diff --git a/docs/api/docgen.py b/docs/api/docgen.py
index effef38..560ac2d 100644
--- a/docs/api/docgen.py
+++ b/docs/api/docgen.py
@@ -162,7 +162,7 @@ def doc_dir(self) -> str:
       return ''
     if isinstance(self, Leaf):
       dir_segments.pop(-1)
-    return os.path.join(self.source_category, *dir_segments)
+    return os.path.join(self.source_category, *dir_segments)  # pyrefly: ignore[no-matching-overload]
 
   @property
   @abc.abstractmethod
diff --git a/docs/conf.py b/docs/conf.py
index d1e1c43..73c46eb 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -100,7 +100,7 @@ def get_git_location(module_name, entity_name):
   except TypeError:
     # e.g. target is constant number, etc.
     return None
-  file = os.path.relpath(file, os.path.abspath('..'))
+  file = os.path.relpath(file, os.path.abspath('..'))  # pyrefly: ignore[no-matching-overload]
   if not file.startswith('pyglove'):
     return None
   start, end = lines[1], lines[1] + len(lines[0]) - 1
diff --git a/pyglove/core/tuning/sample.py b/pyglove/core/tuning/sample.py
index 752f671..d8e80e0 100644
--- a/pyglove/core/tuning/sample.py
+++ b/pyglove/core/tuning/sample.py
@@ -258,7 +258,7 @@ def fun():
 
   while True:
     try:
-      feedback = backend.next()
+      feedback = backend.next()  # pyrefly: ignore[missing-attribute]
       dna = feedback.dna
       reward = dna.metadata.get('reward')
       if reward is None:
diff --git a/pyglove/core/typing/json_schema.py b/pyglove/core/typing/json_schema.py
index 1955c9f..34a6203 100644
--- a/pyglove/core/typing/json_schema.py
+++ b/pyglove/core/typing/json_schema.py
@@ -218,7 +218,7 @@ def _remove_type_name(_, v: Dict[str, Any]):
   if not ignore_nonable and value_spec.is_noneable:
     nullable = {'type': 'null'}
     if 'anyOf' in definition:
-      definition['anyOf'].append(nullable)
+      definition['anyOf'].append(nullable)  # pyrefly: ignore[missing-attribute]
     else:
       definition = {'anyOf': [definition, nullable]}
     if value_spec.default is None:
diff --git a/pyglove/core/typing/value_specs.py b/pyglove/core/typing/value_specs.py
index 072110f..835af58 100644
--- a/pyglove/core/typing/value_specs.py
+++ b/pyglove/core/typing/value_specs.py
@@ -2031,7 +2031,7 @@ def format(
     if self._forward_ref is not None:
       name = self._forward_ref.name
     else:
-      name = self._value_type.__name__
+      name = self._value_type.__name__  # pyrefly: ignore[missing-attribute]
     return utils.kvlist_str(
         [
             ('', utils.RawText(name), None),
diff --git a/pyglove/dev/reloader.py b/pyglove/dev/reloader.py
index 83ab203..0aeaf44 100644
--- a/pyglove/dev/reloader.py
+++ b/pyglove/dev/reloader.py
@@ -102,7 +102,7 @@ def _reload(m: types.ModuleType):
     reloaded_modules = []
     for m in modules:
       if verbose:
-        print(f'Reloading [{m.__name__}]...')
+        print(f'Reloading [{m.__name__}]...')  # pyrefly: ignore[missing-attribute]
       reloaded_modules.append(_reload(m))  # pyrefly: ignore[bad-argument-type]
 
   elapse = time.time() - start_time
diff --git a/pyglove/ext/evolution/recombinators.py b/pyglove/ext/evolution/recombinators.py
index 01e34c4..5e0160d 100644
--- a/pyglove/ext/evolution/recombinators.py
+++ b/pyglove/ext/evolution/recombinators.py
@@ -826,14 +826,14 @@ def possible_permutation_points(
         # subchoices of a multi-choice.
         permutation_proposals: List[List[int]] = self.permutate(
             permutation_point,
-            [[dna.value for dna in p[permutation_point]] for p in parent_dicts])  # pyrefly: ignore[not-iterable]
+            [[dna.value for dna in p[permutation_point]] for p in parent_dicts])  # pyrefly: ignore[missing-attribute, not-iterable]
 
         # For each child proposal, merge it back with each parent's DNA to
         # produce an output. Therefore if there are N parents and M permuation
         # proposals, the maximum number of output is N * M. Duplicates will be
         # removed so it may lead to a smaller number than N * M.
         for parent_dict in parent_dicts:
-          subdna_map = {d.value: d for d in parent_dict[permutation_point]}  # pyrefly: ignore[not-iterable]
+          subdna_map = {d.value: d for d in parent_dict[permutation_point]}  # pyrefly: ignore[missing-attribute, not-iterable]
           for proposal in permutation_proposals:
             parent_dict[permutation_point] = [subdna_map[v] for v in proposal]  # pyrefly: ignore[unsupported-operation]
             outputs.append(pg.DNA.from_dict(parent_dict, dna_spec))  # pyrefly: ignore[bad-argument-type]