From 79a4ebd28d34dc920a4bfa36f822a9f03a8fecff Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 25 Sep 2024 17:47:14 +0100
Subject: [PATCH] Enable ``ignore-without-code`` mypy error code

---
 lib/galaxy/celery/base_task.py                    | 2 +-
 lib/galaxy/schema/schema.py                       | 2 +-
 lib/galaxy/webapps/galaxy/api/history_contents.py | 6 +++---
 mypy.ini                                          | 1 +
 tools/filters/sff_extract.py                      | 4 ++--
 5 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 94bb8d75956f..c4e986cc94b6 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -80,7 +80,7 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     We take advantage of efficiencies in its dialect.
     """
 
-    def calculate_task_start_time(  # type: ignore
+    def calculate_task_start_time(
         self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         with transaction(sa_session):
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 8b9c1ecc0bdd..9e461bd5655d 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -3338,7 +3338,7 @@ class HDACustom(HDADetailed):
     # TODO: Fix this workaround for partial_model not supporting UUID fields for some reason.
     # The error otherwise is: `PydanticUserError: 'UuidVersion' cannot annotate 'nullable'.`
     # Also ignoring mypy complaints about the type redefinition.
-    uuid: Optional[UUID4]  # type: ignore
+    uuid: Optional[UUID4]  # type: ignore[assignment]
 
     # Add fields that are not part of any view here
     visualizations: Annotated[
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 95641f244c85..2386807211ba 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -7,6 +7,7 @@
     List,
     Literal,
     Optional,
+    Set,
     Union,
 )
 
@@ -335,11 +336,10 @@ def parse_content_types(types: Union[List[str], str]) -> List[HistoryContentType
 def parse_dataset_details(details: Optional[str]):
     """Parses the different values that the `dataset_details` parameter
     can have from a string."""
-    dataset_details = None
     if details is not None and details != "all":
-        dataset_details = set(util.listify(details))
+        dataset_details: Union[None, Set[str], str] = set(util.listify(details))
     else:  # either None or 'all'
-        dataset_details = details  # type: ignore
+        dataset_details = details
     return dataset_details
 
 
diff --git a/mypy.ini b/mypy.ini
index 0ec6ae269986..70250f4d521f 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,4 +1,5 @@
 [mypy]
+enable_error_code = ignore-without-code
 plugins = pydantic.mypy
 show_error_codes = True
 ignore_missing_imports = True
diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index 9c67a644c8ff..d7bcf05bf196 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -42,9 +42,9 @@
 fake_sff_name = "fake_sff_name"
 
 # readname as key: lines with matches from SSAHA, one best match
-ssahapematches = {}  # type: ignore
+ssahapematches = {}  # type: ignore[var-annotated]
 # linker readname as key: length of linker sequence
-linkerlengths = {}  # type: ignore
+linkerlengths = {}  # type: ignore[var-annotated]
 
 # set to true if something really fishy is going on with the sequences
 stern_warning = False