Merge branch 'main' into proper-global-var-singleton

.github/workflows/benchmark.yml

@@ -56,7 +56,7 @@ jobs:
         python-version: '3.10'
 
     - name: Run benchmarks
-      run: pytest --benchmark-only --benchmark-json benchmark.json
+      run: pytest --db-backend psql --benchmark-only --benchmark-json benchmark.json tests/
 
     - name: Store benchmark result
       uses: aiidateam/github-action-benchmark@v3
@@ -73,4 +73,4 @@ jobs:
         alert-threshold: 200%
         comment-on-alert: true
         fail-on-alert: false
-        alert-comment-cc-users: '@chrisjsewell,@giovannipizzi'
+        alert-comment-cc-users: '@giovannipizzi,@agoscinski,@GeigerJ2,@khsrali,@unkcpz'

.github/workflows/ci-code.yml

@@ -104,7 +104,7 @@ jobs:
         AIIDA_WARN_v3: 1
       # Python 3.12 has a performance regression when running with code coverage
       # so run code coverage only for python 3.9.
-      run: pytest -v tests -m 'not nightly' ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
+      run: pytest --db-backend psql -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
 
     - name: Upload coverage report
       if: matrix.python-version == 3.9 && github.repository == 'aiidateam/aiida-core'
@@ -139,7 +139,7 @@ jobs:
     - name: Run test suite
       env:
         AIIDA_WARN_v3: 0
-      run: pytest -m 'presto'
+      run: pytest -m 'presto' tests/
 
 
   verdi:

.github/workflows/nightly.yml

@@ -104,19 +104,6 @@ jobs:
         rabbitmq-version: ['3.11', '3.12', '3.13']
 
     services:
-      postgres:
-        image: postgres:16
-        env:
-          POSTGRES_DB: test_aiida
-          POSTGRES_PASSWORD: ''
-          POSTGRES_HOST_AUTH_METHOD: trust
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-        - 5432:5432
       rabbitmq:
         image: rabbitmq:${{ matrix.rabbitmq-version }}-management
         ports:
@@ -132,9 +119,6 @@ jobs:
       with:
         python-version: '3.11'
 
-    - name: Install system dependencies
-      run: sudo apt update && sudo apt install postgresql
-
     - name: Setup SSH on localhost
       run: .github/workflows/setup_ssh.sh
 
@@ -145,7 +129,7 @@ jobs:
       id: tests
       env:
         AIIDA_WARN_v3: 0
-      run: pytest -sv -m 'requires_rmq'
+      run: pytest -s --db-backend sqlite -m 'requires_rmq' tests/
 
     - name: Slack notification
       # Always run this step (otherwise it would be skipped if any of the previous steps fail) but only if the

.github/workflows/release.yml

@@ -54,19 +54,6 @@ jobs:
     timeout-minutes: 30
 
     services:
-      postgres:
-        image: postgres:10
-        env:
-          POSTGRES_DB: test_aiida
-          POSTGRES_PASSWORD: ''
-          POSTGRES_HOST_AUTH_METHOD: trust
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-        - 5432:5432
       rabbitmq:
         image: rabbitmq:3.8.14-management
         ports:
@@ -76,16 +63,11 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Install system dependencies
-      run: |
-        sudo apt update
-        sudo apt install postgresql graphviz
-
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
 
     - name: Run sub-set of test suite
-      run: pytest -sv -k 'requires_rmq'
+      run: pytest -s -m requires_rmq --db-backend=sqlite tests/
 
   publish:
 

.github/workflows/test-install.yml

@@ -229,7 +229,7 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest --verbose tests -m 'not nightly'
+      run: pytest --db-backend psql tests -m 'not nightly' tests/
 
     - name: Freeze test environment
       run: pip freeze | sed '1d' | tee requirements-py-${{ matrix.python-version }}.txt

.github/workflows/tests_nightly.sh

@@ -13,4 +13,4 @@ verdi -p test_aiida run ${SYSTEM_TESTS}/test_containerized_code.py
 bash ${SYSTEM_TESTS}/test_polish_workchains.sh
 verdi daemon stop
 
