diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ebbb369c..db2503f5 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: pre-commit/action@v2.0.0
 
   tests:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0dfe77ac..996a2bb0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -20,7 +20,7 @@ repos:
     - id: trailing-whitespace
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.34.0
+    rev: v2.37.3
     hooks:
     - id: pyupgrade
       args: [--py37-plus]
@@ -36,13 +36,13 @@ repos:
     - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 5.0.2
     hooks:
     - id: flake8
       additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v0.971
     hooks:
     - id: mypy
       args: [--config-file=pyproject.toml]
diff --git a/myst_nb/core/loggers.py b/myst_nb/core/loggers.py
index f060acf7..d898d364 100644
--- a/myst_nb/core/loggers.py
+++ b/myst_nb/core/loggers.py
@@ -98,7 +98,8 @@ def process(self, msg, kwargs):
         for keyword in self.KEYWORDS:
             if keyword in kwargs:
                 kwargs["extra"][keyword] = kwargs.pop(keyword)
-        return f"{msg} [{self.extra['type']}{subtype}]", kwargs
+        etype = "" if not self.extra else self.extra.get("type", "")
+        return f"{msg} [{etype}{subtype}]", kwargs
 
 
 class DocutilsLogHandler(logging.Handler):
diff --git a/myst_nb/ext/glue/crossref.py b/myst_nb/ext/glue/crossref.py
index 76f11146..f2f0c76c 100644
--- a/myst_nb/ext/glue/crossref.py
+++ b/myst_nb/ext/glue/crossref.py
@@ -47,7 +47,7 @@ class ReplacePendingGlueReferences(SphinxPostTransform):
     def apply(self, **kwargs):
         """Apply the transform."""
         cache_folder = self.env.mystnb_config.output_folder  # type: ignore
-        bname = self.app.builder.name  # type: ignore
+        bname = self.app.builder.name
         priority_list = get_mime_priority(
             bname, self.config["nb_mime_priority_overrides"]
         )
diff --git a/myst_nb/sphinx_.py b/myst_nb/sphinx_.py
index 3d504654..4a3a57a0 100644
--- a/myst_nb/sphinx_.py
+++ b/myst_nb/sphinx_.py
@@ -320,7 +320,7 @@ def run(self, **kwargs: Any) -> None:
         """Run the transform."""
         # get priority list for this builder
         # TODO allow for per-notebook/cell priority dicts?
-        bname = self.app.builder.name  # type: ignore
+        bname = self.app.builder.name
         priority_list = get_mime_priority(
             bname, self.config["nb_mime_priority_overrides"]
         )