Pre-commit: move yapf and mypy config to pyproject.toml

The libraries `yapf` and `mypy` support the `pyproject.toml` file for
their configuration starting from v0.31 and v0.9, respectively.

Co-authored-by: Jason Eu <morty.yu@yahoo.com>

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         ]
 
 -   repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.30.0
+    rev: v0.31.0
     hooks:
     -   id: yapf
         name: yapf
@@ -28,6 +28,7 @@ repos:
                 docs/.*|
             )$
         args: ['-i']
+        additional_dependencies: ['toml']
 
 -   repo: local
 

aiida/engine/daemon/execmanager.py

@@ -77,7 +77,7 @@ def upload_calculation(
     link_label = 'remote_folder'
     if node.get_outgoing(RemoteData, link_label_filter=link_label).first():
         EXEC_LOGGER.warning(f'CalcJobNode<{node.pk}> already has a `{link_label}` output: skipping upload')
-        return calc_info
+        return
 
     computer = node.computer
 

aiida/engine/processes/calcjobs/manager.py

@@ -263,7 +263,7 @@ class JobManager:
 
     def __init__(self, transport_queue: 'TransportQueue') -> None:
         self._transport_queue = transport_queue
-        self._job_lists: Dict[Hashable, 'JobInfo'] = {}
+        self._job_lists: Dict[Hashable, 'JobsList'] = {}
 
     def get_jobs_list(self, authinfo: AuthInfo) -> JobsList:
         """Get or create a new `JobLists` instance for the given authinfo.

aiida/manage/configuration/profile.py

@@ -21,6 +21,7 @@
 
 if TYPE_CHECKING:
     from aiida.repository import Repository  # pylint: disable=ungrouped-imports
+    from aiida.repository.backend import DiskObjectStoreRepositoryBackend
 
 __all__ = ('Profile',)
 
@@ -130,12 +131,16 @@ def __init__(self, name, attributes, from_config=False):
 
     def get_repository(self) -> 'Repository':
         """Return the repository configured for this profile."""
-        from disk_objectstore import Container
         from aiida.repository import Repository
+        backend = self.get_repository_backend()
+        return Repository(backend=backend)
+
+    def get_repository_backend(self) -> 'DiskObjectStoreRepositoryBackend':
+        """Return the backend of the repository configured for this profile."""
+        from disk_objectstore import Container
         from aiida.repository.backend import DiskObjectStoreRepositoryBackend
         container = Container(self.repository_path / 'container')
-        backend = DiskObjectStoreRepositoryBackend(container=container)
-        return Repository(backend=backend)
+        return DiskObjectStoreRepositoryBackend(container=container)
 
     @property
     def uuid(self):

aiida/manage/manager.py

@@ -158,6 +158,8 @@ def _load_backend(self, schema_check: bool = True, repository_check: bool = True
         elif backend_type == BACKEND_SQLA:
             from aiida.orm.implementation.sqlalchemy.backend import SqlaBackend
             self._backend = SqlaBackend()
+        else:
+            raise AssertionError('Could not load the backend.')
 
         # Reconfigure the logging with `with_orm=True` to make sure that profile specific logging configuration options
         # are taken into account and the `DbLogHandler` is configured.
@@ -206,7 +208,7 @@ def get_backend(self) -> 'Backend':
 
         """
         if self._backend is None:
-            self._load_backend()
+            return self._load_backend()
 
         return self._backend
 
@@ -269,7 +271,7 @@ def create_communicator(
             # used by verdi status to get a communicator without needing to load the dbenv
             from aiida.common import json
             encoder = functools.partial(json.dumps, encoding='utf-8')
-            decoder = json.loads
+            decoder = json.loads  # type: ignore[assignment]
 
         return kiwipy.rmq.RmqThreadCommunicator.connect(
             connection_params={'url': profile.get_rmq_url()},
@@ -289,14 +291,18 @@ def get_daemon_client(self) -> 'DaemonClient':
         """Return the daemon client for the current profile.
 
