Added new mypy tags and fixed all new mypy errors

Makefile

@@ -3,7 +3,7 @@ default:
 
 SOURCE_DIR_NAME=vistautils
 
-MYPY:=mypy $(SOURCE_DIR_NAME) tests
+MYPY:=mypy $(SOURCE_DIR_NAME) tests --disallow-any-generics --disallow-any-unimported
 
 # Suppressed warnings:
 # Too many arguments, Unexpected keyword arguments: can't do static analysis on attrs __init__

tests/test_range.py

@@ -1,4 +1,5 @@
 import sys
+from typing import Any
 from unittest import TestCase
 
 from immutablecollections import ImmutableSet
@@ -233,15 +234,15 @@ def check_contains(self, rng: Range[int]) -> None:
         self.assertTrue(7 in rng)
         self.assertFalse(8 in rng)
 
-    def assert_unbounded_below(self, rng: Range):
+    def assert_unbounded_below(self, rng: Range[Any]):
         self.assertFalse(rng.has_lower_bound())
         with self.assertRaises(ValueError):
             rng.lower_endpoint()
         # pylint: disable=pointless-statement
         with self.assertRaises(AssertionError):
             rng.lower_bound_type
 
-    def assert_unbounded_above(self, rng: Range):
+    def assert_unbounded_above(self, rng: Range[Any]):
         self.assertFalse(rng.has_upper_bound())
         with self.assertRaises(ValueError):
             rng.upper_endpoint()

vistautils/attrutils.py

@@ -9,7 +9,7 @@
 import vistautils.preconditions
 
 
-def attrib_instance_of(type_: Union[Type, Tuple[Type, ...]], *args, **kwargs):
+def attrib_instance_of(type_: Union[Type[Any], Tuple[Type[Any], ...]], *args, **kwargs):
     warnings.warn(
         "Deprecated, use attrib(validator=instance_of(type))", DeprecationWarning
     )
@@ -22,7 +22,7 @@ def attrib_instance_of(type_: Union[Type, Tuple[Type, ...]], *args, **kwargs):
 # TODO cannot currently be used with additional validators:
 # https://github.com/isi-nlp/isi-flexnlp/issues/188
 def attrib_opt_instance_of(
-    type_: Union[Type, Tuple[Type, ...]], *args, default=None, **kwargs
+    type_: Union[Type[Any], Tuple[Type[Any], ...]], *args, default=None, **kwargs
 ):
     warnings.warn(
         "Deprecated, use attrib(default=<default>, validator=optional(instance_of(<type>)))",
@@ -34,14 +34,14 @@ def attrib_opt_instance_of(
     )
 
 
-def attrib_factory(factory: Callable, *args, **kwargs):
+def attrib_factory(factory: Callable[[Any], Any], *args, **kwargs):
     warnings.warn("Deprecated, use attrib(factory=<factory>)", DeprecationWarning)
     # Mypy does not understand these arguments
     return attrib(default=Factory(factory), *args, **kwargs)  # type: ignore
 
 
 def attrib_immutable(
-    type_: Type[immutablecollections.ImmutableCollection], *args, **kwargs
+    type_: Type[immutablecollections.ImmutableCollection[Any]], *args, **kwargs
 ):
     warnings.warn(
         "Deprecated, use attrib(converter=<collection factory>)", DeprecationWarning
@@ -52,7 +52,7 @@ def attrib_immutable(
 
 
 def attrib_private_immutable_builder(
-    type_: Type[immutablecollections.ImmutableCollection], *args, **kwargs
+    type_: Type[immutablecollections.ImmutableCollection[Any]], *args, **kwargs
 ):
     """
     Create an immutable collection builder private attribute.
@@ -75,7 +75,7 @@ def attrib_private_immutable_builder(
 # TODO: The use of Type[ImmutableCollection] causes Mypy warnings
 # Perhaps the solution is to make ImmutableCollection a Protocol?
 def attrib_opt_immutable(
-    type_: Type[immutablecollections.ImmutableCollection], *args, **kwargs
+    type_: Type[immutablecollections.ImmutableCollection[Any]], *args, **kwargs
 ):
     """Return a attrib with a converter for optional collections.
 
