From f618e7c97d583e24a07202c3f40169e6b4babe0b Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 13:11:30 +0100
Subject: [PATCH 1/9] Docker image for out-of-box qe calculation running

---
 docker/Dockerfile                             | 27 +++++++++++++
 docker/_static/Si.cif                         | 28 ++++++++++++++
 docker/docker-bake.hcl                        | 38 +++++++++++++++++++
 .../s6-assets/init/run-before-daemon-start.sh | 31 +++++++++++++++
 .../dependencies.d/aiida-prepare              |  0
 .../dependencies.d/base                       |  0
 .../run-before-daemon-start/timeout-up        |  1 +
 .../s6-rc.d/run-before-daemon-start/type      |  1 +
 .../s6-rc.d/run-before-daemon-start/up        |  6 +++
 .../user/contents.d/run-before-daemon-start   |  0
 10 files changed, 132 insertions(+)
 create mode 100644 docker/Dockerfile
 create mode 100644 docker/_static/Si.cif
 create mode 100644 docker/docker-bake.hcl
 create mode 100755 docker/s6-assets/init/run-before-daemon-start.sh
 create mode 100644 docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
 create mode 100644 docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
 create mode 100644 docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
 create mode 100644 docker/s6-assets/s6-rc.d/run-before-daemon-start/type
 create mode 100644 docker/s6-assets/s6-rc.d/run-before-daemon-start/up
 create mode 100644 docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start

diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 000000000..f4f1f8d56
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,27 @@
+#FROM aiidateam/aiida-core-with-services:edge
+FROM aiidateam/aiida-core-with-services:newly-baked
+
+USER root
+
+ARG QE_VERSION
+ENV QE_VERSION ${QE_VERSION}
+
+# Install aiida-quantumespresso from source code
+COPY --from=src . /tmp/aiida-quantumespresso
+RUN pip install /tmp/aiida-quantumespresso --no-cache-dir && \
+    rm -rf /tmp/aiida-quantumespresso
+
+# Install quantum espresso from conda (the latest version)
+RUN mamba install -y -c conda-forge qe=${QE_VERSION} && \
+    mamba clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${SYSTEM_USER}"
+
+COPY s6-assets/s6-rc.d /etc/s6-overlay/s6-rc.d
+COPY s6-assets/init /etc/init
+
+# Static example files
+RUN mkdir -p /opt/examples
+COPY _static/ /opt/examples
+
+USER ${SYSTEM_UID}
\ No newline at end of file
diff --git a/docker/_static/Si.cif b/docker/_static/Si.cif
new file mode 100644
index 000000000..deb07daa9
--- /dev/null
+++ b/docker/_static/Si.cif
@@ -0,0 +1,28 @@
+# generated using pymatgen
+data_Si
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   3.86697465
+_cell_length_b   3.86697465
+_cell_length_c   3.86697465
+_cell_angle_alpha   60.00000000
+_cell_angle_beta   60.00000000
+_cell_angle_gamma   60.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Si
+_chemical_formula_sum   Si2
+_cell_volume   40.88829285
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Si  Si0  1  0.75000000  0.75000000  0.75000000  1
+  Si  Si1  1  0.50000000  0.50000000  0.50000000  1
diff --git a/docker/docker-bake.hcl b/docker/docker-bake.hcl
new file mode 100644
index 000000000..5a992dd6a
--- /dev/null
+++ b/docker/docker-bake.hcl
@@ -0,0 +1,38 @@
+# docker-bake.hcl
+variable "ORGANIZATION" {
+  default = "aiidateam"
+}
+
+variable "REGISTRY" {
+  default = "docker.io/"
+}
+
+variable "PLATFORMS" {
+  default = ["linux/amd64"]
+}
+
+variable "QE_VERSION" {
+  default = "7.2"
+}
+
+function "tags" {
+  params = [image]
+  result = [
+    "${REGISTRY}${ORGANIZATION}/${image}:newly-baked"
+  ]
+}
+
+group "default" {
+  targets = ["aiida-quantumespresso"]
+}
+
+target "aiida-quantumespresso" {
+  tags = tags("aiida-quantumespresso")
+  contexts = {
+    src = ".."
+  }
+  platforms = "${PLATFORMS}"
+  args = {
+    "QE_VERSION" = "${QE_VERSION}"
+  }
+}
\ No newline at end of file
diff --git a/docker/s6-assets/init/run-before-daemon-start.sh b/docker/s6-assets/init/run-before-daemon-start.sh
new file mode 100755
index 000000000..dbef58500
--- /dev/null
+++ b/docker/s6-assets/init/run-before-daemon-start.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# If lock file exists, then we have already run this script
+if [ -f ${HOME}/.run-before-daemon-start-done ]; then
+    exit 0
+else
+    touch ${HOME}/.run-before-daemon-start-done
+fi
+
+# Install pseudopotential libraries
+aiida-pseudo install sssp --functional PBE -p efficiency
+aiida-pseudo install sssp --functional PBE -p precision
+aiida-pseudo install sssp --functional PBEsol -p efficiency
+aiida-pseudo install sssp --functional PBEsol -p precision
+
+# Loop over executables to set up
+for code_name in pw ph; do
+    # Set up caching
+    verdi config set -a caching.enabled_for aiida.calculations:quantumespresso.${code_name}
+    # Set up code
+    verdi code create core.code.installed \
+        --non-interactive \
+        --label ${code_name}-${QE_VERSION} \
+        --description "${code_name}.x code on localhost" \
+        --default-calc-job-plugin quantumespresso.${code_name} \
+        --computer localhost --prepend-text 'eval "$(conda shell.posix hook)"\nconda activate base\nexport OMP_NUM_THREADS=1' \
+        --filepath-executable ${code_name}.x
+done
+
+# Import example structures
+verdi data core.structure import ase /opt/examples/Si.cif
\ No newline at end of file
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare b/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
new file mode 100644
index 000000000..e69de29bb
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base b/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
new file mode 100644
index 000000000..e69de29bb
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up b/docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
new file mode 100644
index 000000000..573541ac9
--- /dev/null
+++ b/docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
@@ -0,0 +1 @@
+0
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/type b/docker/s6-assets/s6-rc.d/run-before-daemon-start/type
new file mode 100644
index 000000000..bdd22a185
--- /dev/null
+++ b/docker/s6-assets/s6-rc.d/run-before-daemon-start/type
@@ -0,0 +1 @@
+oneshot
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/up b/docker/s6-assets/s6-rc.d/run-before-daemon-start/up
new file mode 100644
index 000000000..37d82070a
--- /dev/null
+++ b/docker/s6-assets/s6-rc.d/run-before-daemon-start/up
@@ -0,0 +1,6 @@
+#!/command/execlineb -S0
+
+with-contenv
+
+foreground { s6-echo "Calling /etc/init/run-before-daemon-start" }
+/etc/init/run-before-daemon-start.sh
diff --git a/docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start b/docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
new file mode 100644
index 000000000..e69de29bb

