[feature] Add Mypy type checking

[jan-janssen]

List of current issues:

executorlib/standalone/interactive/spawner.py:72: error: Argument "cwd" to "__init__" of "BaseSpawner" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/standalone/interactive/spawner.py:89: error: Incompatible types in assignment (expression has type "Popen[bytes]", variable has type "None")  [assignment]
executorlib/standalone/interactive/spawner.py:114: error: "None" has no attribute "communicate"  [attr-defined]
executorlib/standalone/interactive/spawner.py:115: error: "None" has no attribute "terminate"  [attr-defined]
executorlib/standalone/interactive/spawner.py:117: error: "None" has no attribute "wait"  [attr-defined]
executorlib/interactive/flux.py:36: error: Argument "cwd" to "__init__" of "BaseSpawner" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/interactive/flux.py:98: error: "None" has no attribute "cancel"  [attr-defined]
executorlib/interactive/flux.py:102: error: "None" has no attribute "result"  [attr-defined]
executorlib/standalone/serialize.py:32: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/standalone/serialize.py:32: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/standalone/serialize.py:59: error: callable? has no attribute "__name__"  [attr-defined]
executorlib/standalone/interactive/backend.py:6: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/standalone/interactive/backend.py:6: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/standalone/interactive/backend.py:7: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/standalone/interactive/backend.py:7: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/standalone/__init__.py:12: error: Type of __all__ must be "Sequence[str]", not "list[object]"  [misc]
executorlib/backend/interactive_parallel.py:27: error: Accessing "__init__" on an instance is unsound, since instance.__init__ could be from an incompatible subclass  [misc]
executorlib/backend/interactive_parallel.py:54: error: Argument "socket" to "interface_receive" has incompatible type "Socket[Any] | None"; expected "Socket[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:60: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:60: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/backend/interactive_parallel.py:62: error: Argument "socket" to "interface_send" has incompatible type "Socket[Any] | None"; expected "Socket[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:63: error: Argument "socket" to "interface_shutdown" has incompatible type "Socket[Any] | None"; expected "Socket[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:63: error: Argument "context" to "interface_shutdown" has incompatible type "Context[Any] | None"; expected "Context[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:67: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:68: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:69: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:70: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:74: error: Argument "input_dict" to "call_funct" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:82: error: Argument "socket" to "interface_send" has incompatible type "Socket[Any] | None"; expected "Socket[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:88: error: Argument "socket" to "interface_send" has incompatible type "Socket[Any] | None"; expected "Socket[Any]"  [arg-type]
executorlib/backend/interactive_parallel.py:90: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:91: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/backend/interactive_parallel.py:92: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:93: error: Item "None" of "dict[Any, Any] | None" has no attribute "keys"  [union-attr]
executorlib/backend/interactive_parallel.py:95: error: Argument "input_dict" to "call_funct" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/standalone/inputcheck.py:111: error: Unsupported operand types for + ("str" and "None")  [operator]
executorlib/standalone/inputcheck.py:111: note: Right operand is of type "str | None"
executorlib/standalone/inputcheck.py:177: error: Unsupported operand types for / ("int" and "None")  [operator]
executorlib/standalone/inputcheck.py:177: note: Right operand is of type "int | None"
executorlib/standalone/inputcheck.py:178: error: Incompatible return value type (got "int | None", expected "int")  [return-value]
