CI: fix failed test_containerized.py integration test for containeriz…

…ed code (#6707)

fixes #6709

The test is run in nightly.yml as integration test for running containerized code.
The problem may because the new ubuntu don't allow the container to get root permission even for singularity. Since singularity is anyway outdated and we support docker as containerized code engine. I change it to use docker to run the code from a image.
This also remove the CI action (which has no maintains for around 2 years) of building singularity.

.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/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"