More type checking fixes

pyproject.toml

@@ -24,7 +24,8 @@ dependencies = [
     "rich",
     "rich-click",
     "structlog",
-    "us"
+    "urllib3",
+    "us",
 ]
 
 [project.optional-dependencies]
@@ -63,3 +64,6 @@ lint.extend-select = ["I"]
 [tools.setuptools]
 packages = ["virus_clade_utils"]
 
+[tool.mypy]
+ignore_missing_imports = true
+

requirements/requirements-dev.txt

@@ -145,6 +145,7 @@ tzdata==2024.1
     # via pandas
 urllib3==2.2.1
     # via
+    #   virus-clade-utils (pyproject.toml)
     #   botocore
     #   requests
     #   responses

requirements/requirements.txt

@@ -81,6 +81,7 @@ tzdata==2024.1
     # via pandas
 urllib3==2.2.1
     # via
+    #   virus-clade-utils (pyproject.toml)
     #   botocore
     #   requests
 us==3.2.0

src/virus_clade_utils/util/sequence.py

@@ -9,7 +9,7 @@
 
 import polars as pl
 import structlog
-import us  # type: ignore
+import us
 from requests import Session
 
 from virus_clade_utils.util.reference import _get_s3_object_url

src/virus_clade_utils/util/session.py

@@ -3,12 +3,12 @@
 import requests
 import structlog
 from requests.adapters import HTTPAdapter
-from requests.packages.urllib3.util.retry import Retry  # type: ignore
+from urllib3.util import Retry
 
 logger = structlog.get_logger()
 
 
-def _get_session(session: requests.Session = None) -> requests.Session:
+def _get_session() -> requests.Session:
     """Return a requests session with retry logic."""
 
     headers = {

tests/unit/test_cladetime.py

@@ -5,8 +5,8 @@
 import dateutil.tz
 import pytest
 from freezegun import freeze_time
-from virus_clade_utils.cladetime import CladeTime  # type: ignore
-from virus_clade_utils.exceptions import CladeTimeInvalidDateError  # type: ignore
+from virus_clade_utils.cladetime import CladeTime
+from virus_clade_utils.exceptions import CladeTimeInvalidDateError
 from virus_clade_utils.util.config import Config