Devops: Update pyproject.toml configuration (#6085)

Added stricter rules for `mypy` and `pytest`. Suggestions taken after
automated analysis by the following tool:
https://learn.scientific-python.org/development/guides/repo-review/

aiida/cmdline/commands/cmd_config.py

@@ -8,6 +8,8 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """`verdi config` command."""
+from __future__ import annotations
+
 import json
 from pathlib import Path
 import textwrap
@@ -40,7 +42,7 @@ def verdi_config_list(ctx, prefix, description: bool):
     from aiida.manage.configuration import Config, Profile
 
     config: Config = ctx.obj.config
-    profile: Profile = ctx.obj.get('profile', None)
+    profile: Profile | None = ctx.obj.get('profile', None)
 
     if not profile:
         echo.echo_warning('no profiles configured: run `verdi setup` to create one')
@@ -78,7 +80,7 @@ def verdi_config_show(ctx, option):
     from aiida.manage.configuration.options import NO_DEFAULT
 
     config: Config = ctx.obj.config
-    profile: Profile = ctx.obj.profile
+    profile: Profile | None = ctx.obj.profile
 
     dct = {
         'schema': option.schema,
@@ -124,7 +126,7 @@ def verdi_config_set(ctx, option, value, globally, append, remove):
         echo.echo_critical('Cannot flag both append and remove')
 
     config: Config = ctx.obj.config
-    profile: Profile = ctx.obj.profile
+    profile: Profile | None = ctx.obj.profile
 
     if option.global_only:
         globally = True
@@ -164,7 +166,7 @@ def verdi_config_unset(ctx, option, globally):
     from aiida.manage.configuration import Config, Profile
 
     config: Config = ctx.obj.config
-    profile: Profile = ctx.obj.profile
+    profile: Profile | None = ctx.obj.profile
 
     if option.global_only:
         globally = True

aiida/cmdline/groups/verdi.py

@@ -62,7 +62,7 @@ class VerdiCommandGroup(click.Group):
     def add_verbosity_option(cmd: click.Command):
         """Apply the ``verbosity`` option to the command, which is common to all ``verdi`` commands."""
         # Only apply the option if it hasn't been already added in a previous call.
-        if cmd is not None and 'verbosity' not in [param.name for param in cmd.params]:
+        if 'verbosity' not in [param.name for param in cmd.params]:
             cmd = options.VERBOSITY()(cmd)
 
         return cmd

aiida/common/lang.py

@@ -72,7 +72,7 @@ def wrapped_fn(self, *args, **kwargs):  # pylint: disable=missing-docstring
         else:
             wrapped_fn = func
 
-        return wrapped_fn  # type: ignore
+        return wrapped_fn  # type: ignore[return-value]
 
     return wrap
 

aiida/common/progress_reporter.py

@@ -156,7 +156,7 @@ def set_progress_reporter(reporter: Optional[Type[ProgressReporterAbstract]] = N
     if reporter is None:
         PROGRESS_REPORTER = ProgressReporterNull
     elif kwargs:
-        PROGRESS_REPORTER = partial(reporter, **kwargs)  # type: ignore
+        PROGRESS_REPORTER = partial(reporter, **kwargs)  # type: ignore[assignment]
     else:
         PROGRESS_REPORTER = reporter
 

aiida/engine/daemon/client.py

@@ -713,8 +713,7 @@ def _start_daemon(self, number_workers: int = 1, foreground: bool = False) -> No
         pidfile.create(os.getpid())
 
         # Configure the logger
-        loggerconfig = None
-        loggerconfig = loggerconfig or arbiter.loggerconfig or None
+        loggerconfig = arbiter.loggerconfig or None
         configure_logger(circus_logger, loglevel, logoutput, loggerconfig)
 
         # Main loop

aiida/engine/launch.py

@@ -17,6 +17,7 @@
 from .processes.builder import ProcessBuilder
 from .processes.functions import FunctionProcess
 from .processes.process import Process
+from .runners import ResultAndPk
 from .utils import instantiate_process, is_process_scoped  # pylint: disable=no-name-in-module
 
 __all__ = ('run', 'run_get_pk', 'run_get_node', 'submit')
@@ -60,7 +61,7 @@ def run_get_node(process: TYPE_RUN_PROCESS, *args: Any, **inputs: Any) -> Tuple[
     return runner.run_get_node(process, *args, **inputs)
 
 
-def run_get_pk(process: TYPE_RUN_PROCESS, *args: Any, **inputs: Any) -> Tuple[Dict[str, Any], int]:
+def run_get_pk(process: TYPE_RUN_PROCESS, *args: Any, **inputs: Any) -> ResultAndPk:
     """Run the process with the supplied inputs in a local runner that will block until the process is completed.
 
