Add back pre-commit job for mypy type-checking (#6827)

The pre-commit hook cannot install dependencies therefore the mypy hook (and
others) were skipped in it. We reintroduce the pre-commit CI job to run these
hooks on the CI.

Author: danielhollas

.github/workflows/pre-commit.yml

@@ -0,0 +1,32 @@
+name: pre-commit
+# NOTE: This job is not duplicating pre-commit.ci job,
+# since that once skips running mypy type-checking\
+# due to technical limitations of pre-commit.ci runners.
+
+on:
+  push:
+    branches-ignore: [gh-pages]
+  pull_request:
+    branches-ignore: [gh-pages]
+
+env:
+  FORCE_COLOR: 1
+
+jobs:
+
+  pre-commit:
+
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install python dependencies
+      uses: ./.github/actions/install-aiida-core
+      with:
+        python-version: '3.11'
+        from-lock: 'true'
+
+    - name: Run pre-commit
+      run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.pre-commit-config.yaml

@@ -201,7 +201,8 @@ repos:
     files: >-
       (?x)^(
         pyproject.toml|
-        utils/dependency_management.py
+        utils/dependency_management.py|
+        environment.yml|
       )$
 
   - id: validate-conda-environment

docs/source/reference/command_line.rst

@@ -451,7 +451,7 @@ Below is a list with all available subcommands.
       --broker-host HOSTNAME          Hostname for the message broker.  [default: 127.0.0.1]
       --broker-port INTEGER           Port for the message broker.  [default: 5672]
       --broker-virtual-host TEXT      Name of the virtual host for the message broker without
-                                      leading forward slash.
+                                      leading forward slash.  [default: ""]
       --repository DIRECTORY          Absolute path to the file repository.
       --test-profile                  Designate the profile to be used for running the test
                                       suite only.

environment.yml

@@ -37,4 +37,4 @@ dependencies:
 - typing-extensions~=4.0
 - upf_to_json~=0.9.2
 - wrapt~=1.11
-- chardet~=5.2.0 # [win]
+- chardet~=5.2.0

src/aiida/orm/nodes/data/code/portable.py

@@ -63,7 +63,7 @@ class Model(AbstractCode.Model):
             description='Relative filepath of executable with directory of code files.',
             short_name='-X',
             priority=1,
-            orm_to_model=lambda node, _: str(node.filepath_executable),
+            orm_to_model=lambda node, _: str(node.filepath_executable),  # type: ignore[attr-defined]
         )
         filepath_files: str = MetadataField(
             ...,
@@ -72,7 +72,7 @@ class Model(AbstractCode.Model):
             short_name='-F',
             is_attribute=False,
             priority=2,
-            orm_to_model=_export_filpath_files_from_repo,
+            orm_to_model=_export_filpath_files_from_repo,  # type: ignore[arg-type]
         )
 
     def __init__(
@@ -104,7 +104,7 @@ def __init__(
         if not filepath_files_path.is_dir():
             raise ValueError(f'The filepath `{filepath_files}` is not a directory.')
 
-        self.filepath_executable = filepath_executable
+        self.filepath_executable = filepath_executable  # type: ignore[assignment] # should be fixed in mypy 1.15 see mypy/commit/1eb9d4c
         self.base.repository.put_object_from_tree(str(filepath_files))
 
     def _validate(self):

src/aiida/orm/nodes/node.py

@@ -13,13 +13,13 @@
 import base64
 import datetime
 from functools import cached_property
-from logging import Logger
 from typing import TYPE_CHECKING, Any, ClassVar, Dict, Generic, Iterator, List, Optional, Tuple, Type, TypeVar
 from uuid import UUID
 
 from aiida.common import exceptions
 from aiida.common.lang import classproperty, type_check
 from aiida.common.links import LinkType
+from aiida.common.log import AIIDA_LOGGER
 from aiida.common.pydantic import MetadataField
 from aiida.common.warnings import warn_deprecation
 from aiida.manage import get_manager
@@ -43,6 +43,8 @@
 if TYPE_CHECKING:
     from importlib_metadata import EntryPoint
 
+    from aiida.common.log import AiidaLoggerType
+
     from ..implementation import StorageBackend
     from ..implementation.nodes import BackendNode  # noqa: F401
     from .repository import NodeRepository
@@ -174,8 +176,8 @@ def _query_type_string(cls) -> str:  # noqa: N805
             cls.__query_type_string = get_query_type_from_type_string(cls._plugin_type_string)  # type: ignore[misc]
         return cls.__query_type_string
 
-    # This will be set by the metaclass call
-    _logger: Optional[Logger] = None
+    # This will be set by the metaclass call but we set default
+    _logger: AiidaLoggerType = AIIDA_LOGGER
 
     # A tuple of attribute names that can be updated even after node is stored
     # Requires Sealable mixin, but needs empty tuple for base class
@@ -407,7 +409,7 @@ def entry_point(cls) -> Optional['EntryPoint']:  # noqa: N805
         return get_entry_point_from_class(cls.__module__, cls.__name__)[1]
 
     @property
-    def logger(self) -> Optional[Logger]:
+    def logger(self) -> Optional[AiidaLoggerType]:
         """Return the logger configured for this Node.
 
         :return: Logger object

src/aiida/storage/sqlite_zip/utils.py

@@ -72,7 +72,7 @@ def _json_contains(lhs: Union[str, bytes, bytearray, dict, list], rhs: Union[str
             rhs = json.loads(rhs)
     except json.JSONDecodeError:
         return 0
-    return int(_contains(lhs, rhs))
+    return int(_contains(lhs, rhs))  # type: ignore[arg-type]
 
 
 def register_json_contains(dbapi_connection, _):