Merge branch 'main' of github.com:rabbull/aiida-core into bulk-update…

…-json

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

@@ -7,16 +7,18 @@ inputs:
     default: '3.9'              # Lowest supported version
     required: false
   extras:
-    description: aiida-core extras (including brackets)
-    default: ''
+    description: list of optional dependencies
+    # NOTE: The default 'pre-commit' extra recursively contains
+    # other extras needed to run the tests.
+    default: pre-commit
     required: false
   # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-(
   # https://stackoverflow.com/a/76294014
   # NOTE2: When installing from lockfile, aiida-core and its dependencies
   # are installed in a virtual environment located in .venv directory.
   # Subsuquent jobs steps must either activate the environment or use `uv run`
   from-lock:
-    description: Install aiida-core dependencies from a uv lock file
+    description: Install aiida-core dependencies from uv lock file
     default: 'true'
     required: false
 
@@ -29,19 +31,18 @@ runs:
       python-version: ${{ inputs.python-version }}
 
   - name: Set up uv
-    uses: astral-sh/setup-uv@v4
+    uses: astral-sh/setup-uv@v5
     with:
-      version: 0.5.6
+      version: 0.5.x
+      python-version: ${{ inputs.python-version }}
 
   - name: Install dependencies from uv lock
     if: ${{ inputs.from-lock == 'true' }}
     # NOTE: We're asserting that the lockfile is up to date
-    # NOTE2: 'pre-commit' extra recursively contains other extras
-    # needed to run the tests.
-    run: uv sync --locked --extra pre-commit
+    run: uv sync --locked ${{ inputs.extras && format('--extra {0}', inputs.extras) || '' }}
     shell: bash
 
   - name: Install aiida-core
     if: ${{ inputs.from-lock != 'true' }}
-    run: uv pip install --system -e .${{ inputs.extras }}
+    run: uv pip install -e .${{ inputs.extras }}
     shell: bash

.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

@@ -20,14 +20,17 @@ jobs:
 
   tests:
 
-    runs-on: ubuntu-latest
-    timeout-minutes: 90
+    runs-on: ubuntu-24.04
+    timeout-minutes: 45
 
     strategy:
       fail-fast: false
       matrix:
         python-version: ['3.9', '3.12']
-        database-backend: [psql, sqlite]
+        database-backend: [psql]
+        include:
+        - python-version: '3.9'
+          database-backend: sqlite
 
     services:
       postgres:
@@ -65,16 +68,19 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Setup environment
-      # Note: The virtual environment in .venv was created by uv in previous step
-      run: source .venv/bin/activate && .github/workflows/setup.sh
+      run: .github/workflows/setup.sh
 
     - name: Run test suite
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      # Python 3.12 has a performance regression when running with code coverage
+      # NOTE1: Python 3.12 has a performance regression when running with code coverage
       # so run code coverage only for python 3.9.
-      run: uv run pytest --db-backend ${{ matrix.database-backend }} -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
+      # 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
       if: matrix.python-version == 3.9 && github.repository == 'aiidateam/aiida-core'
@@ -92,10 +98,9 @@ jobs:
       with:
         wait-timeout-minutes: 60
 
-
   tests-presto:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 20
 
     steps:
@@ -120,7 +125,7 @@ jobs:
 
   verdi:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 10
 
     steps:
@@ -130,7 +135,10 @@ jobs:
       uses: ./.github/actions/install-aiida-core
       with:
         python-version: '3.12'
-        from-lock: 'false'
+        from-lock: 'true'
+        # NOTE: The `verdi devel check-undesired-imports` fails if
+        # the 'tui' extra is installed.
+        extras: ''
 
     - name: Run verdi tests
       run: |

.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/docker-build-test.yml

@@ -26,7 +26,7 @@ jobs:
   build-and-test:
     if: ${{ github.event.pull_request.head.repo.fork }}
     name: build and test amd64 images
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 60
     defaults:
       run:

.github/workflows/docs-build.yml

@@ -14,7 +14,7 @@ jobs:
 
   docs-linkcheck:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 30
 
     steps:

.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-latest
+    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
@@ -70,18 +67,25 @@ jobs:
         from-lock: 'true'
 
     - name: Setup environment
-      # NOTE: virtual env in .venv created by uv in previous step
-      run: source .venv/bin/activate && .github/workflows/setup.sh
+      run: .github/workflows/setup.sh
 
-    - name: Run tests
-      id: tests
-      run: source .venv/bin/activate && .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 }}
@@ -95,7 +99,7 @@ jobs:
   # Run a subset of test suite to ensure compatibility with latest RabbitMQ releases
   rabbitmq-tests:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 10
 
     strategy:

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
 
     # Only run this job on the main repository and not on forks
     if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     steps:
     - uses: actions/checkout@v4
@@ -31,7 +31,7 @@ jobs:
   pre-commit:
 
     needs: [check-release-tag]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 30
 
     steps:
@@ -50,7 +50,7 @@ jobs:
   tests:
 
     needs: [check-release-tag]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 30
 
     services:
@@ -75,7 +75,7 @@ jobs:
 
     needs: [check-release-tag, pre-commit, tests]
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Checkout source

.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

@@ -11,6 +11,9 @@ on:
   schedule:
   - cron: 30 02 * * *      # nightly build
 
+env:
+  FORCE_COLOR: 1
+
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
   # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
@@ -23,7 +26,7 @@ jobs:
     # Note: The specification is also validated by the pre-commit hook.
 
     if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 5
 
     steps:
@@ -32,18 +35,18 @@ jobs:
     - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/setup-uv@v4
+      uses: astral-sh/setup-uv@v5
       with:
-        version: 0.5.6
+        version: 0.5.x
 
     - name: Install utils/ dependencies
       run: uv pip install --system -r utils/requirements.txt
 
     - name: Validate uv lockfile
-      run: uv lock --locked
+      run: uv lock --check
 
     - name: Validate conda environment file
       run: python ./utils/dependency_management.py validate-environment-yml
@@ -53,7 +56,7 @@ jobs:
 
     needs: [validate-dependency-specification]
     if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 5
 
     steps:
@@ -73,7 +76,7 @@ jobs:
   install-with-pip:
 
     if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 15
 
     strategy:
@@ -104,7 +107,7 @@ jobs:
     # Verify that we can install AiiDA with conda.
 
     if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 25
 
     strategy:
@@ -156,7 +159,7 @@ jobs:
   tests:
 
     needs: [install-with-pip]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     timeout-minutes: 45
 
     strategy:
@@ -209,4 +212,8 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest --db-backend ${{ matrix.database-backend }} tests -m 'not nightly' tests/
+      # 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/