DevOps: Update the mypy pre-commit dependency (#246)

The requirement is updated to `mypy==0.930`. This allows us to move the
configuration from `tox.ini` to the `pyproject.toml` file. The config in
`.pre-commit-config.yaml` is also corrected as the include path did not
properly include the `src` starting folder.

The remaining configuration for `tox.ini` is also moved to the
`pyproject.toml` and deleted.

.pre-commit-config.yaml

@@ -28,14 +28,17 @@ repos:
         additional_dependencies: ['toml']
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.790
+    rev: v0.982
     hooks:
     -   id: mypy
-        args: [--config-file=tox.ini]
-        additional_dependencies: ['aio_pika~=6.6']
+        args: [--config-file=pyproject.toml]
+        additional_dependencies: [
+            'toml',
+            'types-pyyaml',
+        ]
         files: >
             (?x)^(
-                plumpy/.*py|
+                src/plumpy/.*py|
             )$
 
 -   repo: https://github.com/PyCQA/pylint

pyproject.toml

@@ -53,6 +53,7 @@ pre-commit = [
     'mypy==0.982',
     'pre-commit~=2.2',
     'pylint==2.12.2',
+    'types-pyyaml'
 ]
 tests = [
     'ipykernel==6.12.1',
@@ -83,6 +84,28 @@ include_trailing_comma = true
 line_length = 120
 multi_line_output = 3
 
+[tool.mypy]
+show_error_codes = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+
+[[tool.mypy.overrides]]
+module = 'test.*'
+check_untyped_defs = false
+
+[[tool.mypy.overrides]]
+module = [
+    'aio_pika.*',
+    'aiocontextvars.*',
+    'kiwipy.*',
+    'nest_asyncio.*',
+    'tblib.*',
+]
+ignore_missing_imports = true
+
 [tool.pylint.format]
 max-line-length = 120
 
@@ -118,3 +141,43 @@ column_limit = 120
 dedent_closing_brackets = true
 indent_dictionary_value = false
 split_arguments_when_comma_terminated = true
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py37
+
+[testenv]
+usedevelop = true
+
+[testenv:py{37,38,39,310}]
+description = Run the unit tests
+extras =
+    tests
+commands = pytest {posargs}
+
+[testenv:py{37,38,39,310}-pre-commit]
+description = Run the style checks and formatting
+extras =
+    pre-commit
+    tests
+commands = pre-commit run {posargs}
+
+[testenv:docs-{update,clean}]
+description = Build the documentation
+extras = docs
+whitelist_externals = rm
+commands =
+    clean: rm -rf docs/_build
+    sphinx-build -nW --keep-going -b {posargs:html} docs/source/ docs/_build/{posargs:html}
+
+[testenv:docs-live]
+description = Build the documentation and launch browser (with live updates)
+extras = docs
+deps = sphinx-autobuild
+commands =
+    sphinx-autobuild \
+        --re-ignore _build/.* \
+        --port 0 --open-browser \
+        -n -b {posargs:html} docs/source/ docs/_build/{posargs:html}
+"""

src/plumpy/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
+# mypy: disable-error-code=name-defined
 # pylint: disable=undefined-variable
-# type: ignore[name-defined]
 __version__ = '0.21.0'
 
 import logging
@@ -33,7 +33,7 @@
 # for more details
 class NullHandler(logging.Handler):
 
-    def emit(self, record):
+    def emit(self, record: logging.LogRecord) -> None:
         pass
 
 

src/plumpy/base/state_machine.py

@@ -76,12 +76,12 @@ def event(
     """A decorator to check for correct transitions, raising ``EventError`` on invalid transitions."""
     if from_states != '*':
         if inspect.isclass(from_states):
-            from_states = (from_states,)  # type: ignore
+            from_states = (from_states,)
         if not all(issubclass(state, State) for state in from_states):  # type: ignore
             raise TypeError(f'from_states: {from_states}')
     if to_states != '*':
         if inspect.isclass(to_states):
-            to_states = (to_states,)  # type: ignore
+            to_states = (to_states,)
         if not all(issubclass(state, State) for state in to_states):  # type: ignore
             raise TypeError(f'to_states: {to_states}')
 