     :param process: the process class, instance, builder or function to run

aiida/engine/processes/builder.py

@@ -79,7 +79,7 @@ def fgetter(self, name=name):
                     return self._data.get(name)
             elif port.has_default():
 
-                def fgetter(self, name=name, default=port.default):  # type: ignore # pylint: disable=cell-var-from-loop
+                def fgetter(self, name=name, default=port.default):  # type: ignore[misc] # pylint: disable=cell-var-from-loop
                     return self._data.get(name, default)
             else:
 

aiida/engine/processes/calcjobs/calcjob.py

@@ -517,7 +517,7 @@ def get_state_classes(cls) -> Dict[Hashable, Type[plumpy.process_states.State]]:
 
     @property
     def node(self) -> orm.CalcJobNode:
-        return super().node  # type: ignore
+        return super().node  # type: ignore[return-value]
 
     @override
     def on_terminated(self) -> None:
@@ -616,7 +616,7 @@ def _perform_dry_run(self):
                 calc_info = self.presubmit(folder)
                 transport.chdir(folder.abspath)
                 upload_calculation(self.node, transport, calc_info, folder, inputs=self.inputs, dry_run=True)
-                self.node.dry_run_info = {  # type: ignore
+                self.node.dry_run_info = {  # type: ignore[attr-defined]
                     'folder': folder.abspath,
                     'script_filename': self.node.get_option('submit_script_filename')
                 }
@@ -768,7 +768,7 @@ def parse_scheduler_output(self, retrieved: orm.Node) -> Optional[ExitCode]:
             return None
 
         if exit_code is not None and not isinstance(exit_code, ExitCode):
-            args = (scheduler.__class__.__name__, type(exit_code))
+            args = (scheduler.__class__.__name__, type(exit_code))  # type: ignore[unreachable]
             raise ValueError('`{}.parse_output` returned neither an `ExitCode` nor None, but: {}'.format(*args))
 
         return exit_code
@@ -797,7 +797,7 @@ def parse_retrieved_output(self, retrieved_temporary_folder: Optional[str] = Non
                 break
 
         if exit_code is not None and not isinstance(exit_code, ExitCode):
-            args = (parser_class.__name__, type(exit_code))
+            args = (parser_class.__name__, type(exit_code))  # type: ignore[unreachable]
             raise ValueError('`{}.parse` returned neither an `ExitCode` nor None, but: {}'.format(*args))
 
         return exit_code
@@ -894,7 +894,7 @@ def presubmit(self, folder: Folder) -> CalcInfo:
         # Set resources, also with get_default_mpiprocs_per_machine
         resources = self.node.get_option('resources')
         scheduler.preprocess_resources(resources or {}, computer.get_default_mpiprocs_per_machine())
-        job_tmpl.job_resource = scheduler.create_job_resource(**resources)  # type: ignore
+        job_tmpl.job_resource = scheduler.create_job_resource(**resources)  # type: ignore[arg-type]
 
         subst_dict = {'tot_num_mpiprocs': job_tmpl.job_resource.get_tot_num_mpiprocs()}
 

aiida/engine/processes/functions.py

@@ -81,7 +81,7 @@ def get_stack_size(size: int = 2) -> int:  # type: ignore[return]
         for size in itertools.count(size, 8):  # pylint: disable=redefined-argument-from-local
             frame = frame.f_back.f_back.f_back.f_back.f_back.f_back.f_back.f_back  # type: ignore[assignment,union-attr]
     except AttributeError:
-        while frame:
+        while frame:  # type: ignore[truthy-bool]
             frame = frame.f_back  # type: ignore[assignment]
             size += 1
         return size - 1
@@ -234,6 +234,7 @@ def run_get_pk(*args, **kwargs) -> tuple[dict[str, t.Any] | None, int]:
 
             """
             result, node = run_get_node(*args, **kwargs)
+            assert node.pk is not None
             return result, node.pk
 
         @functools.wraps(function)
@@ -323,10 +324,13 @@ def build(func: FunctionType, node_class: t.Type['ProcessNode']) -> t.Type['Func
 