From f4ec7e6d98308cf51dddbd9e3824a4c0e3faa92b Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 15:44:51 +0100
Subject: [PATCH 2/9] Add github action to build and push

---
 .github/workflows/docker.yml | 90 ++++++++++++++++++++++++++++++++++++
 docker/Dockerfile            |  4 +-
 docker/requirements.txt      |  8 ++++
 3 files changed, 100 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/docker.yml
 create mode 100644 docker/requirements.txt

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 000000000..76a0a9cc0
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,90 @@
+---
+name: Build, test and push Docker Images
+
+on:
+    pull_request:
+        paths-ignore:
+            - "docs/**"
+            - "tests/**"
+    push:
+        branches:
+            - main
+        tags:
+            - "v*"
+        paths-ignore:
+            - "docs/**"
+            - "tests/**"
+    workflow_dispatch:
+
+# 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
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    amd64-build:
+        runs-on: ubuntu-latest
+        defaults:
+            run:
+              shell: bash
+              working-directory: .docker
+
+        steps:
+            - name: Checkout Repo ⚡️
+              uses: actions/checkout@v3
+            - name: Set Up Python 🐍
+              uses: actions/setup-python@v4
+              with:
+                  python-version: 3.x
+
+            - name: Install Dev Dependencies 📦
+              run: |
+                  pip install --upgrade pip
+                  pip install --upgrade -r .docker/requirements.txt
+
+            - name: Build image 
+              run: docker buildx bake -f docker-bake.hcl -f --set *.platform=linux/amd64 --load
+              env:
+                  # Full logs for CI build
+                  BUILDKIT_PROGRESS: plain
+
+            #- name: Run tests ✅
+            #  run: TAG=newly-baked python -m pytest -s tests
+
+
+            #- name: Docker meta 📝
+            #  id: meta
+            #  uses: docker/metadata-action@v4
+            #  env: ${{ fromJson(steps.build_vars.outputs.vars) }}
+            #  with:
+            #      images: |
+            #          name=${{ inputs.registry }}/${{ env.OWNER }}/${{ matrix.image }}
+            #      tags: |
+            #          type=edge,enable={{is_default_branch}}
+            #          type=sha,enable=${{ github.ref_type != 'tag' }}
+            #          type=ref,event=pr
+            #          type=match,pattern=v(\d+\.\d+.\d+),group=1
+            #          type=raw,value={{tag}},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+            #          type=raw,value=python-${{ env.PYTHON_VERSION }},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+            #          type=raw,value=postgresql-${{ env.PGSQL_VERSION }},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+
+            #- name: Login to Container Registry 🔑
+            #  uses: docker/login-action@v2
+            #  with:
+            #      registry: ${{ inputs.registry }}
+            #      username: ${{ secrets.REGISTRY_USERNAME }}
+            #      password: ${{ secrets.REGISTRY_TOKEN }}
+
+            #- name: Set tags for image and push 🏷️📤💾
+            #  run: |
+            #      declare -a arr=(${{ steps.meta.outputs.tags }})
+            #      for tag in "${arr[@]}"; do
+            #          arch_tag=$(echo ${tag} | sed "s/:/:${{ inputs.architecture }}-/")
+            #          docker tag ${{ env.OWNER }}/${{ matrix.image }}:newly-baked ${arch_tag}
+            #          docker push ${arch_tag}
+
+            #          # write tag to file
+            #          mkdir -p /tmp/aiida-core
+            #          echo ${arch_tag} >> /tmp/aiida-core/${{ matrix.image }}-${{ inputs.architecture }}-tags.txt
+            #      done
diff --git a/docker/Dockerfile b/docker/Dockerfile
index f4f1f8d56..e6370ea3d 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,5 +1,5 @@
-#FROM aiidateam/aiida-core-with-services:edge
-FROM aiidateam/aiida-core-with-services:newly-baked
+FROM aiidateam/aiida-core-with-services:edge
+#FROM aiidateam/aiida-core-with-services:newly-baked
 