@@ -111,7 +111,7 @@ def transition(self: Any, *a: Any, **kw: Any) -> Any:
         return transition
 
     if inspect.isfunction(from_states):
-        return wrapper(from_states)  # type: ignore
+        return wrapper(from_states)
 
     return wrapper
 
@@ -397,8 +397,8 @@ def _create_state_instance(self, state: Union[Hashable, State, Type[State]], *ar
         return state_cls(self, *args, **kwargs)
 
     def _ensure_state_class(self, state: Union[Hashable, Type[State]]) -> Type[State]:
-        if inspect.isclass(state) and issubclass(state, State):  # type: ignore
-            return cast(Type[State], state)
+        if inspect.isclass(state) and issubclass(state, State):
+            return state
 
         try:
             return self.get_states_map()[cast(Hashable, state)]  # pylint: disable=unsubscriptable-object

src/plumpy/events.py

@@ -23,7 +23,7 @@ def new_event_loop(*args: Any, **kwargs: Any) -> asyncio.AbstractEventLoop:
     raise NotImplementedError('this method is not implemented because `plumpy` uses a single reentrant loop')
 
 
-class PlumpyEventLoopPolicy(asyncio.DefaultEventLoopPolicy):  # type: ignore
+class PlumpyEventLoopPolicy(asyncio.DefaultEventLoopPolicy):
     """Custom event policy that always returns the same event loop that is made reentrant by ``nest_asyncio``."""
 
     _loop: Optional[asyncio.AbstractEventLoop] = None

src/plumpy/mixins.py

@@ -15,7 +15,7 @@ class ContextMixin(persistence.Savable):
     CONTEXT: str = '_context'
 
     def __init__(self, *args: Any, **kwargs: Any):
-        super().__init__(*args, **kwargs)  # type: ignore
+        super().__init__(*args, **kwargs)
         self._context: Optional[AttributesDict] = AttributesDict()
 
     @property

src/plumpy/persistence.py

@@ -73,7 +73,7 @@ def _bundle_constructor(loader: yaml.Loader, data: Any) -> Generator[Bundle, Non
 
 
 yaml.add_representer(Bundle, _bundle_representer)
-yaml.add_constructor(_BUNDLE_TAG, _bundle_constructor)
+yaml.add_constructor(_BUNDLE_TAG, _bundle_constructor)  # type: ignore[arg-type]
 
 
 class Persister(metaclass=abc.ABCMeta):
@@ -340,7 +340,7 @@ def delete_process_checkpoints(self, pid: PID_TYPE) -> None:
             del self._checkpoints[pid]
 
 
-SavableClsType = TypeVar('SavableClsType', bound='Type[Savable]')
+SavableClsType = TypeVar('SavableClsType', bound='Type[Savable]')  # type: ignore[name-defined]
 
 
 def auto_persist(*members: str) -> Callable[[SavableClsType], SavableClsType]:
@@ -650,5 +650,5 @@ def load_instance_state(self, saved_state: SAVED_STATE_TYPE, load_context: LoadS
         super().load_instance_state(saved_state, load_context)
         if self._callbacks:
             # typing says asyncio.Future._callbacks needs to be called, but in the python 3.7 code it is a simple list
-            for callback in self._callbacks:  # type: ignore
-                self.remove_done_callback(callback)
+            for callback in self._callbacks:
+                self.remove_done_callback(callback)  # type: ignore[arg-type]

src/plumpy/processes.py

@@ -72,7 +72,10 @@ class ProcessStateMachineMeta(abc.ABCMeta, state_machine.StateMachineMeta):
 
 
 # Make ProcessStateMachineMeta instances (classes) YAML - able
-yaml.representer.Representer.add_representer(ProcessStateMachineMeta, yaml.representer.Representer.represent_name)
+yaml.representer.Representer.add_representer(
+    ProcessStateMachineMeta,
+    yaml.representer.Representer.represent_name  # type: ignore[arg-type]
+)
 
 
 def ensure_not_closed(func: Callable[..., Any]) -> Callable[..., Any]:

src/plumpy/utils.py

@@ -171,7 +171,7 @@ def load_function(name: str, instance: Optional[Any] = None) -> Callable[..., An
     obj = load_object(name)
     if inspect.ismethod(obj):
         if instance is not None:
-            return obj.__get__(instance, instance.__class__)
+            return obj.__get__(instance, instance.__class__)  # type: ignore[attr-defined]
 
         return obj