Dependencies: Update requirement mypy~=1.7 (#6188)

This allows to get rid of many exclude statements since those
corresponded to bugs in `mypy` that have now been fixed.

aiida/engine/processes/process.py

@@ -366,7 +366,7 @@ def kill(self, msg: Union[str, None] = None) -> Union[bool, plumpy.futures.Futur
 
                 def done(done_future: plumpy.futures.Future):
                     is_all_killed = all(done_future.result())
-                    result.set_result(is_all_killed)  # type: ignore[union-attr]
+                    result.set_result(is_all_killed)
 
                 kill_future.add_done_callback(done)
 

aiida/engine/processes/workchains/utils.py

@@ -112,9 +112,7 @@ def wrapper(wrapped, instance, args, kwargs):
         # When the handler will be called by the `BaseRestartWorkChain` it will pass the node as the only argument
         node = args[0]
 
-        if exit_codes is not None and node.exit_status not in [
-            exit_code.status for exit_code in exit_codes  # type: ignore[union-attr]
-        ]:
+        if exit_codes is not None and node.exit_status not in [exit_code.status for exit_code in exit_codes]:
             result = None
         else:
             result = wrapped(*args, **kwargs)

aiida/engine/transports.py

@@ -84,7 +84,7 @@ async def transport_task(transport_queue, authinfo):
 
             def do_open():
                 """ Actually open the transport """
-                if transport_request and transport_request.count > 0:
+                if transport_request.count > 0:
                     # The user still wants the transport so open it
                     _LOGGER.debug('Transport request opening transport for %s', authinfo)
                     try:

aiida/orm/nodes/data/singlefile.py

@@ -78,7 +78,7 @@ def open(self, path: str, mode: t.Literal['rb']) -> t.Iterator[t.BinaryIO]:
     def open(self, path: None, mode: t.Literal['rb']) -> t.Iterator[t.BinaryIO]:
         ...
 
-    @contextlib.contextmanager  # type: ignore[misc]
+    @contextlib.contextmanager
     def open(self, path: str | None = None, mode: t.Literal['r', 'rb'] = 'r') -> t.Iterator[t.BinaryIO | t.TextIO]:
         """Return an open file handle to the content of this data node.
 

aiida/storage/psql_dos/backend.py

@@ -214,9 +214,8 @@ def _clear(self) -> None:
 
             with self.transaction() as session:
                 session.execute(
-                    DbSetting.__table__.update().where(
-                        DbSetting.key == REPOSITORY_UUID_KEY  # type: ignore[attr-defined]
-                    ).values(val=repository_uuid)
+                    DbSetting.__table__.update().where(DbSetting.key == REPOSITORY_UUID_KEY
+                                                       ).values(val=repository_uuid)
                 )
 
     def get_repository(self) -> 'DiskObjectStoreRepositoryBackend':
@@ -358,17 +357,14 @@ def delete_nodes_and_connections(self, pks_to_delete: Sequence[int]) -> None:
 
         session = self.get_session()
         # Delete the membership of these nodes to groups.
-        session.query(DbGroupNode).filter(DbGroupNode.dbnode_id.in_(list(pks_to_delete))  # type: ignore[attr-defined]
+        session.query(DbGroupNode).filter(DbGroupNode.dbnode_id.in_(list(pks_to_delete))
                                           ).delete(synchronize_session='fetch')
         # Delete the links coming out of the nodes marked for deletion.
-        session.query(DbLink).filter(DbLink.input_id.in_(list(pks_to_delete))
-                                     ).delete(synchronize_session='fetch')  # type: ignore[attr-defined]
+        session.query(DbLink).filter(DbLink.input_id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
         # Delete the links pointing to the nodes marked for deletion.
-        session.query(DbLink).filter(DbLink.output_id.in_(list(pks_to_delete))
-                                     ).delete(synchronize_session='fetch')  # type: ignore[attr-defined]
+        session.query(DbLink).filter(DbLink.output_id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
         # Delete the actual nodes
-        session.query(DbNode).filter(DbNode.id.in_(list(pks_to_delete))
-                                     ).delete(synchronize_session='fetch')  # type: ignore[attr-defined]
+        session.query(DbNode).filter(DbNode.id.in_(list(pks_to_delete))).delete(synchronize_session='fetch')
 
     def get_backend_entity(self, model: base.Base) -> BackendEntity:
         """
@@ -386,10 +382,9 @@ def set_global_variable(
 
