Merge branch 'master' of github.com:neurostuff/PyMARE into fix/scipy_dependency

Author: jdkent

.github/workflows/testing.yml

@@ -4,13 +4,18 @@ on:
   push:
     branches:
       - "master"
-  pull_request:
+  pull_request_target:
     branches:
       - "*"
   schedule:
     # Run tests every Sunday at 12am
     - cron: "0 0 * * 0"
 
+permissions:
+  contents: read
+  checks: write
+  pull-requests: write
+
 concurrency:
   group: environment-${{ github.ref }}
   cancel-in-progress: true
@@ -38,7 +43,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-12"]
+        os: ["ubuntu-latest", "macos-13"]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}

docs/conf.py

@@ -22,7 +22,7 @@
 from distutils.version import LooseVersion
 
 import sphinx
-from m2r import MdInclude
+from m2r2 import MdInclude
 
 sys.path.insert(0, os.path.abspath("sphinxext"))
 sys.path.insert(0, os.path.abspath(os.path.pardir))
@@ -214,6 +214,7 @@ def setup(app):
     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_config_value("m2r_use_mermaid", True, "env")
     app.add_directive("mdinclude", MdInclude)
 
 

setup.cfg

@@ -47,9 +47,9 @@ include_package_data = False
 
 [options.extras_require]
 doc =
-    m2r
+    m2r2
     matplotlib
-    mistune<2  # just temporary until m2r addresses this issue
+    mistune
     numpydoc
     pillow
     recommonmark
@@ -60,6 +60,8 @@ doc =
     sphinx_gallery
     sphinx_rtd_theme
     sphinxcontrib-bibtex
+    sphinxcontrib-mermaid
+    docutils>=0.18.1,<0.21
 tests =
     codecov
     coverage