         """
         # pylint: disable=too-many-statements
-        if not issubclass(node_class, ProcessNode) or not issubclass(node_class, FunctionCalculationMixin):
+        if (
+            not issubclass(node_class, ProcessNode) or  # type: ignore[redundant-expr]
+            not issubclass(node_class, FunctionCalculationMixin)  # type: ignore[unreachable]
+        ):
             raise TypeError('the node_class should be a sub class of `ProcessNode` and `FunctionCalculationMixin`')
 
-        signature = inspect.signature(func)
+        signature = inspect.signature(func)  # type: ignore[unreachable]
 
         args: list[str] = []
         varargs: str | None = None
@@ -519,7 +523,7 @@ def get_or_create_db_record(cls) -> 'ProcessNode':
     def __init__(self, *args, **kwargs) -> None:
         if kwargs.get('enable_persistence', False):
             raise RuntimeError('Cannot persist a function process')
-        super().__init__(enable_persistence=False, *args, **kwargs)  # type: ignore
+        super().__init__(enable_persistence=False, *args, **kwargs)  # type: ignore[misc]
 
     @property
     def process_class(self) -> t.Callable[..., t.Any]:
@@ -586,11 +590,11 @@ def run(self) -> 'ExitCode' | None:
 
         result = self._func(*args, **kwargs)
 
-        if result is None or isinstance(result, ExitCode):
-            return result
+        if result is None or isinstance(result, ExitCode):  # type: ignore[redundant-expr]
+            return result  # type: ignore[unreachable]
 
-        if isinstance(result, Data):
-            self.out(self.SINGLE_OUTPUT_LINKNAME, result)
+        if isinstance(result, Data):  # type: ignore[unreachable]
+            self.out(self.SINGLE_OUTPUT_LINKNAME, result)  # type: ignore[unreachable]
         elif isinstance(result, collections.abc.Mapping):
             for name, value in result.items():
                 self.out(name, value)

aiida/engine/processes/process.py

@@ -251,7 +251,6 @@ def metadata(self) -> AttributeDict:
 
         """
         try:
-            assert self.inputs is not None
             return self.inputs.metadata
         except (AssertionError, AttributeError):
             return AttributeDict()
@@ -297,7 +296,6 @@ def get_provenance_inputs_iterator(self) -> Iterator[Tuple[str, Union[InputPort,
 
         :rtype: filter
         """
-        assert self.inputs is not None
         return filter(lambda kv: not kv[0].startswith('_'), self.inputs.items())
 
     @override
@@ -321,7 +319,7 @@ def load_instance_state(
         super().load_instance_state(saved_state, load_context)
 
         if self.SaveKeys.CALC_ID.value in saved_state:
-            self._node = orm.load_node(saved_state[self.SaveKeys.CALC_ID.value])  # type: ignore
+            self._node = orm.load_node(saved_state[self.SaveKeys.CALC_ID.value])  # type: ignore[assignment]
             self._pid = self.node.pk  # pylint: disable=attribute-defined-outside-init
         else:
             self._pid = self._create_and_setup_db_record()  # pylint: disable=attribute-defined-outside-init
@@ -429,7 +427,7 @@ def on_entered(self, from_state: Optional[plumpy.process_states.State]) -> None:
         except ValueError:  # pylint: disable=try-except-raise
             raise
         finally:
-            self.node.set_process_state(self._state.LABEL)  # type: ignore
+            self.node.set_process_state(self._state.LABEL)  # type: ignore[arg-type]
 
         self._save_checkpoint()
         set_process_state_change_timestamp(self)
@@ -464,7 +462,7 @@ def on_except(self, exc_info: Tuple[Any, Exception, TracebackType]) -> None:
         self.report(''.join(traceback.format_exception(*exc_info)))
 
     @override
-    def on_finish(self, result: Union[int, ExitCode], successful: bool) -> None:
+    def on_finish(self, result: Union[int, ExitCode, None], successful: bool) -> None:
         """ Set the finish status on the process node.
 