executorlib/cache/subprocess_spawner.py:36: error: Argument "file_name" to "check_file_exists" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/base/executor.py:48: error: "RaisingThread" has no attribute "_kwargs"  [attr-defined]
executorlib/base/executor.py:65: error: Signature of "submit" incompatible with supertype "Executor"  [override]
executorlib/base/executor.py:65: note:      Superclass:
executorlib/base/executor.py:65: note:          def [_P`-1, _T] submit(self, Callable[_P, _T], /, *args: _P.args, **kwargs: _P.kwargs) -> Future[_T]
executorlib/base/executor.py:65: note:      Subclass:
executorlib/base/executor.py:65: note:          def submit(self, fn: callable?, *args: Any, resource_dict: dict[Any, Any] = ..., **kwargs: Any) -> Future[Any]
executorlib/base/executor.py:65: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/base/executor.py:65: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/base/executor.py:100: error: Need type annotation for "f"  [var-annotated]
executorlib/base/executor.py:135: error: Incompatible types in assignment (expression has type "None", variable has type "Queue[Any]")  [assignment]
executorlib/interactive/shared.py:25: error: Signature of "submit" incompatible with supertype "Executor"  [override]
executorlib/interactive/shared.py:25: note:      Superclass:
executorlib/interactive/shared.py:25: note:          def [_P`-1, _T] submit(self, Callable[_P, _T], /, *args: _P.args, **kwargs: _P.kwargs) -> Future[_T]
executorlib/interactive/shared.py:25: note:      Subclass:
executorlib/interactive/shared.py:25: note:          def submit(self, fn: callable?, *args: Any, resource_dict: dict[Any, Any] = ..., **kwargs: Any) -> Future[Any]
executorlib/interactive/shared.py:25: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/interactive/shared.py:25: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/interactive/shared.py:52: error: Need type annotation for "f"  [var-annotated]
executorlib/interactive/shared.py:73: error: Argument 1 to "len" has incompatible type "RaisingThread"; expected "Sized"  [arg-type]
executorlib/interactive/shared.py:76: error: "RaisingThread" has no attribute "__iter__" (not iterable)  [attr-defined]
executorlib/interactive/shared.py:80: error: Incompatible types in assignment (expression has type "None", variable has type "Queue[Any]")  [assignment]
executorlib/interactive/shared.py:82: error: Argument 1 of "_set_process" is incompatible with supertype "ExecutorBase"; supertype defines the argument type as "RaisingThread"  [override]
executorlib/interactive/shared.py:82: note: This violates the Liskov substitution principle
executorlib/interactive/shared.py:82: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides
executorlib/interactive/shared.py:89: error: Incompatible types in assignment (expression has type "list[RaisingThread]", variable has type "RaisingThread | None")  [assignment]
executorlib/interactive/shared.py:90: error: Item "RaisingThread" of "RaisingThread | None" has no attribute "__iter__" (not iterable)  [union-attr]
executorlib/interactive/shared.py:90: error: Item "None" of "RaisingThread | None" has no attribute "__iter__" (not iterable)  [union-attr]
executorlib/interactive/shared.py:91: error: "list[RaisingThread]" has no attribute "start"  [attr-defined]
executorlib/interactive/shared.py:132: error: Incompatible default for argument "spawner" (default has type "type[MpiExecSpawner]", argument has type "BaseSpawner")  [assignment]
executorlib/interactive/shared.py:185: error: Incompatible default for argument "spawner" (default has type "type[MpiExecSpawner]", argument has type "BaseSpawner")  [assignment]
executorlib/interactive/shared.py:203: error: Incompatible default for argument "spawner" (default has type "type[MpiExecSpawner]", argument has type "BaseSpawner")  [assignment]
executorlib/interactive/shared.py:230: error: "BaseSpawner" not callable  [operator]
executorlib/interactive/shared.py:260: error: Incompatible default for argument "spawner" (default has type "type[MpiExecSpawner]", argument has type "BaseSpawner")  [assignment]
executorlib/interactive/shared.py:284: error: Need type annotation for "active_task_dict" (hint: "active_task_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/interactive/shared.py:285: error: Need type annotation for "process_lst" (hint: "process_lst: list[<type>] = ...")  [var-annotated]
executorlib/interactive/shared.py:297: error: Need type annotation for "qtask"  [var-annotated]
