Merge branch 'main' into uv-update

.github/actions/install-aiida-core/action.yml

@@ -31,7 +31,7 @@ runs:
       python-version: ${{ inputs.python-version }}
 
   - name: Set up uv
-    uses: astral-sh/setup-uv@v5
+    uses: astral-sh/setup-uv@v5.2.0
     with:
       version: 0.5.x
       python-version: ${{ inputs.python-version }}

.github/config/add-singularity.yaml → .github/config/add-containerized.yaml

@@ -3,7 +3,7 @@ description: Bash run in Docker image through Singularity
 default_calc_job_plugin: core.arithmetic.add
 computer: localhost
 filepath_executable: /bin/sh
-image_name: docker://alpine:3
-engine_command: singularity exec --bind $PWD:$PWD {image_name}
+image_name: alpine:3
+engine_command: docker run --user 1001:100 -v $PWD:$PWD -w $PWD -i {image_name}
 prepend_text: ' '
 append_text: ' '

.github/workflows/ci-code.yml

@@ -76,10 +76,7 @@ jobs:
         AIIDA_WARN_v3: 1
       # NOTE1: Python 3.12 has a performance regression when running with code coverage
       # so run code coverage only for python 3.9.
-      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
-      # https://github.com/astral-sh/setup-uv/issues/219
       run: |
-        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
         pytest -n auto --db-backend ${{ matrix.database-backend }} -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
 
     - name: Upload coverage report

.github/workflows/tests_nightly.sh → .github/workflows/daemon_tests.sh

@@ -12,5 +12,3 @@ verdi -p test_aiida run ${SYSTEM_TESTS}/test_daemon.py
 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 --db-backend psql -m nightly tests/

.github/workflows/nightly.yml

@@ -27,7 +27,7 @@ jobs:
   nightly-tests:
 
     if: github.repository == 'aiidateam/aiida-core'      # Prevent running the builds on forks as well
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     services:
       postgres:
@@ -55,9 +55,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: eWaterCycle/setup-singularity@v7        # for containerized code test
-      with:
-        singularity-version: 3.8.7
 
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql
@@ -72,15 +69,23 @@ jobs:
     - name: Setup environment
       run: .github/workflows/setup.sh
 
-    - name: Run tests
-      id: tests
-      run: .github/workflows/tests_nightly.sh
+    - name: Run pytest nigthly tests
+      id: pytest-tests
+      env:
+        AIIDA_TEST_PROFILE: test_aiida
+        AIIDA_WARN_v3: 1
+      run: |
+        pytest --db-backend psql -m nightly tests/
+
+    - name: Run daemon nightly tests
+      id: daemon-tests
+      run: .github/workflows/daemon_tests.sh
 
     - name: Slack notification
       # Always run this step (otherwise it would be skipped if any of the previous steps fail) but only if the
       # `install` or `tests` steps failed, and the `SLACK_WEBHOOK` is available. The latter is not the case for
       # pull requests that come from forks. This is a limitation of secrets on GHA
-      if: always() && (steps.install.outcome == 'failure' || steps.tests.outcome == 'failure') && env.SLACK_WEBHOOK != null
+      if: always() && (steps.install.outcome == 'failure' || steps.pytest-tests.outcome == 'failure' || steps.daemon-tests.outcome == 'failure') && env.SLACK_WEBHOOK != null
       uses: rtCamp/action-slack-notify@v2
       env:
         SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}

.github/workflows/setup.sh

@@ -19,7 +19,7 @@ verdi computer configure core.local localhost --config "${CONFIG}/localhost-conf
 verdi computer test localhost
 verdi code create core.code.installed --non-interactive --config "${CONFIG}/doubler.yaml"
 verdi code create core.code.installed --non-interactive --config "${CONFIG}/add.yaml"
-verdi code create core.code.containerized --non-interactive --config "${CONFIG}/add-singularity.yaml"
+verdi code create core.code.containerized --non-interactive --config "${CONFIG}/add-containerized.yaml"
 
 # set up slurm-ssh computer
 verdi computer setup --non-interactive --config "${CONFIG}/slurm-ssh.yaml"

.github/workflows/test-install.yml

@@ -38,7 +38,7 @@ jobs:
         python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v5.2.0
       with:
         version: 0.5.x
 