         session = self.get_session()
         with (nullcontext() if self.in_transaction else self.transaction()):
-            if session.query(DbSetting).filter(DbSetting.key == key).count():  # type: ignore[attr-defined]
+            if session.query(DbSetting).filter(DbSetting.key == key).count():
                 if overwrite:
-                    session.query(DbSetting).filter(DbSetting.key == key
-                                                    ).update(dict(val=value))  # type: ignore[attr-defined]
+                    session.query(DbSetting).filter(DbSetting.key == key).update(dict(val=value))
                 else:
                     raise ValueError(f'The setting {key} already exists')
             else:
@@ -400,7 +395,7 @@ def get_global_variable(self, key: str) -> Union[None, str, int, float]:
 
         session = self.get_session()
         with (nullcontext() if self.in_transaction else self.transaction()):
-            setting = session.query(DbSetting).filter(DbSetting.key == key).one_or_none()  # type: ignore[attr-defined]
+            setting = session.query(DbSetting).filter(DbSetting.key == key).one_or_none()
             if setting is None:
                 raise KeyError(f'No setting found with key {key}')
             return setting.val

aiida/storage/psql_dos/migrations/utils/provenance_redesign.py

@@ -126,9 +126,8 @@ def migrate_infer_calculation_entry_point(alembic_op):
                 fallback_cases.append([uuid, type_string, entry_point_string])
 
         connection.execute(
-            DbNode.update().where(
-                DbNode.c.type == alembic_op.inline_literal(type_string)  # type: ignore[attr-defined]
-            ).values(process_type=alembic_op.inline_literal(entry_point_string))
+            DbNode.update().where(DbNode.c.type == alembic_op.inline_literal(type_string)
+                                  ).values(process_type=alembic_op.inline_literal(entry_point_string))
         )
 
     if fallback_cases:

aiida/storage/psql_dos/migrations/versions/12536798d4d3_trajectory_symbols_to_attribute.py

@@ -50,15 +50,15 @@ def upgrade():
         column('attributes', JSONB),
     )
 
-    nodes = connection.execute(  # type: ignore[var-annotated]
+    nodes = connection.execute(
         select(DbNode.c.id,
                DbNode.c.uuid).where(DbNode.c.type == op.inline_literal('node.data.array.trajectory.TrajectoryData.'))
     ).fetchall()
 
     for pk, uuid in nodes:
         symbols = load_numpy_array_from_repository(repo_path, uuid, 'symbols').tolist()
         connection.execute(
-            DbNode.update().where(DbNode.c.id == pk).values(  # type: ignore[attr-defined]
+            DbNode.update().where(DbNode.c.id == pk).values(
                 attributes=func.jsonb_set(DbNode.c.attributes, op.inline_literal('{"symbols"}'), cast(symbols, JSONB))
             )
         )

aiida/storage/psql_dos/migrations/versions/ce56d84bcc35_delete_trajectory_symbols_array.py

@@ -45,7 +45,7 @@ def upgrade():
         column('attributes', JSONB),
     )
 
-    nodes = connection.execute(  # type: ignore[var-annotated]
+    nodes = connection.execute(
         select(DbNode.c.id,
                DbNode.c.uuid).where(DbNode.c.type == op.inline_literal('node.data.array.trajectory.TrajectoryData.'))
     ).fetchall()

aiida/storage/psql_dos/migrations/versions/django_0026_trajectory_symbols_to_attribute.py

@@ -42,7 +42,7 @@ def upgrade():
         sa.column('type', sa.String),
     )
 
-    nodes = connection.execute(  # type: ignore[var-annotated]
+    nodes = connection.execute(
         sa.select(node_model.c.id, node_model.c.uuid).where(
             node_model.c.type == op.inline_literal('node.data.array.trajectory.TrajectoryData.')
         )

aiida/storage/psql_dos/migrations/versions/django_0027_delete_trajectory_symbols_array.py

@@ -44,7 +44,7 @@ def upgrade():
         # sa.column('attributes', JSONB),
     )
 
-    nodes = connection.execute(  # type: ignore[var-annotated]
+    nodes = connection.execute(
         sa.select(node_tbl.c.id, node_tbl.c.uuid).where(
             node_tbl.c.type == op.inline_literal('node.data.array.trajectory.TrajectoryData.')
         )

aiida/storage/psql_dos/migrations/versions/django_0037_attributes_extras_settings_json.py