@@ -98,7 +98,9 @@ def attrib_opt_immutable(
     )
 
 
-def opt_instance_of(type_: Union[Type, Tuple[Type, ...]]) -> Callable:
+def opt_instance_of(
+    type_: Union[Type[Any], Tuple[Type[Any], ...]]
+) -> Callable[[Any], Any]:
     warnings.warn("Deprecated, use optional(instance_of(<type>))", DeprecationWarning)
     # Mypy does not understand these arguments
     return validators.instance_of((type_, type(None)))  # type: ignore
@@ -112,8 +114,8 @@ def _check_immutable_collection(type_):
 
 
 def _empty_immutable_if_none(
-    val: Any, type_: Type[immutablecollections.ImmutableCollection]
-) -> immutablecollections.ImmutableCollection:
+    val: Any, type_: Type[immutablecollections.ImmutableCollection[Any]]
+) -> immutablecollections.ImmutableCollection[Any]:
     if val is None:
         return type_.empty()
     else:

vistautils/io_utils.py

@@ -11,7 +11,6 @@
     Any,
     AnyStr,
     BinaryIO,
-    Callable,
     Iterable,
     Iterator,
     List,
@@ -229,7 +228,7 @@ def open(self) -> TextIO:
             ret = CharSource.from_string(tgz_data.read().decode(self._encoding)).open()
             # we need to fiddle with the close method on the returned TextIO so that when it is
             # closed the containing zip file is closed as well
-            old_close: Callable = ret.close
+            old_close = ret.close
         else:
             raise IOError(
                 f"Could not extract path {self._path_within_tgz} from {self._tgz_path}"

vistautils/key_value.py

@@ -166,7 +166,9 @@ def zip_bytes_sink(
         )
 
 
-class KeyValueLinearSource(Generic[K, V], AbstractContextManager, metaclass=ABCMeta):
+class KeyValueLinearSource(
+    Generic[K, V], AbstractContextManager, metaclass=ABCMeta  # type: ignore
+):
     """
     Anything which provide a sequence of key-value pairs.
 
@@ -875,7 +877,7 @@ def byte_key_value_linear_source_from_params(
     params: Parameters,
     *,
     input_namespace: str = "input",
-    eval_context: Optional[Dict] = None,
+    eval_context: Optional[Dict[Any, Any]] = None,
 ) -> KeyValueLinearSource[str, bytes]:
     """
     Get a key-value source based on parameters.
@@ -918,7 +920,7 @@ def char_key_value_source_from_params(
     params: Parameters,
     *,
     input_namespace: str = "input",
-    eval_context: Optional[Dict] = None,
+    eval_context: Optional[Dict[Any, Any]] = None,
 ) -> KeyValueSource[str, str]:
     """
     Get a random-access key-value source based on parameters.
@@ -957,7 +959,7 @@ def byte_key_value_source_from_params(
     params: Parameters,
     *,
     input_namespace: str = "input",
-    eval_context: Optional[Dict] = None,
+    eval_context: Optional[Dict[Any, Any]] = None,
 ) -> KeyValueSource[str, bytes]:
     """
     Get a random-access key-value source based on parameters.
@@ -1007,7 +1009,7 @@ def char_key_value_sink_from_params(
     params: Parameters,
     *,
     output_namespace: str = "output",
-    eval_context: Optional[Dict] = None,
+    eval_context: Optional[Dict[Any, Any]] = None,
 ) -> KeyValueSink[str, str]:
     """
     Get a key-value sink based on parameters.
@@ -1044,7 +1046,7 @@ def byte_key_value_sink_from_params(
     params: Parameters,
     *,
     output_namespace: str = "output",
-    eval_context: Optional[Dict] = None,
+    eval_context: Optional[Dict[Any, Any]] = None,
 ) -> KeyValueSink[str, bytes]:
     """
     Get a binary key-value sink based on parameters.