-AIIDA_TEST_PROFILE=test_aiida pytest -v tests -m 'nightly'
+AIIDA_TEST_PROFILE=test_aiida pytest --db-backend psql -m nightly tests/

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Changelog
 
+## v2.6.3 - 2024-11-6
+
+### Fixes
+- CLI: Fix exception for `verdi plugin list` (#6560) [[c3b10b7]](https://github.com/aiidateam/aiida-core/commit/c3b10b759a9cd062800ef120591d5c7fd0ae4ee7)
+- `DirectScheduler`: Ensure killing child processes (#6572) [[fddffca]](https://github.com/aiidateam/aiida-core/commit/fddffca67b4f7e3b76b19df7db8e1511c449d2d9)   
+- Engine: Fix state change broadcast before process node is updated  (#6580) [[867353c]](https://github.com/aiidateam/aiida-core/commit/867353c415c61d94a2427d5225dd5224a1b95fb9)
+
+### Devops
+- Docker: Replace sleep with `s6-notifyoncheck` (#6475) [[9579378b]](https://github.com/aiidateam/aiida-core/commit/9579378ba063237baa5b73380eb8e9f0a28529ee)
+- Fix failed docker CI using more reasoning grep regex to parse python version (#6581) [[332a4a91]](https://github.com/aiidateam/aiida-core/commit/332a4a915771afedcb144463b012558e4669e529)
+- DevOps: Fix json query in reading the docker names to filter out fields not starting with aiida (#6573) [[e1467edc]](https://github.com/aiidateam/aiida-core/commit/e1467edca902867e53605e0e60b67f8767bf8d3e)
+
+
 ## v2.6.2 - 2024-08-07
 
 ### Fixes
@@ -31,7 +44,7 @@
 
 ## v2.6.1 - 2024-07-01
 
-### Fixes:
+### Fixes
 - Fixtures: Make `pgtest` truly an optional dependency [[9fe8fd2e0]](https://github.com/aiidateam/aiida-core/commit/9fe8fd2e0b88e746ee2156eccb71b7adbab6b2c5)
 
 

pyproject.toml

@@ -211,7 +211,7 @@ notebook = [
 ]
 pre-commit = [
   'aiida-core[atomic_tools,rest,tests,tui]',
-  'mypy~=1.10.0',
+  'mypy~=1.13.0',
   'packaging~=23.0',
   'pre-commit~=3.5',
   'sqlalchemy[mypy]~=2.0',
@@ -255,6 +255,7 @@ runaiida = 'aiida.cmdline.commands.cmd_run:run'
 verdi = 'aiida.cmdline.commands.cmd_verdi:verdi'
 
 [project.urls]
+Changelog = 'https://github.com/aiidateam/aiida-core/blob/main/CHANGELOG.md'
 Documentation = 'https://aiida.readthedocs.io'
 Home = 'http://www.aiida.net/'
 Source = 'https://github.com/aiidateam/aiida-core'

src/aiida/common/lang.py

@@ -96,4 +96,4 @@ def __init__(self, getter: Callable[[SelfType], ReturnType]) -> None:
         self.getter = getter
 
     def __get__(self, instance: Any, owner: SelfType) -> ReturnType:
-        return self.getter(owner)
+        return self.getter(owner)  # type: ignore[arg-type]

src/aiida/common/pydantic.py

@@ -41,7 +41,7 @@ class Model(BaseModel):
     field_info = Field(default, **kwargs)
 
     for key, value in (('priority', priority), ('short_name', short_name), ('option_cls', option_cls)):
-        if value is not None:
+        if value is not None and field_info is not None:
             field_info.metadata.append({key: value})
 
     return field_info

src/aiida/engine/processes/calcjobs/calcjob.py

@@ -1062,7 +1062,7 @@ def presubmit(self, folder: Folder) -> CalcInfo:
 
         def encoder(obj):
             if dataclasses.is_dataclass(obj):
-                return dataclasses.asdict(obj)
+                return dataclasses.asdict(obj)  # type: ignore[arg-type]
             raise TypeError(f' {obj!r} is not JSON serializable')
 