 USER root
 
diff --git a/docker/requirements.txt b/docker/requirements.txt
new file mode 100644
index 000000000..3ba15482b
--- /dev/null
+++ b/docker/requirements.txt
@@ -0,0 +1,8 @@
+docker
+pre-commit
+pytest
+requests
+tabulate
+pytest-docker
+docker-compose
+pyyaml<=5.3.1

From 852853ce42a988b1b47785129a218a5d617502a2 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 15:47:55 +0100
Subject: [PATCH 3/9] f-m

---
 {docker => .docker}/Dockerfile                       |  0
 {docker => .docker}/_static/Si.cif                   |  0
 {docker => .docker}/docker-bake.hcl                  |  0
 {docker => .docker}/requirements.txt                 |  0
 .../s6-assets/init/run-before-daemon-start.sh        |  0
 .../dependencies.d/aiida-prepare                     |  0
 .../run-before-daemon-start/dependencies.d/base      |  0
 .../s6-rc.d/run-before-daemon-start/timeout-up       |  0
 .../s6-assets/s6-rc.d/run-before-daemon-start/type   |  0
 .../s6-assets/s6-rc.d/run-before-daemon-start/up     |  0
 .../s6-rc.d/user/contents.d/run-before-daemon-start  |  0
 .github/workflows/docker.yml                         | 12 ++++++------
 12 files changed, 6 insertions(+), 6 deletions(-)
 rename {docker => .docker}/Dockerfile (100%)
 rename {docker => .docker}/_static/Si.cif (100%)
 rename {docker => .docker}/docker-bake.hcl (100%)
 rename {docker => .docker}/requirements.txt (100%)
 rename {docker => .docker}/s6-assets/init/run-before-daemon-start.sh (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/run-before-daemon-start/type (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/run-before-daemon-start/up (100%)
 rename {docker => .docker}/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start (100%)

diff --git a/docker/Dockerfile b/.docker/Dockerfile
similarity index 100%
rename from docker/Dockerfile
rename to .docker/Dockerfile
diff --git a/docker/_static/Si.cif b/.docker/_static/Si.cif
similarity index 100%
rename from docker/_static/Si.cif
rename to .docker/_static/Si.cif
diff --git a/docker/docker-bake.hcl b/.docker/docker-bake.hcl
similarity index 100%
rename from docker/docker-bake.hcl
rename to .docker/docker-bake.hcl
diff --git a/docker/requirements.txt b/.docker/requirements.txt
similarity index 100%
rename from docker/requirements.txt
rename to .docker/requirements.txt
diff --git a/docker/s6-assets/init/run-before-daemon-start.sh b/.docker/s6-assets/init/run-before-daemon-start.sh
similarity index 100%
rename from docker/s6-assets/init/run-before-daemon-start.sh
rename to .docker/s6-assets/init/run-before-daemon-start.sh
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
similarity index 100%
rename from docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
rename to .docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
similarity index 100%
rename from docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
rename to .docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
similarity index 100%
rename from docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
rename to .docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/type b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/type
similarity index 100%
rename from docker/s6-assets/s6-rc.d/run-before-daemon-start/type
rename to .docker/s6-assets/s6-rc.d/run-before-daemon-start/type
diff --git a/docker/s6-assets/s6-rc.d/run-before-daemon-start/up b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/up
similarity index 100%
rename from docker/s6-assets/s6-rc.d/run-before-daemon-start/up
rename to .docker/s6-assets/s6-rc.d/run-before-daemon-start/up
diff --git a/docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start b/.docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
similarity index 100%
rename from docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
rename to .docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 76a0a9cc0..9cf639a56 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -7,10 +7,10 @@ on:
             - "docs/**"
             - "tests/**"
     push:
-        branches:
-            - main
-        tags:
-            - "v*"
+        #branches:
+        #    - main
+        #tags:
+        #    - "v*"
         paths-ignore:
             - "docs/**"
             - "tests/**"
@@ -41,10 +41,10 @@ jobs:
             - name: Install Dev Dependencies 📦
               run: |
                   pip install --upgrade pip
-                  pip install --upgrade -r .docker/requirements.txt
+                  pip install --upgrade -r requirements.txt
 