         :return: the daemon client
-
-        :raises aiida.common.MissingConfigurationError: if the configuration file cannot be found
-        :raises aiida.common.ProfileConfigurationError: if the given profile does not exist
         """
+        from aiida.common import ConfigurationError
         from aiida.engine.daemon.client import DaemonClient
 
+        profile = self.get_profile()
+        if profile is None:
+            raise ConfigurationError(
+                'Could not determine the current profile. Consider loading a profile using `aiida.load_profile()`.'
+            )
+
         if self._daemon_client is None:
-            self._daemon_client = DaemonClient(self.get_profile())
+            self._daemon_client = DaemonClient(profile)
 
         return self._daemon_client
 

aiida/orm/nodes/node.py

@@ -207,7 +207,7 @@ def validate_storability(self) -> None:
     def class_node_type(cls) -> str:
         """Returns the node type of this node (sub) class."""
         # pylint: disable=no-self-argument,no-member
-        return cls._plugin_type_string
+        return cls._plugin_type_string  # type: ignore[attr-defined]
 
     @property
     def logger(self) -> Optional[Logger]:
@@ -324,7 +324,7 @@ def computer(self, computer: Optional[Computer]) -> None:
         if computer is not None:
             computer = computer.backend_entity
 
-        self.backend_entity.computer = computer
+        self.backend_entity.computer = computer  # type: ignore[misc] # See: https://github.com/python/mypy/issues/4165
 
     @property
     def user(self) -> User:
@@ -345,7 +345,8 @@ def user(self, user: User) -> None:
             raise exceptions.ModificationNotAllowed('cannot set the user on a stored node')
 
         type_check(user, User)
-        self.backend_entity.user = user.backend_entity
+        # See: https://github.com/python/mypy/issues/4165
+        self.backend_entity.user = user.backend_entity  # type: ignore[misc]
 
     @property
     def ctime(self) -> datetime.datetime:
@@ -507,7 +508,7 @@ def get_stored_link_triples(
         :param link_direction: `incoming` or `outgoing` to get the incoming or outgoing links, respectively.
         :param only_uuid: project only the node UUID instead of the instance onto the `NodeTriple.node` entries
         """
-        if not isinstance(link_type, tuple):
+        if isinstance(link_type, LinkType):
             link_type = (link_type,)
 
         if link_type and not all([isinstance(t, LinkType) for t in link_type]):
@@ -565,7 +566,7 @@ def get_incoming(
         """
         assert self._incoming_cache is not None, 'incoming_cache not initialised'
 
-        if not isinstance(link_type, tuple):
+        if isinstance(link_type, LinkType):
             link_type = (link_type,)
 
         if self.is_stored:

aiida/tools/graph/graph_traversers.py

@@ -250,7 +250,7 @@ def traverse_graph(
     elif missing_pks and missing_callback is not None:
         missing_callback(missing_pks)
 
-    rules = []
+    rules = []  # type: List[UpdateRule|RuleSaveWalkers|RuleSetWalkers]
     basket = Basket(nodes=existing_pks)
 
     # When max_iterations is finite, the order of traversal may affect the result

aiida/tools/groups/paths.py

@@ -184,7 +184,7 @@ def is_virtual(self) -> bool:
 
     def get_or_create_group(self) -> Tuple[orm.Group, bool]:
         """Return the concrete group associated with this path or, create it, if it does not already exist."""
-        return self.cls.objects.get_or_create(label=self.path)
+        return self.cls.objects.get_or_create(label=self.path)  # type: ignore[attr-defined]
 
     def delete_group(self):
         """Delete the concrete group associated with this path.
@@ -196,7 +196,7 @@ def delete_group(self):
             raise GroupNotFoundError(self)
         if len(ids) > 1:
             raise GroupNotUniqueError(self)
-        self.cls.objects.delete(ids[0])
+        self.cls.objects.delete(ids[0])  # type: ignore[attr-defined]
 
     @property
     def children(self) -> Iterator['GroupPath']:

aiida/tools/importexport/archive/migrators.py

@@ -47,7 +47,7 @@ def get_migrator(file_format: str) -> Type['ArchiveMigratorAbstract']:
             f'Can only migrate in the formats: {tuple(migrators.keys())}, please specify one for "file_format".'
         )
 
-    return cast(Type[ArchiveMigratorAbstract], migrators[file_format])
+    return cast(Type[ArchiveMigratorAbstract], migrators[file_format])  # type: ignore[index]
 
 
 class ArchiveMigratorAbstract(ABC):

aiida/tools/importexport/common/config.py

@@ -9,6 +9,7 @@
 ###########################################################################
 # pylint: disable=invalid-name
 """ Configuration file for AiiDA Import/Export module """
+from typing import Dict
 from enum import Enum
 from aiida.orm import Computer, Group, Node, User, Log, Comment
 