         subfolder = folder.get_subfolder('.aiida', create=True)

src/aiida/engine/processes/workchains/restart.py

@@ -29,7 +29,7 @@
 
 
 def validate_handler_overrides(
-    process_class: 'BaseRestartWorkChain', handler_overrides: Optional[orm.Dict], ctx: 'PortNamespace'
+    process_class: type['BaseRestartWorkChain'], handler_overrides: Optional[orm.Dict], ctx: 'PortNamespace'
 ) -> Optional[str]:
     """Validator for the ``handler_overrides`` input port of the ``BaseRestartWorkChain``.
 

src/aiida/manage/manager.py

@@ -430,7 +430,7 @@ def create_runner(self, with_persistence: bool = True, **kwargs: Any) -> 'Runner
         if with_persistence and 'persister' not in settings:
             settings['persister'] = self.get_persister()
 
-        return runners.Runner(**settings)
+        return runners.Runner(**settings)  # type: ignore[arg-type]
 
     def create_daemon_runner(self, loop: Optional['asyncio.AbstractEventLoop'] = None) -> 'Runner':
         """Create and return a new daemon runner.

src/aiida/orm/nodes/data/array/projection.py

@@ -278,7 +278,7 @@ def array_list_checker(array_list, array_name, orb_length):
                 raise exceptions.ValidationError('Tags must set a list of strings')
             self.base.attributes.set('tags', tags)
 
-    def set_orbitals(self, **kwargs):
+    def set_orbitals(self, **kwargs):  # type: ignore[override]
         """This method is inherited from OrbitalData, but is blocked here.
         If used will raise a NotImplementedError
         """

src/aiida/orm/nodes/data/list.py

@@ -81,15 +81,15 @@ def remove(self, value):
             self.set_list(data)
         return item
 
-    def pop(self, **kwargs):
+    def pop(self, **kwargs):  # type: ignore[override]
         """Remove and return item at index (default last)."""
         data = self.get_list()
         item = data.pop(**kwargs)
         if not self._using_list_reference():
             self.set_list(data)
         return item
 
-    def index(self, value):
+    def index(self, value):  # type: ignore[override]
         """Return first index of value.."""
         return self.get_list().index(value)
 

src/aiida/orm/nodes/data/singlefile.py

@@ -71,9 +71,7 @@ def open(self, path: FilePath, mode: t.Literal['rb']) -> t.Iterator[t.BinaryIO]:
 
     @t.overload
     @contextlib.contextmanager
-    def open(  # type: ignore[overload-overlap]
-        self, path: None = None, mode: t.Literal['r'] = ...
-    ) -> t.Iterator[t.TextIO]: ...
+    def open(self, path: None = None, mode: t.Literal['r'] = ...) -> t.Iterator[t.TextIO]: ...
 
     @t.overload
     @contextlib.contextmanager

src/aiida/plugins/utils.py

@@ -38,7 +38,7 @@ def __init__(self):
     def logger(self) -> Logger:
         return self._logger
 
-    def get_version_info(self, plugin: str | type) -> dict[t.Any, dict[t.Any, t.Any]]:
+    def get_version_info(self, plugin: str | t.Any) -> dict[t.Any, dict[t.Any, t.Any]]:
         """Get the version information for a given plugin.
 
         .. note::

src/aiida/tools/pytest_fixtures/daemon.py

@@ -116,7 +116,7 @@ def test(submit_and_await):
     from aiida.engine import ProcessState
 
     def factory(
-        submittable: 'Process' | 'ProcessBuilder' | 'ProcessNode',
+        submittable: type[Process] | ProcessBuilder | ProcessNode | t.Any,
         state: ProcessState = ProcessState.FINISHED,
         timeout: int = 20,
         **kwargs,

tests/cmdline/groups/test_dynamic.py

@@ -17,7 +17,7 @@ class Model(BaseModel):
         union_type: t.Union[int, float] = Field(title='Union type')
         without_default: str = Field(title='Without default')
         with_default: str = Field(title='With default', default='default')
-        with_default_factory: str = Field(title='With default factory', default_factory=lambda: True)
+        with_default_factory: str = Field(title='With default factory', default_factory=lambda: True)  # type: ignore[assignment]
 
 
 def test_list_options(entry_points):

tests/conftest.py

@@ -22,6 +22,7 @@
 import types
 import typing as t
 import warnings
+from enum import Enum
 from pathlib import Path
 
 import click
@@ -37,7 +38,14 @@
 pytest_plugins = ['aiida.tools.pytest_fixtures', 'sphinx.testing.fixtures']
 
