fix deprecation warnings

chrisjsewell · chrisjsewell · commit 9a6ed16c3b8f · 2022-06-07T11:43:44.000+02:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -50,7 +50,7 @@ repos:
     - id: mypy
       args: [--config-file=pyproject.toml]
       additional_dependencies:
-      - sphinx~=4.1
+      - sphinx~=5.0
       - markdown-it-py>=1.0.0,<3.0.0
       - mdit-py-plugins~=0.3.0
       files: >
diff --git a/myst_parser/_compat.py b/myst_parser/_compat.py
@@ -0,0 +1,11 @@
+"""Helpers for cross compatibility across dependency versions."""
+from typing import Callable, Iterable
+
+from docutils.nodes import Element
+
+
+def findall(node: Element) -> Callable[..., Iterable[Element]]:
+    """Iterate through"""
+    # findall replaces traverse in docutils v0.18
+    # note a difference is that findall is an iterator
+    return getattr(node, "findall", node.traverse)
diff --git a/myst_parser/mdit_to_docutils/base.py b/myst_parser/mdit_to_docutils/base.py
@@ -32,6 +32,7 @@
 from markdown_it.token import Token
 from markdown_it.tree import SyntaxTreeNode
 
+from myst_parser._compat import findall
 from myst_parser.config.main import MdParserConfig
 from myst_parser.mocking import (
     MockIncludeDirective,
@@ -41,7 +42,7 @@
     MockState,
     MockStateMachine,
 )
-from ..parsers.directives import DirectiveParsingError, parse_directive_text
+from myst_parser.parsers.directives import DirectiveParsingError, parse_directive_text
 from .html_to_nodes import html_to_nodes
 from .utils import is_external_url
 
@@ -260,7 +261,7 @@ def _render_finalise(self) -> None:
         # those from the initial markdown parse
         # instead we gather them from a walk of the created document
         foot_refs = OrderedDict()
-        for refnode in self.document.traverse(nodes.footnote_reference):
+        for refnode in findall(self.document)(nodes.footnote_reference):
             if refnode["refname"] not in foot_refs:
                 foot_refs[refnode["refname"]] = True
 
diff --git a/myst_parser/sphinx_ext/myst_refs.py b/myst_parser/sphinx_ext/myst_refs.py
@@ -16,6 +16,8 @@
 from sphinx.util import docname_join, logging
 from sphinx.util.nodes import clean_astext, make_refnode
 
+from myst_parser._compat import findall
+
 try:
     from sphinx.errors import NoUri
 except ImportError:
@@ -35,7 +37,7 @@ class MystReferenceResolver(ReferencesResolver):
 
     def run(self, **kwargs: Any) -> None:
         self.document: document
-        for node in self.document.traverse(addnodes.pending_xref):
+        for node in findall(self.document)(addnodes.pending_xref):
             if node["reftype"] != "myst":
                 continue
 
diff --git a/tests/test_sphinx/conftest.py b/tests/test_sphinx/conftest.py
@@ -39,6 +39,8 @@ def test_basic(app, status, warning, get_sphinx_app_output):
 from bs4 import BeautifulSoup
 from sphinx.testing.path import path
 
+from myst_parser._compat import findall
+
 SOURCE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "sourcedirs"))
 
 
@@ -109,7 +111,7 @@ def read(
             extension = regress_ext
 
         # convert absolute filenames
-        for node in doctree.traverse(
+        for node in findall(doctree)(
             lambda n: "source" in n and not isinstance(n, str)
         ):
             node["source"] = pathlib.Path(node["source"]).name
diff --git a/tox.ini b/tox.ini
@@ -57,7 +57,6 @@ addopts = --ignore=setup.py
 markers =
     sphinx: set parameters for the sphinx `app` fixture (see ipypublish/sphinx/tests/conftest.py)
 filterwarnings =
-    ignore::DeprecationWarning:sphinx.jinja2glue.*
 
 [flake8]
 max-line-length = 100
