abs/2009.13534), and takes inspiration from the code they released with that paper, [PhonoDark](https://github.com/tanner-trickle/PhonoDark). 
 
-DarkMAGIC is currently in pre-alpha testing, so not all features are implemented and not everything has been tested. Development is in progress, and once at a satisfying stage, a manuscript will be prepared.
+DarkMAGIC is currently in pre-alpha testing, so not all features are implemented, the public API is unstable, and not everything has been tested. Development is in progress, and once at a satisfying stage, a manuscript will be prepared.
 
 ## Features
 * Calculate scattering rates from single phonons and magnons.

docs/overrides/main.html

@@ -0,0 +1,8 @@
+{% extends "base.html" %}
+
+{% block outdated %}
+  You're not viewing the latest version.
+  <a href="{{ '../' ~ base_url }}"> 
+    <strong>Click here to go to latest.</strong>
+  </a>
+{% endblock %}

mkdocs.yml

@@ -1,12 +1,13 @@
 site_name: "DarkMAGIC"
-site_url: "https://oashour.github.io/DarkMAGIC/"
-repo_url: "https://github.com/oashour/DarkMAGIC/"
-repo_name: "oashour/DarkMAGIC"
+site_url: "https://Griffin-Group.github.io/DarkMAGIC/"
+repo_url: "https://github.com/Griffin-Group/DarkMAGIC/"
+repo_name: "Griffin-Group/DarkMAGIC"
 copyright: Copyright © 2024 Omar A. Ashour
-edit_uri: edit/main/docs/
+edit_uri: blob/main/docs/
 
 nav:
   - Home: index.md
+  - Examples: examples.md
   - Formalism: formalism.md
   - Code Reference: reference/
 
@@ -44,6 +45,7 @@ theme:
 
 extra:
   version:
+    default: develop
     provider: mike
 
 plugins:

pyproject.toml

@@ -5,9 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "dark-magic"
 version = "0.0.1"
-authors = [
-  { name="Omar A. Ashour", email="ashour@berkeley.edu" },
-]
+authors = [{ name = "Omar A. Ashour", email = "ashour@berkeley.edu" }]
 description = "Dark Matter Ab initio maGnon/phonon Interaction Calculator (DarkMAGIC) is a python package for computing DM interaction rates with collective excitations based on ab initio calculations of material properties."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -17,9 +15,9 @@ dependencies = [
     "rad-tools",
     "h5py",
     "mpi4py",
-    "setuptools",
+    "setuptools; python_version=='3.12'",
 ]
-classifiers=[
+classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -32,11 +30,21 @@ classifiers=[
 ]
 
 [project.urls]
-Homepage = "https://github.com/oashour/DarkMAGIC"
-Issues = "https://github.com/oashour/DarkMAGIC/issues"
+Homepage = "https://github.com/Griffin-Group/DarkMAGIC"
+Issues = "https://github.com/Griffin-Group/DarkMAGIC/issues"
 
+[project.optional-dependencies]
+docs = [ # Optional dependencies for building documentation
+    "mkdocs-material",
+    "mike",
+    "mkdocstrings",
+    "mkdocstrings-python",
+    "mkdocs-literate-nav",
+    "mkdocs-gen-files",
+    "mkdocs-section-index",
+]
 [tool.setuptools.packages]
-find = {}  # Scan the project directory with the default parameters
+find = {} # Scan the project directory with the default parameters
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
@@ -74,8 +82,8 @@ exclude = [
 line-length = 88
 indent-width = 4
 
-# Assume Python 3.8
-target-version = "py38"
+# Assume Python 3.10
+target-version = "py310"
 
 [tool.ruff.lint]
 # Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.