Merge branch 'main' into bump-ruff

.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 --db-backend psql -m 'not nightly' tests/ ${{ 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'

.github/workflows/nightly.yml

@@ -129,7 +129,7 @@ jobs:
       id: tests
       env:
         AIIDA_WARN_v3: 0
-      run: pytest -sv --db-backend sqlite -m 'requires_rmq' tests/
+      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

@@ -67,7 +67,7 @@ jobs:
       uses: ./.github/actions/install-aiida-core
 
     - name: Run sub-set of test suite
-      run: pytest -sv -m requires_rmq --db-backend=sqlite tests/
+      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 -v --db-backend psql tests -m 'not nightly' tests/
+      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 --db-backend psql -m nightly tests/
+AIIDA_TEST_PROFILE=test_aiida pytest --db-backend psql -m nightly tests/

.pre-commit-config.yaml

@@ -84,6 +84,7 @@ repos:
         .docker/.*|
         docs/.*|
         utils/.*|
+        tests/.*|
 
         src/aiida/calculations/arithmetic/add.py|
         src/aiida/calculations/diff_tutorial/calculations.py|
@@ -186,17 +187,6 @@ repos:
         src/aiida/transports/plugins/local.py|
         src/aiida/transports/plugins/ssh.py|
         src/aiida/workflows/arithmetic/multiply_add.py|
-
-        tests/conftest.py|
-        tests/repository/conftest.py|
-        tests/repository/test_repository.py|
-        tests/sphinxext/sources/workchain/conf.py|
-        tests/sphinxext/sources/workchain_broken/conf.py|
-        tests/storage/psql_dos/migrations/conftest.py|
-        tests/storage/psql_dos/migrations/django_branch/test_0026_0027_traj_data.py|
-        tests/test_calculation_node.py|
-        tests/test_nodes.py|
-
       )$
 
   - id: dm-generate-all

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

@@ -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/cmdline/utils/ascii_vis.py

@@ -29,7 +29,7 @@ def calc_info(node, call_link_label: bool = False) -> str:
         raise TypeError(f'Unknown type: {type(node)}')
 
     process_label = node.process_label
-    process_state = node.process_state.value.capitalize()
+    process_state = 'None' if node.process_state is None else node.process_state.value.capitalize()
     exit_status = node.exit_status
 
     if call_link_label and (caller := node.caller):

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

@@ -9,6 +9,7 @@
 """`Data` sub class to represent a list."""
 
 from collections.abc import MutableSequence
+from typing import Any
 
 from .base import to_aiida_type
 from .data import Data
@@ -81,15 +82,15 @@ def remove(self, value):
             self.set_list(data)
         return item
 
-    def pop(self, **kwargs):  # type: ignore[override]
+    def pop(self, index: int = -1) -> Any:
         """Remove and return item at index (default last)."""
         data = self.get_list()
-        item = data.pop(**kwargs)
+        item = data.pop(index)
         if not self._using_list_reference():
             self.set_list(data)
         return item
 
-    def index(self, value):  # type: ignore[override]
+    def index(self, value: Any, start: int = 0, stop: int = 0) -> int:
         """Return first index of value.."""
         return self.get_list().index(value)
 

src/aiida/tools/pytest_fixtures/daemon.py

@@ -116,7 +116,7 @@ def test(submit_and_await):
     from aiida.engine import ProcessState
 
     def factory(
-        submittable: type[Process] | ProcessBuilder | ProcessNode | t.Any,
+        submittable: type[Process] | ProcessBuilder | ProcessNode,
         state: ProcessState = ProcessState.FINISHED,
         timeout: int = 20,
         **kwargs,

tests/cmdline/utils/test_ascii_vis.py

@@ -0,0 +1,20 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
+"""Tests for the :mod:`aiida.cmdline.utils.ascii_vis` module."""
+
+from aiida.orm.nodes.process.process import ProcessNode
+
+
+def test_build_call_graph():
+    from aiida.cmdline.utils.ascii_vis import build_call_graph
+
+    node = ProcessNode()
+
+    call_graph = build_call_graph(node)
+    assert call_graph == 'None<None> None'

tests/orm/test_querybuilder.py

@@ -9,6 +9,7 @@
 """Tests for the QueryBuilder."""
 