@@ -211,8 +211,5 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
-      # https://github.com/astral-sh/setup-uv/issues/219
       run: |
-        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
         pytest -n auto --db-backend psql -m 'not nightly' tests/

.readthedocs.yml

@@ -17,8 +17,8 @@ build:
     # https://docs.readthedocs.io/en/stable/build-customization.html#install-dependencies-with-uv
     pre_create_environment:
     - asdf plugin add uv
-    - asdf install uv 0.5.17
-    - asdf global uv 0.5.17
+    - asdf install uv 0.5.20
+    - asdf global uv 0.5.20
     create_environment:
     - uv venv
     install:

pyproject.toml

@@ -510,3 +510,6 @@ passenv =
     AIIDA_TEST_WORKERS
 commands = molecule {posargs:test}
 """
+
+[tool.uv]
+required-version = ">=0.5.20"

src/aiida/tools/pytest_fixtures/daemon.py

@@ -2,13 +2,15 @@
 
 from __future__ import annotations
 
+import logging
 import pathlib
 import typing as t
 
 import pytest
 
 if t.TYPE_CHECKING:
     from aiida.engine import Process, ProcessBuilder
+    from aiida.engine.daemon.client import DaemonClient
     from aiida.orm import ProcessNode
 
 
@@ -47,7 +49,7 @@ def test(daemon_client):
 
 
 @pytest.fixture
-def started_daemon_client(daemon_client):
+def started_daemon_client(daemon_client: 'DaemonClient'):
     """Ensure that the daemon is running for the test profile and return the associated client.
 
     Usage::
@@ -60,11 +62,14 @@ def test(started_daemon_client):
         daemon_client.start_daemon()
         assert daemon_client.is_daemon_running
 
+    logger = logging.getLogger('tests.daemon:started_daemon_client')
+    logger.debug(f'Daemon log file is located at: {daemon_client.daemon_log_file}')
+
     yield daemon_client
 
 
 @pytest.fixture
-def stopped_daemon_client(daemon_client):
+def stopped_daemon_client(daemon_client: 'DaemonClient'):
     """Ensure that the daemon is not running for the test profile and return the associated client.
 
     Usage::

src/aiida/tools/pytest_fixtures/orm.py

@@ -183,6 +183,7 @@ def factory(label: str | None = None, configure: bool = True) -> 'Computer':
             computer.configure(
                 key_filename=str(ssh_key),
                 key_policy='AutoAddPolicy',
+                safe_interval=1.0,
             )
 
         return computer

tests/engine/test_memory_leaks.py

@@ -65,7 +65,6 @@ def test_leak_local_calcjob(aiida_code_installed):
 
 
 @pytest.mark.skipif(sys.version_info >= (3, 12), reason='Garbage collecting hangs on Python 3.12')
-@pytest.mark.nightly
 @pytest.mark.usefixtures('aiida_profile', 'check_memory_leaks')
 def test_leak_ssh_calcjob(aiida_computer_ssh):
     """Test whether running a CalcJob over SSH leaks memory.

tests/tools/archive/orm/test_links.py

@@ -8,14 +8,16 @@
 ###########################################################################
 """orm links tests for the export and import routines"""
 
+import pytest
+
 from aiida import orm
 from aiida.common.links import LinkType
 from aiida.orm.entities import EntityTypes
 from aiida.tools.archive import ArchiveFormatSqlZip, create_archive, import_archive
 from tests.tools.archive.utils import get_all_node_links
 
 
-def test_links_to_unknown_nodes(tmp_path, aiida_profile):
+def test_links_to_unknown_nodes(tmp_path, aiida_profile_clean):
     """Test importing of nodes, that have links to unknown nodes."""
     # store a node
     node = orm.Data()
@@ -46,7 +48,7 @@ def test_links_to_unknown_nodes(tmp_path, aiida_profile):
     with ArchiveFormatSqlZip().open(filename, 'r') as archive:
         assert archive.querybuilder().append(entity_type='link').count() == 1
 
