Extend mypy config to more modules, fix revealed errors.

At least a couple of real bugs in this bunch, as well as a lot of
annotation problems and missing annotations.

mypy.ini

@@ -11,6 +11,15 @@ ignore_missing_imports = True
 [mypy-backoff]
 ignore_missing_imports = True
 
+[mypy-numpy.*]
+ignore_missing_imports = True
+
+[mypy-pyarrow.*]
+ignore_missing_imports = True
+
+[mypy-pandas.*]
+ignore_missing_imports = True
+
 [mypy-boto3]
 ignore_missing_imports = True
 
@@ -27,9 +36,9 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 ignore_errors = True
 
-# Check all of core...
+# Check all of daf.butler...
 
-[mypy-lsst.daf.butler.core.*]
+[mypy-lsst.daf.butler.*]
 ignore_missing_imports = False
 ignore_errors = False
 disallow_untyped_defs = True
@@ -42,58 +51,19 @@ warn_unused_ignores = True
 # breaks in the lists of modules).
 
 [mypy-lsst.daf.butler.core.config]
-ignore_errors = True
-
-# Check registry subpackage.
-
-[mypy-lsst.daf.butler.registry.*]
-ignore_missing_imports = False
-ignore_errors = False
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-strict_equality = True
-warn_unreachable = True
-warn_unused_ignores = True
+disallow_untyped_defs = False
 
 [mypy-lsst.daf.butler.registry.queries.exprParser.ply.*]
 ignore_errors = True
 
-[mypy-lsst.daf.butler.registry.tests.*]
+[mypy-lsst.daf.butler.tests.*]
 ignore_errors = True
 
-# Check transfers subpackage
-
-[mypy-lsst.daf.butler.transfers.*]
-ignore_missing_imports = False
-ignore_errors = False
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-strict_equality = True
-warn_unreachable = True
-warn_unused_ignores = True
-
-
-# Check concrete datastores.
-
-[mypy-lsst.daf.butler.datastores.*]
-ignore_missing_imports = False
-ignore_errors = False
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-strict_equality = True
-warn_unreachable = True
-warn_unused_ignores = True
+[mypy-lsst.daf.butler.cli.*]
+ignore_errors = True
 
-# Formatters
+[mypy-lsst.daf.butler.script.*]
+disallow_untyped_defs = False
 
-[mypy-lsst.daf.butler.formatters.*]
-ignore_missing_imports = False
-ignore_errors = False
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-strict_equality = True
-warn_unreachable = True
-warn_unused_ignores = True
-
-[mypy-lsst.daf.butler.formatters.parquet]
+[mypy-lsst.daf.butler.registry.tests.*]
 ignore_errors = True