Run mypy on all packages' files

Also:
- mypy fixes.
- Use `with` statement to open/close files.

lib/galaxy_ext/expressions/handle_job.py

@@ -16,7 +16,7 @@ warnings.filterwarnings("ignore", message=r"[\n.]DEPRECATION: Python 2", module=
 try:
     from cwltool import expression
 except ImportError:
-    expression = None
+    expression = None  # type: ignore[assignment]
 
 from galaxy.tools.expressions import evaluate
 

lib/galaxy_test/base/populators.py

@@ -67,7 +67,7 @@ from typing import (
     Union,
 )
 
-import cwltest
+import cwltest.utils
 import requests
 import yaml
 from bioblend.galaxy import GalaxyClient
@@ -2102,7 +2102,7 @@ class CwlPopulator:
         try:
             for key, value in expected_outputs.items():
                 actual_output = run.get_output_as_object(key)
-                cwltest.compare(value, actual_output)
+                cwltest.utils.compare(value, actual_output)
         except Exception:
             self.dataset_populator._summarize_history(run.history_id)
             raise