         :param result: result of the process
@@ -559,7 +557,7 @@ def get_parent_calc(self) -> Optional[orm.ProcessNode]:
         if self._parent_pid is None:
             return None
 
-        return orm.load_node(pk=self._parent_pid)  # type: ignore
+        return orm.load_node(pk=self._parent_pid)  # type: ignore[return-value]
 
     @classmethod
     def build_process_type(cls) -> str:
@@ -702,7 +700,6 @@ def _setup_db_record(self) -> None:
         In addition, the parent calculation will be setup with a CALL link if applicable and all inputs will be
         linked up as well.
         """
-        assert self.inputs is not None
         assert not self.node.is_sealed, 'process node cannot be sealed when setting up the database record'
 
         # Store important process attributes in the node proxy
@@ -731,9 +728,6 @@ def _setup_version_info(self) -> None:
         """Store relevant plugin version information."""
         from aiida.plugins.entry_point import format_entry_point_string
 
-        if self.inputs is None:
-            return
-
         version_info = self.runner.plugin_version_provider.get_version_info(self.__class__)
 
         for key, monitor in self.inputs.get('monitors', {}).items():
@@ -836,7 +830,6 @@ def _flat_inputs(self) -> Dict[str, Any]:
         :return: flat dictionary of parsed inputs
 
         """
-        assert self.inputs is not None
         inputs = {key: value for key, value in self.inputs.items() if key != self.spec().metadata_key}
         return dict(self._flatten_inputs(self.spec().inputs, inputs))
 
@@ -890,7 +883,9 @@ def _flatten_inputs(
                 items.extend(sub_items)
             return items
 
-        assert (port is None) or (isinstance(port, InputPort) and (port.is_metadata or port.non_db))
+        assert (port is None) or (
+            isinstance(port, InputPort) and (port.is_metadata or port.non_db)  # type: ignore[redundant-expr]
+        )
         return []
 
     def _flatten_outputs(

aiida/engine/processes/utils.py

@@ -14,12 +14,14 @@ def prune_mapping(value):
     :param value: A nested mapping of port values.
     :return: The same mapping but without any nested namespace that is completely empty.
     """
-    if isinstance(value, Mapping) and not isinstance(value, Node):
+    if isinstance(value, Mapping) and not isinstance(value, Node):  # type: ignore[unreachable]
         result = {}
         for key, sub_value in value.items():
             pruned = prune_mapping(sub_value)
             # If `pruned` is an "empty'ish" mapping and not an instance of `Node`, skip it, otherwise keep it.
-            if not (isinstance(pruned, Mapping) and not pruned and not isinstance(pruned, Node)):
+            if not (
+                isinstance(pruned, Mapping) and not pruned and not isinstance(pruned, Node)  # type: ignore[unreachable]
+            ):
                 result[key] = pruned
         return result
 

aiida/engine/processes/workchains/restart.py

@@ -427,7 +427,8 @@ def _wrap_bare_dict_inputs(self, port_namespace: 'PortNamespace', inputs: Dict[s
                 continue
 
             port = port_namespace[key]
-            valid_types = port.valid_type if isinstance(port.valid_type, (list, tuple)) else (port.valid_type,)
+            valid_types = port.valid_type \
+                if isinstance(port.valid_type, (list, tuple)) else (port.valid_type,)  # type: ignore[redundant-expr]
 
             if isinstance(port, PortNamespace):
                 wrapped[key] = self._wrap_bare_dict_inputs(port, value)

aiida/engine/processes/workchains/workchain.py

@@ -139,7 +139,7 @@ def spec(cls) -> WorkChainSpec:
 
     @property
     def node(self) -> WorkChainNode:
-        return super().node  # type: ignore
+        return super().node  # type: ignore[return-value]
 
     @property
     def ctx(self) -> AttributeDict:
@@ -408,7 +408,7 @@ def _on_awaitable_finished(self, awaitable: Awaitable) -> None:
         if awaitable.outputs:
             value = {entry.link_label: entry.node for entry in node.base.links.get_outgoing()}
         else:
-            value = node  # type: ignore
+            value = node  # type: ignore[assignment]
 
         self._resolve_awaitable(awaitable, value)
 

aiida/engine/runners.py

@@ -9,6 +9,8 @@
 ###########################################################################
 # pylint: disable=global-statement
 """Runners that can run and submit processes."""
+from __future__ import annotations
+
 import asyncio
 import functools
 import logging
@@ -43,7 +45,7 @@ class ResultAndNode(NamedTuple):
 
 class ResultAndPk(NamedTuple):
     result: Dict[str, Any]
-    pk: int
+    pk: int | None
 
 
 TYPE_RUN_PROCESS = Union[Process, Type[Process], ProcessBuilder]  # pylint: disable=invalid-name

aiida/manage/caching.py

@@ -40,7 +40,7 @@ def __init__(self):
 
     def clear(self):
         """Clear caching overrides."""
-        self.__init__()  # type: ignore
+        self.__init__()  # type: ignore[misc]
 
     def enable_all(self):
         self._default_all = 'enable'