             - name: Build image 
-              run: docker buildx bake -f docker-bake.hcl -f --set *.platform=linux/amd64 --load
+              run: docker buildx bake -f docker-bake.hcl --set *.platform=linux/amd64 --load
               env:
                   # Full logs for CI build
                   BUILDKIT_PROGRESS: plain

From 8b41937349ef68def5b3956aaadf2c4e67c15769 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 16:05:49 +0100
Subject: [PATCH 4/9] Implement unit test for the built image

---
 .../docker-compose.aiida-quantumespresso.yml  | 15 +++++
 .docker/tests/conftest.py                     | 61 +++++++++++++++++++
 .docker/tests/test_aiida.py                   | 39 ++++++++++++
 .github/workflows/docker.yml                  |  5 +-
 4 files changed, 117 insertions(+), 3 deletions(-)
 create mode 100644 .docker/docker-compose.aiida-quantumespresso.yml
 create mode 100644 .docker/tests/conftest.py
 create mode 100644 .docker/tests/test_aiida.py

diff --git a/.docker/docker-compose.aiida-quantumespresso.yml b/.docker/docker-compose.aiida-quantumespresso.yml
new file mode 100644
index 000000000..ab8725175
--- /dev/null
+++ b/.docker/docker-compose.aiida-quantumespresso.yml
@@ -0,0 +1,15 @@
+---
+version: '3.4'
+
+services:
+
+    aiida:
+        image: ${REGISTRY:-}${BASE_IMAGE:-aiidateam/aiida-quantumespresso}:${TAG:-latest}
+        environment:
+            TZ: Europe/Zurich
+            SETUP_DEFAULT_AIIDA_PROFILE: 'true'
+        #volumes:
+        #    - aiida-home-folder:/home/aiida
+
+volumes:
+    aiida-home-folder:
diff --git a/.docker/tests/conftest.py b/.docker/tests/conftest.py
new file mode 100644
index 000000000..f347c8df8
--- /dev/null
+++ b/.docker/tests/conftest.py
@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+# pylint: disable=missing-docstring, redefined-outer-name
+import json
+import re
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture(scope='session', params=['aiida-quantumespresso'])
+def variant(request):
+    return request.param
+
+
+@pytest.fixture(scope='session')
+def docker_compose_file(pytestconfig, variant):  # pylint: disable=unused-argument
+    return f'docker-compose.{variant}.yml'
+
+
+@pytest.fixture(scope='session')
+def docker_compose(docker_services):
+    # pylint: disable=protected-access
+    return docker_services._docker_compose
+
+
+@pytest.fixture
+def timeout():
+    """Container and service startup timeout"""
+    return 60
+
+
+@pytest.fixture
+def container_user():
+    return 'aiida'
+
+
+@pytest.fixture
+def aiida_exec(docker_compose):
+
+    def execute(command, user=None, **kwargs):
+        if user:
+            command = f'exec -T --user={user} aiida {command}'
+        else:
+            command = f'exec -T aiida {command}'
+        return docker_compose.execute(command, **kwargs)
+
+    return execute
+
+@pytest.fixture
+def qe_version(aiida_exec):
+    info = json.loads(
+        aiida_exec(
+            "mamba list -n base --json --full-name qe"
+        ).decode()
+    )[0]
+    return info['version']
+
+@pytest.fixture
+def sssp_version(aiida_exec, container_user):
+    output = aiida_exec("aiida-pseudo list", user=container_user).decode().strip()
+    return re.search(r"SSSP/(\d+\.\d+)/PBE/efficiency", output).group(1)
diff --git a/.docker/tests/test_aiida.py b/.docker/tests/test_aiida.py
new file mode 100644
index 000000000..61f2ce798
--- /dev/null
+++ b/.docker/tests/test_aiida.py
@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+# pylint: disable=missing-docstring
+import json
+import time
+
+from packaging.version import parse
+import pytest
+
+
+def test_verdi_status(aiida_exec, container_user, timeout):
+    time.sleep(timeout)
+    output = aiida_exec('verdi status', user=container_user).decode().strip()
+    assert 'Connected to RabbitMQ' in output
+    assert 'Daemon is running' in output
+
+    # check that we have suppressed the warnings
+    assert 'Warning' not in output
+
+
+def test_computer_setup_success(aiida_exec, container_user, timeout):
+    time.sleep(timeout)
+    output = aiida_exec('verdi computer test localhost', user=container_user).decode().strip()
+
+    assert "Success" in output
+    assert "Failed" not in output
+
+def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version, timeout):
+    import re
+
+    time.sleep(timeout)
+    output = aiida_exec("verdi data core.structure import ase /opt/examples/Si.cif", user=container_user).decode().strip()
+    
+    # Find pk 
+    pk = re.search(r"PK = (\d+)", output).group(1)
+
+    cmd = f"aiida-quantumespresso calculation launch pw -X pw-{qe_version}@localhost -F SSSP/{sssp_version}/PBE/efficiency -S {pk} -k 1 1 1"
+    output = aiida_exec(cmd, user=container_user).decode().strip()
+
+    assert "terminated with state: finished [0]" in output
\ No newline at end of file
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 9cf639a56..606189add 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -49,9 +49,8 @@ jobs:
                   # Full logs for CI build
                   BUILDKIT_PROGRESS: plain
 