executorlib/interactive/shared.py:475: error: Incompatible types in assignment (expression has type "list[Any]", variable has type "tuple[Any, ...]")  [assignment]
executorlib/interactive/shared.py:642: error: Incompatible types in assignment (expression has type "object", variable has type "dict[Any, Any]")  [assignment]
executorlib/cache/shared.py:34: error: Incompatible return value type (got "object", expected "str")  [return-value]
executorlib/cache/shared.py:52: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/cache/shared.py:52: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/cache/shared.py:54: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/cache/shared.py:54: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/cache/shared.py:77: error: Need type annotation for "memory_dict" (hint: "memory_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/cache/shared.py:77: error: Need type annotation for "process_dict" (hint: "process_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/cache/shared.py:77: error: Need type annotation for "file_name_dict" (hint: "file_name_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/cache/shared.py:125: error: callable? not callable  [misc]
executorlib/cache/queue_spawner.py:38: error: Argument "file_name" to "check_file_exists" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/cache/queue_spawner.py:39: error: Argument "file_name" to "get_queue_id" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/cache/queue_spawner.py:72: error: Argument "file_name" to "dump" has incompatible type "str | None"; expected "str"  [arg-type]
executorlib/cache/queue_spawner.py:73: error: Incompatible return value type (got "int | None", expected "tuple[int, int]")  [return-value]
executorlib/cache/executor.py:23: error: Incompatible types in assignment (expression has type "Callable[[list[Any], list[Any], str | None, dict[Any, Any] | None, str | None, str | None, str | None], Popen[Any]]", variable has type "Callable[[list[Any], list[int], str | None, dict[Any, Any] | None, str | None, str | None, str | None], tuple[int, int]]")  [assignment]
executorlib/cache/executor.py:31: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/cache/executor.py:31: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/cache/executor.py:32: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/cache/executor.py:32: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/cache/executor.py:61: error: Unsupported left operand type for == (callable?)  [operator]
executorlib/cache/executor.py:94: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/cache/executor.py:94: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/backend/cache_parallel.py:26: error: Accessing "__init__" on an instance is unsound, since instance.__init__ could be from an incompatible subclass  [misc]
executorlib/backend/cache_parallel.py:40: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/standalone/plot.py:20: error: Need type annotation for "node_lst" (hint: "node_lst: list[<type>] = ...")  [var-annotated]
executorlib/standalone/plot.py:21: error: Need type annotation for "hash_id_dict" (hint: "hash_id_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/interactive/executor.py:76: error: Need type annotation for "_future_hash_dict" (hint: "_future_hash_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/interactive/executor.py:77: error: Need type annotation for "_task_hash_dict" (hint: "_task_hash_dict: dict[<type>, <type>] = ...")  [var-annotated]
executorlib/interactive/executor.py:80: error: Signature of "submit" incompatible with supertype "Executor"  [override]
executorlib/interactive/executor.py:80: note:      Superclass:
executorlib/interactive/executor.py:80: note:          def [_P`-1, _T] submit(self, Callable[_P, _T], /, *args: _P.args, **kwargs: _P.kwargs) -> Future[_T]
executorlib/interactive/executor.py:80: note:      Subclass:
executorlib/interactive/executor.py:80: note:          def submit(self, fn: Callable[..., Any], *args: Any, resource_dict: dict[str, Any] = ..., **kwargs: Any) -> Future[Any]
executorlib/interactive/executor.py:137: error: Unexpected keyword argument "exc_type" for "__exit__" of "Executor"  [call-arg]
executorlib/interactive/executor.py:159: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/interactive/executor.py:159: note: Perhaps you meant "typing.Callable" instead of "callable"?