@@ -105,7 +106,8 @@ class ExportFileFormat(str, Enum):
         'dbnode': 'dbnode_id',
         'user': 'user_id'
     }
-}
+}  # type: Dict[str, Dict[str, str]]
+
 # As above but the opposite procedure
 model_fields_to_file_fields = {
     NODE_ENTITY_NAME: {
@@ -124,7 +126,7 @@ class ExportFileFormat(str, Enum):
         'dbnode_id': 'dbnode',
         'user_id': 'user'
     }
-}
+}  # type: Dict[str, Dict[str, str]]
 
 
 def get_all_fields_info():

aiida/tools/importexport/dbexport/__init__.py

@@ -586,7 +586,7 @@ def _write_node_repositories(
 
             profile = get_manager().get_profile()
             assert profile is not None, 'profile not loaded'
-            container_profile = profile.get_repository().backend.container
+            container_profile = profile.get_repository_backend().container
 
             # This should be done more effectively, starting by not having to load the node. Either the repository
             # metadata should be collected earlier when the nodes themselves are already exported or a single separate

aiida/tools/importexport/dbimport/backends/common.py

@@ -45,7 +45,7 @@ def _copy_node_repositories(*, repository_metadatas: List[Dict], reader: Archive
 
     profile = get_manager().get_profile()
     assert profile is not None, 'profile not loaded'
-    container_profile = profile.get_repository().backend.container
+    container_profile = profile.get_repository_backend().container
 
     def collect_hashkeys(objects, hashkeys):
         for obj in objects.values():
@@ -66,7 +66,7 @@ def collect_hashkeys(objects, hashkeys):
         container_export.export(set(hashkeys), container_profile, compress=True, callback=callback)
 
 
-def _make_import_group(*, group: Optional[ImportGroup], node_pks: List[int]) -> ImportGroup:
+def _make_import_group(*, group: Optional[Group], node_pks: List[int]) -> Optional[Group]:
     """Make an import group containing all imported nodes.
 
     :param group: Use an existing group
@@ -79,7 +79,7 @@ def _make_import_group(*, group: Optional[ImportGroup], node_pks: List[int]) ->
         return group
 
     # If user specified a group, import all things into it
-    if not group:
+    if group is None:
         # Get an unique name for the import group, based on the current (local) time
         basename = timezone.localtime(timezone.now()).strftime('%Y%m%d-%H%M%S')
         counter = 0

docs/source/nitpick-exceptions

@@ -62,6 +62,7 @@ py:class ProcessSpec
 py:class Port
 py:class PortNamespace
 py:class Repository
+py:class DiskObjectStoreRepositoryBackend
 py:class Runner
 py:class Transport
 py:class TransportQueue

pyproject.toml

@@ -71,6 +71,46 @@ markers = [
     "sphinx: set parameters for the sphinx `app` fixture"
 ]
 
+[tool.yapf]
+based_on_style = "google"
+column_limit = 120
+dedent_closing_brackets = true
+coalesce_brackets = true
+align_closing_bracket_with_visual_indent = true
+split_arguments_when_comma_terminated = true
+indent_dictionary_value = false
+
+[tool.mypy]
+show_error_codes = true
+check_untyped_defs = true
+scripts_are_modules = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+
+[[tool.mypy.overrides]]
+module = [
+    'tqdm.*',
+    'circus.*',
+    'disk_objectstore.*',
+    'django.*',
+    'sqlalchemy.*',
+    'numpy.*',
+    'kiwipy.*',
+    'scipy.*',
+    'wrapt.*',
+    'ruamel.*',
+    'pymatgen',
+]
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = 'aiida'
+follow_imports = "skip"
+
+[[tool.mypy.overrides]]
+module = 'tests'
+check_untyped_defs = false
+
 [tool.tox]
 legacy_tox_ini = """
 [tox]

setup.json

@@ -95,7 +95,7 @@
         ],
         "pre-commit": [
             "astroid<2.5",
-            "mypy==0.790",
+            "mypy==0.910",
             "packaging==20.3",
             "pre-commit~=2.2",
             "pylint~=2.5.0",