-            #- name: Run tests ✅
-            #  run: TAG=newly-baked python -m pytest -s tests
-
+            - name: Run tests ✅
+              run: TAG=newly-baked python -m pytest -s tests
 
             #- name: Docker meta 📝
             #  id: meta

From ea658a5226248d4471ea68b9c341b812d679019a Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 18:41:48 +0100
Subject: [PATCH 5/9] timeout for session count when test start

---
 .docker/tests/conftest.py   |  2 +-
 .docker/tests/test_aiida.py | 15 +++------------
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/.docker/tests/conftest.py b/.docker/tests/conftest.py
index f347c8df8..31a920d57 100644
--- a/.docker/tests/conftest.py
+++ b/.docker/tests/conftest.py
@@ -23,7 +23,7 @@ def docker_compose(docker_services):
     return docker_services._docker_compose
 
 
-@pytest.fixture
+@pytest.fixture(scope='session')
 def timeout():
     """Container and service startup timeout"""
     return 60
diff --git a/.docker/tests/test_aiida.py b/.docker/tests/test_aiida.py
index 61f2ce798..9f6fbf2a3 100644
--- a/.docker/tests/test_aiida.py
+++ b/.docker/tests/test_aiida.py
@@ -1,14 +1,7 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=missing-docstring
-import json
-import time
 
-from packaging.version import parse
-import pytest
-
-
-def test_verdi_status(aiida_exec, container_user, timeout):
-    time.sleep(timeout)
+def test_verdi_status(aiida_exec, container_user):
     output = aiida_exec('verdi status', user=container_user).decode().strip()
     assert 'Connected to RabbitMQ' in output
     assert 'Daemon is running' in output
@@ -17,17 +10,15 @@ def test_verdi_status(aiida_exec, container_user, timeout):
     assert 'Warning' not in output
 
 
-def test_computer_setup_success(aiida_exec, container_user, timeout):
-    time.sleep(timeout)
+def test_computer_setup_success(aiida_exec, container_user):
     output = aiida_exec('verdi computer test localhost', user=container_user).decode().strip()
 
     assert "Success" in output
     assert "Failed" not in output
 
-def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version, timeout):
+def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version):
     import re
 
-    time.sleep(timeout)
     output = aiida_exec("verdi data core.structure import ase /opt/examples/Si.cif", user=container_user).decode().strip()
     
     # Find pk 

From e1641446c61356ef0a43265cc1a34489b9351b48 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 18:42:27 +0100
Subject: [PATCH 6/9] test

---
 .docker/Dockerfile          |  4 ++--
 .docker/tests/conftest.py   |  6 +++---
 .docker/tests/test_aiida.py | 10 ++++++----
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/.docker/Dockerfile b/.docker/Dockerfile
index e6370ea3d..f4f1f8d56 100644
--- a/.docker/Dockerfile
+++ b/.docker/Dockerfile
@@ -1,5 +1,5 @@
-FROM aiidateam/aiida-core-with-services:edge
-#FROM aiidateam/aiida-core-with-services:newly-baked
+#FROM aiidateam/aiida-core-with-services:edge
+FROM aiidateam/aiida-core-with-services:newly-baked
 
 USER root
 
diff --git a/.docker/tests/conftest.py b/.docker/tests/conftest.py
index 31a920d57..e9139e67f 100644
--- a/.docker/tests/conftest.py
+++ b/.docker/tests/conftest.py
@@ -23,7 +23,7 @@ def docker_compose(docker_services):
     return docker_services._docker_compose
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture
 def timeout():
     """Container and service startup timeout"""
     return 60
@@ -56,6 +56,6 @@ def qe_version(aiida_exec):
     return info['version']
 