vistautils/parameters.py

@@ -92,7 +92,7 @@ def empty(*, namespace_prefix: Iterable[str] = tuple()) -> "Parameters":
 
     @staticmethod
     def from_mapping(
-        mapping: Mapping, *, namespace_prefix: Iterable[str] = tuple()
+        mapping: Mapping[Any, Any], *, namespace_prefix: Iterable[str] = tuple()
     ) -> "Parameters":
         """
         Convert a dictionary of dictionaries into a `Parameter`s
@@ -651,21 +651,23 @@ def namespace_or_empty(self, name: str) -> Optional["Parameters"]:
                 f"Expected a namespace, but got a regular parameters for {name}"
             )
 
-    def arbitrary_list(self, name: str, *, default: Optional[List] = None) -> List:
+    def arbitrary_list(
+        self, name: str, *, default: Optional[List[Any]] = None
+    ) -> List[Any]:
         """
         Get a list with arbitrary structure.
         """
         return self.get(name, List, default=default)
 
     @overload
-    def optional_arbitrary_list(self, name: str) -> Optional[List]:
+    def optional_arbitrary_list(self, name: str) -> Optional[List[Any]]:
         ...
 
     @overload
-    def optional_arbitrary_list(self, name: str, *, default: List) -> List:
+    def optional_arbitrary_list(self, name: str, *, default: List[Any]) -> List[Any]:
         ...
 
-    def optional_arbitrary_list(self, name: str, *, default: Optional[List] = None):
+    def optional_arbitrary_list(self, name: str, *, default: Optional[List[Any]] = None):
         """
         Get a list with arbitrary structure, if available
         """
@@ -710,7 +712,7 @@ def evaluate(
         name: str,
         expected_type: Type[_ParamType],
         *,
-        context: Optional[Mapping] = None,
+        context: Optional[Mapping[Any, Any]] = None,
         namespace_param_name: str = "value",
         special_values: Mapping[str, str] = ImmutableDict.empty(),
         default: Optional[_ParamType] = None,
@@ -743,7 +745,7 @@ def handle_special_values(val: str) -> str:
         namespace = self.optional_namespace(name)
         try:
             to_evaluate = None
-            context_modules: List = []
+            context_modules: List[Any] = []
 
             if namespace:
                 to_evaluate = namespace.string(namespace_param_name)
@@ -773,7 +775,7 @@ def object_from_parameters(
         name: str,
         expected_type: Type[_ParamType],
         *,
-        context: Optional[Mapping] = None,
+        context: Optional[Mapping[Any, Any]] = None,
         creator_namepace_param_name: str = "value",
         special_creator_values: Mapping[str, str] = ImmutableDict.empty(),
         default_creator: Optional[Any] = None,
@@ -1255,7 +1257,7 @@ def _inner_load_from_string(
             raise IOError(f"Failure while loading parameter file {error_string}") from e
 
     @staticmethod
-    def _validate(raw_yaml: Mapping):
+    def _validate(raw_yaml: Mapping[Any, Any]):
         # we don't use check_isinstance so we can have a custom error message
         check_arg(
             isinstance(raw_yaml, Mapping),
@@ -1264,7 +1266,7 @@ def _validate(raw_yaml: Mapping):
         YAMLParametersLoader._check_all_keys_strings(raw_yaml)
 
     @staticmethod
-    def _check_all_keys_strings(mapping: Mapping, path=None):
+    def _check_all_keys_strings(mapping: Mapping[Any, Any], path=None):
         if path is None:
             path = []
 

vistautils/preconditions.py

@@ -5,7 +5,7 @@
 # pylint: disable=invalid-name
 # Type annotation from TypeShed for classinfo argument  of isinstance and issubclass
 
-_ClassInfo = Union[type, Tuple[Union[type, Tuple], ...]]
+_ClassInfo = Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]]
 
