From b80f6c94a8b9763dd9830b54adc32a8adb8de7b6 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Thu, 31 Oct 2024 10:55:24 -0700
Subject: [PATCH] Use myst to build this thing.

---
 make.bat         | 35 -----------------------------------
 requirements.txt |  4 +++-
 source/conf.py   | 11 ++++++-----
 source/index.md  | 17 +++++++++++++++++
 source/index.rst | 17 -----------------
 5 files changed, 26 insertions(+), 58 deletions(-)
 delete mode 100644 make.bat
 create mode 100644 source/index.md
 delete mode 100644 source/index.rst

diff --git a/make.bat b/make.bat
deleted file mode 100644
index 747ffb7..0000000
--- a/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/requirements.txt b/requirements.txt
index 1b3a6e8..ba872ef 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1,3 @@
-sphinx
\ No newline at end of file
+sphinx
+myst-parser
+pydata_sphinx_theme
\ No newline at end of file
diff --git a/source/conf.py b/source/conf.py
index a1f1ac0..1aac9e9 100644
--- a/source/conf.py
+++ b/source/conf.py
@@ -13,15 +13,16 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = []
+extensions = [
+    "myst_parser",
+    ]
 
 templates_path = ['_templates']
-exclude_patterns = []
-
-
+exclude_patterns = ['.DS_Store']
+source_suffix = ['.rst', '.md']
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'alabaster'
+html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
diff --git a/source/index.md b/source/index.md
new file mode 100644
index 0000000..436b729
--- /dev/null
+++ b/source/index.md
@@ -0,0 +1,17 @@
+# Tractometry
+
+## Projects
+
+[*pyAFQ*](https://tractometry.org/pyAFQ): Automated Fiber Quantification in Python
+[*AFQ-Insight*](https://tractometry.org/AFQ-Insight): Machine learning and statistics for tractomtery.
+[*Tractable*](https://tractometry.org/tractable): R-based statistical analysis of tractometry.
+[*AFQ-Browser*](https://tractometry.org/AFQ-Browser): Interactive exploratory visualization and sharing of tractometry studies.
+[*Tractoscope*](https://tractometry.org/tractoscope): Visualization of large openly-available tractometry studies.
+
+```{eval-rst}
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+```
\ No newline at end of file
diff --git a/source/index.rst b/source/index.rst
deleted file mode 100644
index 40a7dce..0000000
--- a/source/index.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-.. tractometry documentation master file, created by
-   sphinx-quickstart on Thu Oct 31 09:45:39 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-tractometry documentation
-=========================
-
-Add your content using ``reStructuredText`` syntax. See the
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
-documentation for details.
-
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-