@@ -92,18 +92,12 @@ def upgrade():
     if node_count:
         with get_progress_reporter()(total=node_count, desc='Updating attributes and extras') as progress:
             for node in conn.execute(select(node_tbl)).all():
-                attr_list = conn.execute(  # type: ignore[var-annotated]
-                    select(attr_tbl).where(attr_tbl.c.dbnode_id == node.id)
-                ).all()
+                attr_list = conn.execute(select(attr_tbl).where(attr_tbl.c.dbnode_id == node.id)).all()
                 attributes, _ = attributes_to_dict(sorted(attr_list, key=lambda a: a.key))
-                extra_list = conn.execute(  # type: ignore[var-annotated]
-                    select(extra_tbl).where(extra_tbl.c.dbnode_id == node.id)
-                ).all()
+                extra_list = conn.execute(select(extra_tbl).where(extra_tbl.c.dbnode_id == node.id)).all()
                 extras, _ = attributes_to_dict(sorted(extra_list, key=lambda a: a.key))
                 conn.execute(
-                    node_tbl.update().where(  # type: ignore[attr-defined]
-                        node_tbl.c.id == node.id
-                    ).values(attributes=attributes, extras=extras)
+                    node_tbl.update().where(node_tbl.c.id == node.id).values(attributes=attributes, extras=extras)
                 )
                 progress.update()
 
@@ -135,9 +129,8 @@ def upgrade():
                     else:
                         val = setting.dval
                 conn.execute(
-                    setting_tbl.update().where(  # type: ignore[attr-defined]
-                        setting_tbl.c.id == setting.id
-                    ).values(val=cast(val, postgresql.JSONB(astext_type=sa.Text())))
+                    setting_tbl.update().where(setting_tbl.c.id == setting.id
+                                               ).values(val=cast(val, postgresql.JSONB(astext_type=sa.Text())))
                 )
                 progress.update()
 

aiida/storage/sqlite_zip/migrations/v1_db_schema.py

@@ -56,8 +56,8 @@ class DbAuthInfo(ArchiveV1Base):
         nullable=True,
         index=True
     )
-    _metadata = Column('metadata', JSON, default=dict, nullable=True)  # type: ignore[var-annotated]
-    auth_params = Column(JSON, default=dict, nullable=True)  # type: ignore[misc]
+    _metadata = Column('metadata', JSON, default=dict, nullable=True)
+    auth_params = Column(JSON, default=dict, nullable=True)
     enabled = Column(Boolean, default=True, nullable=True)
 
 
@@ -96,7 +96,7 @@ class DbComputer(ArchiveV1Base):
     description = Column(Text, default='', nullable=True)
     scheduler_type = Column(String(255), default='', nullable=True)
     transport_type = Column(String(255), default='', nullable=True)
-    _metadata = Column('metadata', JSON, default=dict, nullable=True)  # type: ignore[var-annotated]
+    _metadata = Column('metadata', JSON, default=dict, nullable=True)
 
 
 class DbGroupNodes(ArchiveV1Base):
@@ -126,7 +126,7 @@ class DbGroup(ArchiveV1Base):
     type_string = Column(String(255), default='', nullable=True, index=True)
     time = Column(DateTime(timezone=True), default=timezone.now, nullable=True)
     description = Column(Text, default='', nullable=True)
-    extras = Column(JSON, default=dict, nullable=False)  # type: ignore[misc]
+    extras = Column(JSON, default=dict, nullable=False)
     user_id = Column(
         Integer,
         ForeignKey('db_dbuser.id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'),
@@ -152,7 +152,7 @@ class DbLog(ArchiveV1Base):
         index=True
     )
     message = Column(Text(), default='', nullable=True)
-    _metadata = Column('metadata', JSON, default=dict, nullable=True)  # type: ignore[var-annotated]
+    _metadata = Column('metadata', JSON, default=dict, nullable=True)
 
 
 class DbNode(ArchiveV1Base):
@@ -168,9 +168,9 @@ class DbNode(ArchiveV1Base):
     description = Column(Text(), default='', nullable=True)
     ctime = Column(DateTime(timezone=True), default=timezone.now, nullable=True, index=True)
     mtime = Column(DateTime(timezone=True), default=timezone.now, nullable=True, index=True)
-    attributes = Column(JSON)  # type: ignore[var-annotated]
-    extras = Column(JSON)  # type: ignore[var-annotated]
-    repository_metadata = Column(JSON, nullable=False, default=dict, server_default='{}')  # type: ignore[var-annotated]
+    attributes = Column(JSON)
+    extras = Column(JSON)
+    repository_metadata = Column(JSON, nullable=False, default=dict, server_default='{}')
     dbcomputer_id = Column(
         Integer,
         ForeignKey('db_dbcomputer.id', deferrable=True, initially='DEFERRED', ondelete='RESTRICT'),