 @pytest.fixture
-def sssp_version(aiida_exec, container_user):
-    output = aiida_exec("aiida-pseudo list", user=container_user).decode().strip()
+def sssp_version(aiida_exec):
+    output = aiida_exec("aiida-pseudo list").decode().strip()
     return re.search(r"SSSP/(\d+\.\d+)/PBE/efficiency", output).group(1)
diff --git a/.docker/tests/test_aiida.py b/.docker/tests/test_aiida.py
index 9f6fbf2a3..5f54e1f16 100644
--- a/.docker/tests/test_aiida.py
+++ b/.docker/tests/test_aiida.py
@@ -1,7 +1,9 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=missing-docstring
+import time
 
-def test_verdi_status(aiida_exec, container_user):
+def test_verdi_status(aiida_exec, container_user, timeout):
+    time.sleep(timeout)
     output = aiida_exec('verdi status', user=container_user).decode().strip()
     assert 'Connected to RabbitMQ' in output
     assert 'Daemon is running' in output
@@ -10,20 +12,20 @@ def test_verdi_status(aiida_exec, container_user):
     assert 'Warning' not in output
 
 
-def test_computer_setup_success(aiida_exec, container_user):
+def test_computer_setup_success(aiida_exec, container_user, timeout):
     output = aiida_exec('verdi computer test localhost', user=container_user).decode().strip()
 
     assert "Success" in output
     assert "Failed" not in output
 
-def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version):
+def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version, timeout):
     import re
 
     output = aiida_exec("verdi data core.structure import ase /opt/examples/Si.cif", user=container_user).decode().strip()
     
     # Find pk 
     pk = re.search(r"PK = (\d+)", output).group(1)
-
+    
     cmd = f"aiida-quantumespresso calculation launch pw -X pw-{qe_version}@localhost -F SSSP/{sssp_version}/PBE/efficiency -S {pk} -k 1 1 1"
     output = aiida_exec(cmd, user=container_user).decode().strip()
 

From db854fdb29fb3b27b85593c74d24ee5139245384 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 20:14:12 +0100
Subject: [PATCH 7/9] More proper service wait fixture

---
 .docker/tests/conftest.py   | 33 +++++++++++++++++++--------------
 .docker/tests/test_aiida.py |  7 +++----
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/.docker/tests/conftest.py b/.docker/tests/conftest.py
index e9139e67f..314dd220c 100644
--- a/.docker/tests/conftest.py
+++ b/.docker/tests/conftest.py
@@ -2,19 +2,13 @@
 # pylint: disable=missing-docstring, redefined-outer-name
 import json
 import re
-from pathlib import Path
 
 import pytest
 
 
-@pytest.fixture(scope='session', params=['aiida-quantumespresso'])
-def variant(request):
-    return request.param
-
-
 @pytest.fixture(scope='session')
-def docker_compose_file(pytestconfig, variant):  # pylint: disable=unused-argument
-    return f'docker-compose.{variant}.yml'
+def docker_compose_file(pytestconfig):  # pylint: disable=unused-argument
+    return f'docker-compose.aiida-quantumespresso.yml'
 
 
 @pytest.fixture(scope='session')
@@ -22,12 +16,23 @@ def docker_compose(docker_services):
     # pylint: disable=protected-access
     return docker_services._docker_compose
 
-
-@pytest.fixture
-def timeout():
-    """Container and service startup timeout"""
-    return 60
-
+def is_container_ready(dodkec_compose):
+    output = dodkec_compose.execute('exec -T aiida verdi status').decode().strip()
+    return 'Connected to RabbitMQ' in output and 'Daemon is running' in output
+
+@pytest.fixture(scope='session', autouse=True)
+def _docker_service_wait(docker_services):
+    """Container startup wait."""
+    # XXX: Temporary fail the real run test because daemon start is should depened on
+    # run-before-daemon-start but it does not.
+
+    #docker_compose = docker_services._docker_compose
+    
+    #docker_services.wait_until_responsive(
+    #    timeout=120.0, pause=0.1, check=lambda: is_container_ready(docker_compose)
+    #)
+    import time
+    time.sleep(60)
 
 @pytest.fixture
 def container_user():
diff --git a/.docker/tests/test_aiida.py b/.docker/tests/test_aiida.py
index 5f54e1f16..1f62c5deb 100644
--- a/.docker/tests/test_aiida.py
+++ b/.docker/tests/test_aiida.py
@@ -2,8 +2,7 @@
 # pylint: disable=missing-docstring
 import time
 
-def test_verdi_status(aiida_exec, container_user, timeout):
-    time.sleep(timeout)
+def test_verdi_status(aiida_exec, container_user):
     output = aiida_exec('verdi status', user=container_user).decode().strip()
     assert 'Connected to RabbitMQ' in output
     assert 'Daemon is running' in output
@@ -12,13 +11,13 @@ def test_verdi_status(aiida_exec, container_user, timeout):
     assert 'Warning' not in output
 
 
-def test_computer_setup_success(aiida_exec, container_user, timeout):
+def test_computer_setup_success(aiida_exec, container_user):
     output = aiida_exec('verdi computer test localhost', user=container_user).decode().strip()
 
     assert "Success" in output
     assert "Failed" not in output
 
-def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version, timeout):
+def test_run_real_pw_computation(aiida_exec, container_user, qe_version, sssp_version):
     import re
 
     output = aiida_exec("verdi data core.structure import ase /opt/examples/Si.cif", user=container_user).decode().strip()

