From a98a2815cf4e0dc2fa0ddf9158944b1f20d4a71d Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 15 Oct 2024 09:14:34 -0400
Subject: [PATCH] Fix RTD build (#449)

* Fix RTD build.

* Update conf.py

* Try fixing.

* Drop recommonmark.

* Update index.rst

* Link out to release notes.

* Update index.rst
---
 CHANGES.md       |  2 ++
 docs/changes.rst |  7 -------
 docs/conf.py     | 11 +----------
 docs/index.rst   |  2 +-
 pyproject.toml   |  4 +---
 5 files changed, 5 insertions(+), 21 deletions(-)
 delete mode 100644 docs/changes.rst

diff --git a/CHANGES.md b/CHANGES.md
index 26a35b02b..4388a9a0a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,5 @@
+# What's new
+
 ## 0.7.3
 
 This release fixes a bug in multi-PLD PCASL CBF calculation.
diff --git a/docs/changes.rst b/docs/changes.rst
deleted file mode 100644
index ab149c726..000000000
--- a/docs/changes.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-.. include:: links.rst
-
-##########
-What's new
-##########
-
-.. mdinclude:: ../CHANGES.md
diff --git a/docs/conf.py b/docs/conf.py
index 528bd58b8..e6441fe07 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -24,7 +24,6 @@
 import sys
 from datetime import datetime
 
-from m2r import MdInclude
 from packaging import version as pver
 from sphinx import __version__ as sphinxversion
 
@@ -47,9 +46,9 @@
 # Add any Sphinx extension module names here, as strings.
 # They can be extensions coming with Sphinx (named "sphinx.ext.*") or your custom ones.
 extensions = [
+    "myst_parser",
     "nipype.sphinxext.apidoc",
     "nipype.sphinxext.plot_workflow",
-    "recommonmark",
     "sphinx.ext.autodoc",
     "sphinx.ext.coverage",
     "sphinx.ext.doctest",
@@ -333,11 +332,3 @@ def setup(app):
     app.add_css_file("theme_overrides.css")
     # We need this for the boilerplate script
     app.add_js_file("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")
-    # Fix to https://github.com/sphinx-doc/sphinx/issues/7420
-    # from https://github.com/life4/deal/commit/7f33cbc595ed31519cefdfaaf6f415dada5acd94
-    # from m2r to make `mdinclude` work
-    app.add_config_value("no_underscore_emphasis", False, "env")
-    app.add_config_value("m2r_parse_relative_links", False, "env")
-    app.add_config_value("m2r_anonymous_references", False, "env")
-    app.add_config_value("m2r_disable_inline_math", False, "env")
-    app.add_directive("mdinclude", MdInclude)
diff --git a/docs/index.rst b/docs/index.rst
index 03a34b8ee..8e11ad741 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -26,4 +26,4 @@ Contents
    spaces
    contributors
    api
-   changes
+   What's New <https://github.com/PennLINC/aslprep/releases>
diff --git a/pyproject.toml b/pyproject.toml
index 64f58c7b4..b3f68b948 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,13 +53,11 @@ NiPreps = "https://www.nipreps.org/"
 doc = [
     "doctest-ignore-unicode",
     "lxml_html_clean",
-    "m2r",
-    "mistune < 4",  # just temporary until m2r addresses this issue
+    "myst_parser",
     "nbsphinx",
     "packaging",
     "pydot >= 1.2.3",
     "pydotplus",
-    "recommonmark",
     "sphinx >= 6.2.1",
     "sphinx-argparse",
     "sphinx-markdown-tables",