/Users/janssen/mambaforge/lib/python3.12/site-packages/mypy/typeshed/stdlib/concurrent/futures/_base.pyi:74: note: "__exit__" of "Executor" defined here
executorlib/interactive/executor.py:137: error: Unexpected keyword argument "exc_val" for "__exit__" of "Executor"  [call-arg]
/Users/janssen/mambaforge/lib/python3.12/site-packages/mypy/typeshed/stdlib/concurrent/futures/_base.pyi:74: note: "__exit__" of "Executor" defined here
executorlib/interactive/executor.py:137: error: Unexpected keyword argument "exc_tb" for "__exit__" of "Executor"  [call-arg]
/Users/janssen/mambaforge/lib/python3.12/site-packages/mypy/typeshed/stdlib/concurrent/futures/_base.pyi:74: note: "__exit__" of "Executor" defined here
executorlib/interactive/executor.py:199: error: Argument "init_function" to "check_init_function" has incompatible type "callable? | None"; expected "Callable[..., Any]"  [arg-type]
executorlib/interactive/executor.py:203: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/interactive/executor.py:204: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:205: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:207: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/interactive/executor.py:209: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/interactive/executor.py:211: error: Item "None" of "dict[Any, Any] | None" has no attribute "__delitem__"  [union-attr]
executorlib/interactive/executor.py:212: error: Item "None" of "dict[Any, Any] | None" has no attribute "__delitem__"  [union-attr]
executorlib/interactive/executor.py:213: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:214: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:215: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:217: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:225: error: Argument "executor_kwargs" to "InteractiveExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:226: error: Argument "spawner" to "InteractiveExecutor" has incompatible type "type[FluxPythonSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/interactive/executor.py:232: error: Argument "executor_kwargs" to "InteractiveStepExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:233: error: Argument "spawner" to "InteractiveStepExecutor" has incompatible type "type[FluxPythonSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/interactive/executor.py:239: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:247: error: Argument "executor_kwargs" to "InteractiveExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:248: error: Argument "spawner" to "InteractiveExecutor" has incompatible type "type[SrunSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/interactive/executor.py:254: error: Argument "executor_kwargs" to "InteractiveStepExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:255: error: Argument "spawner" to "InteractiveStepExecutor" has incompatible type "type[SrunSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/interactive/executor.py:260: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/interactive/executor.py:262: error: Value of type "dict[Any, Any] | None" is not indexable  [index]
executorlib/interactive/executor.py:264: error: Item "None" of "dict[Any, Any] | None" has no attribute "__delitem__"  [union-attr]
executorlib/interactive/executor.py:265: error: Item "None" of "dict[Any, Any] | None" has no attribute "__delitem__"  [union-attr]
executorlib/interactive/executor.py:266: error: Item "None" of "dict[Any, Any] | None" has no attribute "__delitem__"  [union-attr]
executorlib/interactive/executor.py:268: error: Unsupported target for indexed assignment ("dict[Any, Any] | None")  [index]
executorlib/interactive/executor.py:276: error: Argument "executor_kwargs" to "InteractiveExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:277: error: Argument "spawner" to "InteractiveExecutor" has incompatible type "type[MpiExecSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/interactive/executor.py:283: error: Argument "executor_kwargs" to "InteractiveStepExecutor" has incompatible type "dict[Any, Any] | None"; expected "dict[Any, Any]"  [arg-type]
executorlib/interactive/executor.py:284: error: Argument "spawner" to "InteractiveStepExecutor" has incompatible type "type[MpiExecSpawner]"; expected "BaseSpawner"  [arg-type]
executorlib/__init__.py:19: error: Need type annotation for "__all__" (hint: "__all__: list[<type>] = ...")  [var-annotated]
executorlib/__init__.py:100: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/__init__.py:100: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/__init__.py:121: error: Function "builtins.callable" is not valid as a type  [valid-type]
executorlib/__init__.py:121: note: Perhaps you meant "typing.Callable" instead of "callable"?
executorlib/__init__.py:172: error: Need type annotation for "default_resource_dict"  [var-annotated]
executorlib/__init__.py:189: error: Argument "max_workers" to "create_file_executor" has incompatible type "int | None"; expected "int"  [arg-type]
executorlib/__init__.py:191: error: Argument "max_cores" to "create_file_executor" has incompatible type "int | None"; expected "int"  [arg-type]
Found 126 errors in 17 files (checked 31 source files)