The error is now clearer:

This is happening because both m2r2 and recommonmark are trying to handle .md files. Let's fix your conf.py by removing one of them. Since you're using m2r2 for the mdinclude directive, let's keep that and remove recommonmark:

docs/conf.py

@@ -36,8 +36,7 @@
     'numpydoc',
     'm2r2',
     'sphinxcontrib.mermaid',
-    'recommonmark',
-    ]
+]
 
 extlinks = {
     'doi': ('https://dx.doi.org/%s', 'doi:%s'),
@@ -68,7 +67,7 @@
 
 source_suffix = {
     '.rst': 'restructuredtext',
-    '.md': 'markdown',
+    '.md': 'm2r2',
 }
 
 # Configure m2r2
@@ -84,12 +83,6 @@
 from recommonmark.transform import AutoStructify
 
 def setup(app):
-    app.add_config_value('recommonmark_config', {
-        'enable_eval_rst': True,
-        'enable_math': True,
-        'enable_inline_math': True,
-    }, True)
-    app.add_transform(AutoStructify)
     app.connect('build-finished', copy_examples)
 
 # Copy ./examples/results images into documentation so they show up when

docs/requirements.txt

@@ -4,5 +4,4 @@ numpydoc
 m2r2
 sphinxcontrib.mermaid
 sphinx_rtd_theme
-sphinxcontrib-apidoc
-recommonmark
+sphinxcontrib-apidoc