 
 T = TypeVar("T")
@@ -29,7 +29,7 @@ def check_not_none(x: T, msg: str = None) -> T:
         return x
 
 
-def check_arg(result: Any, msg: str = None, msg_args: Tuple = None) -> None:
+def check_arg(result: Any, msg: str = None, msg_args: Tuple[Any] = None) -> None:
     if not result:
         if msg:
             raise ValueError(msg % (msg_args or ()))

vistautils/range.py

@@ -914,7 +914,7 @@ def remove_all(
 class _SortedDictRangeSet(RangeSet[T], metaclass=ABCMeta):
     # pylint:disable=protected-access
 
-    def __init__(self, ranges_by_lower_bound: SortedDict) -> None:
+    def __init__(self, ranges_by_lower_bound: SortedDict) -> None:  # type: ignore
         # we store the ranges as a map sorted by their lower bound
         # Note that because we enforce that there are no overlapping or connected ranges,
         # this sorts the ranges by upper bound as well
@@ -1039,7 +1039,7 @@ def leftmost_containing_or_above(self, lower_limit: T) -> Optional[Range[T]]:
         # an AboveValue cut corresponds to a closed upper interval, which catches containment
         # as desired
         # I have no idea why mypy is asking for an explicit type assignment here
-        limit_as_bound: _AboveValue = _AboveValue(lower_limit)
+        limit_as_bound: _AboveValue[Any] = _AboveValue(lower_limit)
 
         # insertion index into the sorted list of sets
         idx = sorted_dict.bisect_left(limit_as_bound)
@@ -1410,7 +1410,7 @@ def immutablerangemap(
 
 
 # utility functions for SortedDict to give it an interface more like Java's NavigableMap
-def _value_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:
+def _value_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:  # type: ignore
     """
     Get item for greatest key strictly less than the given key
 
@@ -1426,7 +1426,7 @@ def _value_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:
         return None
 
 
-def _value_at_or_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:
+def _value_at_or_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:  # type: ignore
     """
     Get item for greatest key less than or equal to a given key.
 
@@ -1445,7 +1445,7 @@ def _value_at_or_below(sorted_dict: SortedDict, key: T) -> Optional[Any]:
     return sorted_dict[key]
 
 
-def _value_at_or_above(sorted_dict: SortedDict, key: T) -> Optional[Any]:
+def _value_at_or_above(sorted_dict: SortedDict, key: T) -> Optional[Any]:  # type: ignore
     if not sorted_dict:
         return None
     idx = sorted_dict.bisect_left(key)
@@ -1455,7 +1455,7 @@ def _value_at_or_above(sorted_dict: SortedDict, key: T) -> Optional[Any]:
     return sorted_dict[sorted_dict.keys()[idx]]
 
 
-def _clear(
+def _clear(  # type: ignore
     sorted_dict: SortedDict, start_key_inclusive: T, stop_key_exclusive: T
 ) -> None:
     # we copy to a list first in case sorted_dict is not happy with modification during iteration

vistautils/scripts/directory_to_key_value_store.py

@@ -55,7 +55,7 @@ def key_function_from_params(params: Parameters) -> Callable[[Path], str]:
     elif key_function_string == STRIP_ONE_EXTENSION:
         return strip_one_extension_key_function
     else:
-        raise NotImplementedError(f"Unknown key function %s", key_function_string)
+        raise NotImplementedError(f"Unknown key function {key_function_string}")
 
 
 IDENTITY = "identity"

vistautils/span.py

@@ -1,4 +1,4 @@
-from typing import Iterable, Optional, Sized, Tuple, TypeVar, Union
+from typing import Any, Iterable, Optional, Sized, Tuple, TypeVar, Union
 
 from attr import attrib, attrs, validators
 
@@ -129,7 +129,7 @@ def __repr__(self):
 
 
 class HasSpan(Protocol):
-    __slots__: tuple = ()
+    __slots__: Tuple[Any, ...] = ()
     span: Span
 
     @property