From 58e074a05bbe86168b88a26d8fb48132c834a598 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 23:15:54 +0100
Subject: [PATCH 8/9] Use run-before-daemon to simplify implementation

---
 .docker/Dockerfile                                  |  3 +--
 .../dependencies.d/aiida-prepare                    |  0
 .../run-before-daemon-start/dependencies.d/base     |  0
 .../s6-rc.d/run-before-daemon-start/timeout-up      |  1 -
 .../s6-assets/s6-rc.d/run-before-daemon-start/type  |  1 -
 .../s6-assets/s6-rc.d/run-before-daemon-start/up    |  6 ------
 .../s6-rc.d/user/contents.d/run-before-daemon-start |  0
 .../60-pseudo-code-setup.sh}                        |  4 ++--
 .docker/tests/conftest.py                           | 13 ++++---------
 .docker/tests/test_aiida.py                         |  1 -
 10 files changed, 7 insertions(+), 22 deletions(-)
 delete mode 100644 .docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
 delete mode 100644 .docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
 delete mode 100644 .docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
 delete mode 100644 .docker/s6-assets/s6-rc.d/run-before-daemon-start/type
 delete mode 100644 .docker/s6-assets/s6-rc.d/run-before-daemon-start/up
 delete mode 100644 .docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
 rename .docker/{s6-assets/init/run-before-daemon-start.sh => scripts/60-pseudo-code-setup.sh} (91%)

diff --git a/.docker/Dockerfile b/.docker/Dockerfile
index f4f1f8d56..0262c8ee4 100644
--- a/.docker/Dockerfile
+++ b/.docker/Dockerfile
@@ -17,8 +17,7 @@ RUN mamba install -y -c conda-forge qe=${QE_VERSION} && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${SYSTEM_USER}"
 
-COPY s6-assets/s6-rc.d /etc/s6-overlay/s6-rc.d
-COPY s6-assets/init /etc/init
+COPY scripts/60-pseudo-code-setup.sh /etc/init/run-before-daemon-start/
 
 # Static example files
 RUN mkdir -p /opt/examples
diff --git a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/aiida-prepare
deleted file mode 100644
index e69de29bb..000000000
diff --git a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/dependencies.d/base
deleted file mode 100644
index e69de29bb..000000000
diff --git a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
deleted file mode 100644
index 573541ac9..000000000
--- a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/timeout-up
+++ /dev/null
@@ -1 +0,0 @@
-0
diff --git a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/type b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/type
deleted file mode 100644
index bdd22a185..000000000
--- a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/type
+++ /dev/null
@@ -1 +0,0 @@
-oneshot
diff --git a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/up b/.docker/s6-assets/s6-rc.d/run-before-daemon-start/up
deleted file mode 100644
index 37d82070a..000000000
--- a/.docker/s6-assets/s6-rc.d/run-before-daemon-start/up
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/command/execlineb -S0
-
-with-contenv
-
-foreground { s6-echo "Calling /etc/init/run-before-daemon-start" }
-/etc/init/run-before-daemon-start.sh
diff --git a/.docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start b/.docker/s6-assets/s6-rc.d/user/contents.d/run-before-daemon-start
deleted file mode 100644
index e69de29bb..000000000
diff --git a/.docker/s6-assets/init/run-before-daemon-start.sh b/.docker/scripts/60-pseudo-code-setup.sh
similarity index 91%
rename from .docker/s6-assets/init/run-before-daemon-start.sh
rename to .docker/scripts/60-pseudo-code-setup.sh
index dbef58500..1e48acd70 100755
--- a/.docker/s6-assets/init/run-before-daemon-start.sh
+++ b/.docker/scripts/60-pseudo-code-setup.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
 
 # If lock file exists, then we have already run this script
-if [ -f ${HOME}/.run-before-daemon-start-done ]; then
+if [ -f ${HOME}/.lock_pseudo_code_setup ]; then
     exit 0
 else
-    touch ${HOME}/.run-before-daemon-start-done
+    touch ${HOME}/.lock_pseudo_code_setup
 fi
 
 # Install pseudopotential libraries
diff --git a/.docker/tests/conftest.py b/.docker/tests/conftest.py
index 314dd220c..266d2be96 100644
--- a/.docker/tests/conftest.py
+++ b/.docker/tests/conftest.py
@@ -23,16 +23,11 @@ def is_container_ready(dodkec_compose):
 @pytest.fixture(scope='session', autouse=True)
 def _docker_service_wait(docker_services):
     """Container startup wait."""
-    # XXX: Temporary fail the real run test because daemon start is should depened on
-    # run-before-daemon-start but it does not.
-
-    #docker_compose = docker_services._docker_compose
+    docker_compose = docker_services._docker_compose
     