 
-def pytest_collection_modifyitems(items):
+class TestDbBackend(Enum):
+    """Options for the '--db-backend' CLI argument when running pytest."""
+
+    SQLITE = 'sqlite'
+    PSQL = 'psql'
+
+
+def pytest_collection_modifyitems(items, config):
     """Automatically generate markers for certain tests.
 
     Most notably, we add the 'presto' marker for all tests that
@@ -47,6 +55,14 @@ def pytest_collection_modifyitems(items):
     filepath_django = Path(__file__).parent / 'storage' / 'psql_dos' / 'migrations' / 'django_branch'
     filepath_sqla = Path(__file__).parent / 'storage' / 'psql_dos' / 'migrations' / 'sqlalchemy_branch'
 
+    # If the user requested the SQLite backend, automatically skip incompatible tests
+    if config.option.db_backend is TestDbBackend.SQLITE:
+        if config.option.markexpr != '':
+            # Don't overwrite markers that the user already provided via '-m ' cmdline argument
+            config.option.markexpr += ' and (not requires_psql)'
+        else:
+            config.option.markexpr = 'not requires_psql'
+
     for item in items:
         filepath_item = Path(item.fspath)
 
@@ -68,6 +84,30 @@ def pytest_collection_modifyitems(items):
             item.add_marker('presto')
 
 
+def db_backend_type(string):
+    """Conversion function for the custom '--db-backend' pytest CLI option
+
+    :param string: String provided by the user via CLI
+    :returns: DbBackend enum corresponding to user input string
+    """
+    try:
+        return TestDbBackend(string)
+    except ValueError:
+        msg = f"Invalid --db-backend option '{string}'\nMust be one of: {tuple(db.value for db in TestDbBackend)}"
+        raise pytest.UsageError(msg)
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        '--db-backend',
+        action='store',
+        default=TestDbBackend.SQLITE,
+        required=False,
+        help=f'Database backend to be used for tests {tuple(db.value for db in TestDbBackend)}',
+        type=db_backend_type,
+    )
+
+
 @pytest.fixture(scope='session')
 def aiida_profile(pytestconfig, aiida_config, aiida_profile_factory, config_psql_dos, config_sqlite_dos):
     """Create and load a profile with ``core.psql_dos`` as a storage backend and RabbitMQ as the broker.
@@ -77,18 +117,22 @@ def aiida_profile(pytestconfig, aiida_config, aiida_profile_factory, config_psql
     be run against the main storage backend, which is ``core.sqlite_dos``.
     """
     marker_opts = pytestconfig.getoption('-m')
+    db_backend = pytestconfig.getoption('--db-backend')
 
-    # By default we use RabbitMQ broker and psql_dos storage
+    # We use RabbitMQ broker by default unless 'presto' marker is specified
     broker = 'core.rabbitmq'
     if 'not requires_rmq' in marker_opts or 'presto' in marker_opts:
         broker = None
 
-    if 'not requires_psql' in marker_opts or 'presto' in marker_opts:
+    if db_backend is TestDbBackend.SQLITE:
         storage = 'core.sqlite_dos'
         config = config_sqlite_dos()
-    else:
+    elif db_backend is TestDbBackend.PSQL:
         storage = 'core.psql_dos'
         config = config_psql_dos()
+    else:
+        # This should be unreachable
+        raise ValueError(f'Invalid DB backend {db_backend}')
 
     with aiida_profile_factory(
         aiida_config, storage_backend=storage, storage_config=config, broker_backend=broker