 import copy
+import json
 import uuid
 import warnings
 from collections import defaultdict
@@ -1703,3 +1704,163 @@ def test_statistics_default_class(self, aiida_localhost):
         # data are correct
         res = next(iter(qb.dict()[0].values()))
         assert res == expected_dict
+
+
+class TestJsonFilters:
+    @pytest.mark.parametrize(
+        'data,filters,is_match',
+        (
+            # contains different types of element
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': [1]}}, True),
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': ['2']}}, True),
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': [None]}}, True),
+            # contains multiple elements of various types
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': [1, None]}}, True),
+            # contains non-exist elements
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': [114514]}}, False),
+            # contains empty set
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'contains': []}}, True),
+            ({'arr': []}, {'attributes.arr': {'contains': []}}, True),
+            # nested arrays
+            ({'arr': [[1, 0], [0, 2]]}, {'attributes.arr': {'contains': [[1, 0]]}}, True),
+            ({'arr': [[2, 3], [0, 1], []]}, {'attributes.arr': {'contains': [[1, 0]]}}, True),
+            ({'arr': [[2, 3], [1]]}, {'attributes.arr': {'contains': [[4]]}}, False),
+            ({'arr': [[1, 0], [0, 2]]}, {'attributes.arr': {'contains': [[3]]}}, False),
+            ({'arr': [[1, 0], [0, 2]]}, {'attributes.arr': {'contains': [3]}}, False),
+            ({'arr': [[1, 0], [0, 2]]}, {'attributes.arr': {'contains': [[2]]}}, True),
+            ({'arr': [[1, 0], [0, 2]]}, {'attributes.arr': {'contains': [2]}}, False),
+            ({'arr': [[1, 0], [0, 2], 3]}, {'attributes.arr': {'contains': [[3]]}}, False),
+            ({'arr': [[1, 0], [0, 2], 3]}, {'attributes.arr': {'contains': [3]}}, True),
+            # negations
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'!contains': [1]}}, False),
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'!contains': []}}, False),
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'!contains': [114514]}}, True),
+            ({'arr': [1, '2', None]}, {'attributes.arr': {'!contains': [1, 114514]}}, True),
+            # TODO: these pass, but why? are these behaviors expected?
+            # non-exist `attr_key`s
+            ({'foo': []}, {'attributes.arr': {'contains': []}}, False),
+            ({'foo': []}, {'attributes.arr': {'!contains': []}}, False),
+        ),
+        ids=json.dumps,
+    )
+    @pytest.mark.usefixtures('aiida_profile_clean')
+    @pytest.mark.requires_psql
+    def test_json_filters_contains_arrays(self, data, filters, is_match):
+        """Test QueryBuilder filter `contains` for JSON array fields"""
+        orm.Dict(data).store()
+        qb = orm.QueryBuilder().append(orm.Dict, filters=filters)
+        assert qb.count() in {0, 1}
+        found = qb.count() == 1
+        assert found == is_match
+
+    @pytest.mark.parametrize(
+        'data,filters,is_match',
+        (
+            # contains different types of values
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'contains': {'k1': 1}}},
+                True,
+            ),
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'contains': {'k1': 1, 'k2': '2'}}},
+                True,
+            ),
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'contains': {'k3': None}}},
+                True,
+            ),
+            # contains empty set
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'contains': {}}},
+                True,
+            ),
+            # doesn't contain non-exist entries
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'contains': {'k1': 1, 'k': 'v'}}},
+                False,
+            ),
+            # negations
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'!contains': {'k1': 1}}},
+                False,
+            ),
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'!contains': {'k1': 1, 'k': 'v'}}},
+                True,
+            ),
+            (
+                {
+                    'dict': {
+                        'k1': 1,
+                        'k2': '2',
+                        'k3': None,
+                    }
+                },
+                {'attributes.dict': {'!contains': {}}},
+                False,
+            ),
+            # TODO: these pass, but why? are these behaviors expected?
+            # non-exist `attr_key`s
+            ({'map': {}}, {'attributes.dict': {'contains': {}}}, False),
+            ({'map': {}}, {'attributes.dict': {'!contains': {}}}, False),
+        ),
+        ids=json.dumps,
+    )
+    @pytest.mark.usefixtures('aiida_profile_clean')
+    @pytest.mark.requires_psql
+    def test_json_filters_contains_object(self, data, filters, is_match):
+        """Test QueryBuilder filter `contains` for JSON object fields"""
+        orm.Dict(data).store()
+        qb = orm.QueryBuilder().append(orm.Dict, filters=filters)
+        assert qb.count() in {0, 1}
+        found = qb.count() == 1
+        assert found == is_match