-    #docker_services.wait_until_responsive(
-    #    timeout=120.0, pause=0.1, check=lambda: is_container_ready(docker_compose)
-    #)
-    import time
-    time.sleep(60)
+    docker_services.wait_until_responsive(
+        timeout=120.0, pause=0.1, check=lambda: is_container_ready(docker_compose)
+    )
 
 @pytest.fixture
 def container_user():
diff --git a/.docker/tests/test_aiida.py b/.docker/tests/test_aiida.py
index 1f62c5deb..c4cbc6acd 100644
--- a/.docker/tests/test_aiida.py
+++ b/.docker/tests/test_aiida.py
@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=missing-docstring
-import time
 
 def test_verdi_status(aiida_exec, container_user):
     output = aiida_exec('verdi status', user=container_user).decode().strip()

From 080637739204731c17d240a2cf4ac9a9a20bbcdf Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Sat, 4 Nov 2023 23:25:08 +0100
Subject: [PATCH 9/9] finalize the docker tag and push

---
 .docker/Dockerfile           |  4 +--
 .github/workflows/docker.yml | 58 ++++++++++++++++--------------------
 2 files changed, 27 insertions(+), 35 deletions(-)

diff --git a/.docker/Dockerfile b/.docker/Dockerfile
index 0262c8ee4..6555ec3fa 100644
--- a/.docker/Dockerfile
+++ b/.docker/Dockerfile
@@ -1,5 +1,5 @@
-#FROM aiidateam/aiida-core-with-services:edge
-FROM aiidateam/aiida-core-with-services:newly-baked
+#FROM ghcr.io/aiidateam/aiida-core-with-services:edge
+FROM ghcr.io/aiidateam/aiida-core-with-services:pr-6170
 
 USER root
 
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 606189add..379fb7fa3 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -52,38 +52,30 @@ jobs:
             - name: Run tests ✅
               run: TAG=newly-baked python -m pytest -s tests
 
-            #- name: Docker meta 📝
-            #  id: meta
-            #  uses: docker/metadata-action@v4
-            #  env: ${{ fromJson(steps.build_vars.outputs.vars) }}
-            #  with:
-            #      images: |
-            #          name=${{ inputs.registry }}/${{ env.OWNER }}/${{ matrix.image }}
-            #      tags: |
-            #          type=edge,enable={{is_default_branch}}
-            #          type=sha,enable=${{ github.ref_type != 'tag' }}
-            #          type=ref,event=pr
-            #          type=match,pattern=v(\d+\.\d+.\d+),group=1
-            #          type=raw,value={{tag}},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
-            #          type=raw,value=python-${{ env.PYTHON_VERSION }},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
-            #          type=raw,value=postgresql-${{ env.PGSQL_VERSION }},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
-
-            #- name: Login to Container Registry 🔑
-            #  uses: docker/login-action@v2
-            #  with:
-            #      registry: ${{ inputs.registry }}
-            #      username: ${{ secrets.REGISTRY_USERNAME }}
-            #      password: ${{ secrets.REGISTRY_TOKEN }}
+            - name: Docker meta 📝
+              id: meta
+              uses: docker/metadata-action@v4
+              with:
+                  images: |
+                      name=ghcr.io/aiidateam/aiida-quantumespresso
+                  tags: |
+                      type=edge,enable={{is_default_branch}}
+                      type=sha,enable=${{ github.ref_type != 'tag' }}
+                      type=ref,event=pr
+                      type=match,pattern=v(\d+\.\d+.\d+),group=1
+                      type=raw,value={{tag}},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
 
-            #- name: Set tags for image and push 🏷️📤💾
-            #  run: |
-            #      declare -a arr=(${{ steps.meta.outputs.tags }})
-            #      for tag in "${arr[@]}"; do
-            #          arch_tag=$(echo ${tag} | sed "s/:/:${{ inputs.architecture }}-/")
-            #          docker tag ${{ env.OWNER }}/${{ matrix.image }}:newly-baked ${arch_tag}
-            #          docker push ${arch_tag}
+            - name: Login to Container Registry 🔑
+              uses: docker/login-action@v2
+              with:
+                  registry: ghcr.io
+                  username: ${{ github.actor }}
+                  password: ${{ secrets.GITHUB_TOKEN }}
 
-            #          # write tag to file
-            #          mkdir -p /tmp/aiida-core
-            #          echo ${arch_tag} >> /tmp/aiida-core/${{ matrix.image }}-${{ inputs.architecture }}-tags.txt
-            #      done
+            - name: Set tags for image and push 🏷️📤💾
+              run: |
+                  declare -a arr=(${{ steps.meta.outputs.tags }})
+                  for tag in "${arr[@]}"; do
+                      docker tag aiidateam/aiida-quantumespresso:newly-baked ${tag}
+                      docker push ${tag}
+                  done