-    aiida_profile.reset_storage()
+    aiida_profile_clean.reset_storage()
 
     # since the query builder only looks for links between known nodes,
     # this should not import the erroneous link
@@ -262,7 +264,8 @@ def test_complex_workflow_graph_links(aiida_profile_clean, tmp_path, aiida_local
     assert set(export_set) == set(import_set)
 
 
-def test_complex_workflow_graph_export_sets(aiida_profile, tmp_path, aiida_localhost_factory):
+@pytest.mark.nightly
+def test_complex_workflow_graph_export_sets(aiida_profile_clean, tmp_path, aiida_localhost_factory):
     """Test ex-/import of individual nodes in complex graph"""
     for export_conf in range(0, 9):
         _, (export_node, export_target) = construct_complex_graph(aiida_localhost_factory, export_conf)
@@ -272,7 +275,7 @@ def test_complex_workflow_graph_export_sets(aiida_profile, tmp_path, aiida_local
         create_archive([export_node], filename=export_file, overwrite=True)
         export_node_str = str(export_node)
 
-        aiida_profile.reset_storage()
+        aiida_profile_clean.reset_storage()
 
         import_archive(export_file)
 
@@ -296,7 +299,8 @@ def test_complex_workflow_graph_export_sets(aiida_profile, tmp_path, aiida_local
         )
 
 
-def test_high_level_workflow_links(aiida_profile, tmp_path, aiida_localhost_factory):
+@pytest.mark.nightly
+def test_high_level_workflow_links(aiida_profile_clean, tmp_path, aiida_localhost_factory):
     """This test checks that all the needed links are correctly exported and imported.
     INPUT_CALC, INPUT_WORK, CALL_CALC, CALL_WORK, CREATE, and RETURN
     links connecting Data nodes and high-level Calculation and Workflow nodes:
@@ -318,7 +322,7 @@ def test_high_level_workflow_links(aiida_profile, tmp_path, aiida_localhost_fact
 
     for calcs in high_level_calc_nodes:
         for works in high_level_work_nodes:
-            aiida_profile.reset_storage()
+            aiida_profile_clean.reset_storage()
 
             graph_nodes, _ = construct_complex_graph(aiida_localhost_factory, calc_nodes=calcs, work_nodes=works)
 
@@ -350,7 +354,7 @@ def test_high_level_workflow_links(aiida_profile, tmp_path, aiida_localhost_fact
             export_file = tmp_path.joinpath('export.aiida')
             create_archive(graph_nodes, filename=export_file, overwrite=True)
 
-            aiida_profile.reset_storage()
+            aiida_profile_clean.reset_storage()
 
             import_archive(export_file)
             import_links = get_all_node_links()
@@ -450,7 +454,8 @@ def link_flags_export_helper(name, all_nodes, tmp_path, nodes_to_export, flags,
     return ret
 
 
-def test_link_flags(aiida_profile, tmp_path, aiida_localhost_factory):
+@pytest.mark.nightly
+def test_link_flags(aiida_profile_clean, tmp_path, aiida_localhost_factory):
     """Verify all link follow flags are working as intended.
 
     Graph (from ``construct_complex_graph()``)::
@@ -584,10 +589,10 @@ def test_link_flags(aiida_profile, tmp_path, aiida_localhost_factory):
         ),
     )
 
-    link_flags_import_helper(input_links_forward, aiida_profile.reset_storage)
-    link_flags_import_helper(create_return_links_backward, aiida_profile.reset_storage)
-    link_flags_import_helper(call_links_backward_calc1, aiida_profile.reset_storage)
-    link_flags_import_helper(call_links_backward_work2, aiida_profile.reset_storage)
+    link_flags_import_helper(input_links_forward, aiida_profile_clean.reset_storage)
+    link_flags_import_helper(create_return_links_backward, aiida_profile_clean.reset_storage)
+    link_flags_import_helper(call_links_backward_calc1, aiida_profile_clean.reset_storage)
+    link_flags_import_helper(call_links_backward_work2, aiida_profile_clean.reset_storage)
 
 
 def test_double_return_links_for_workflows(tmp_path, aiida_profile_clean):