Docs: Migrate from m2r2 to MyST parser

Author: adrien-berchet

dir_content_diff/comparators/voxcell.py

@@ -119,7 +119,8 @@ class Mvd3Comparator(DataframeComparator):
     Note: MVD3 files can contain their creation date, so their hashes are depends on
     this creation date, even if the data are the same.
 
-    This comparator inherits from the :class:`dir_content_diff.pandas.DataframeComparator`, read
+    This comparator inherits from the
+    :class:`dir_content_diff.comparators.pandas.DataframeComparator`, read
     the doc of this comparator for details on args and kwargs.
     """
 
@@ -135,7 +136,8 @@ def save(self, data, path, **kwargs):
 class CellCollectionComparator(DataframeComparator):
     """Comparator for any type of CellCollection file.
 
-    This comparator inherits from the :class:`dir_content_diff.pandas.DataframeComparator`, read
+    This comparator inherits from the
+    :class:`dir_content_diff.comparators.pandas.DataframeComparator`, read
     the doc of this comparator for details on args and kwargs.
     """
 

docs/source/changelog.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../../CHANGELOG.md
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.sphinx_

docs/source/conf.py

@@ -39,12 +39,12 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "myst_parser",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
     "sphinx.ext.todo",
-    "m2r2",
 ]
 
 todo_include_todos = True
@@ -91,7 +91,17 @@
 }
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-    "pandas": ("https://pandas.pydata.org/docs", None),
     "dictdiffer": ("https://dictdiffer.readthedocs.io/en/latest/", None),
+    "morph_tool": ("https://morph-tool.readthedocs.io/en/latest/", None),
+    "morphio": ("https://morphio.readthedocs.io/en/latest/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
+    "python": ("https://docs.python.org/3", None),
+    "voxcell": ("https://voxcell.readthedocs.io/en/latest/", None),
 }
+
+# MyST parser settings
+myst_enable_extensions = []
+myst_heading_anchors = 5
+myst_all_links_external = True
+suppress_warnings = ["myst.header"]

docs/source/contributing.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../../CONTRIBUTING.md
+.. include:: ../../CONTRIBUTING.md
+   :parser: myst_parser.sphinx_

docs/source/index.rst

@@ -1,4 +1,5 @@
-.. mdinclude:: ../../README.md
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
 
 
 .. toctree::

setup.py

@@ -15,8 +15,7 @@
 from setuptools import setup
 
 doc_reqs = [
-    "docutils<0.21",  # Temporary fix for m2r2
-    "m2r2",
+    "myst_parser",
     "sphinx",
     "sphinx-bluebrain-theme",
 ]