Fix/docker build jq

.docker/aiida-core-base/Dockerfile

@@ -104,9 +104,6 @@ USER ${SYSTEM_UID}
 # Pin python version here
 ARG PYTHON_VERSION
 
-# Pin mamba version here
-ARG MAMBA_VERSION
-
 # Download and install Micromamba, and initialize Conda prefix.
 #   <https://github.com/mamba-org/mamba#micromamba>
 #   Similar projects using Micromamba:
@@ -137,7 +134,7 @@ RUN set -x && \
         --prefix="${CONDA_DIR}" \
         --yes \
         "${PYTHON_SPECIFIER}" \
-        "mamba=${MAMBA_VERSION}" && \
+        mamba && \
     rm micromamba && \
     # Pin major.minor version of python
     mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
@@ -146,8 +143,9 @@ RUN set -x && \
     fix-permissions "/home/${SYSTEM_USER}"
 
 # Add ~/.local/bin to PATH where the dependencies get installed via pip
-# This require the package installed with `--user` flag in pip
+# This require the package installed with `--user` flag in pip, which we set as default.
 ENV PATH=${PATH}:/home/${SYSTEM_USER}/.local/bin
+ENV PIP_USER 1
 
 # Switch to root to install AiiDA and set AiiDA as service
 # Install AiiDA from source code

.docker/aiida-core-base/s6-assets/init/aiida-prepare.sh

@@ -18,11 +18,6 @@ verdi config set warnings.development_version False
 # If the environment variable `SETUP_DEFAULT_AIIDA_PROFILE` is not set, set it to `true`.
 if [[ ${SETUP_DEFAULT_AIIDA_PROFILE:-true} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} &> /dev/null; then
 
-    # For the container that includes the services, this script is called as soon as the RabbitMQ startup script has
-    # been launched, but it can take a while for the service to come up. If ``verdi presto`` is called straight away
-    # it is possible it tries to connect to the service before that and it will configure the profile without a broker.
-    sleep 5
-
     # Create AiiDA profile.
     verdi presto \
         --verbosity info \

.docker/aiida-core-with-services/Dockerfile

@@ -22,8 +22,7 @@ RUN mamba install --yes \
 # Install erlang.
 RUN apt-get update --yes && \
      apt-get install --yes --no-install-recommends \
-     erlang \
-     xz-utils && \
+     erlang && \
      apt-get clean && rm -rf /var/lib/apt/lists/* && \
      # Install rabbitmq.
      wget -c --no-check-certificate https://github.com/rabbitmq/rabbitmq-server/releases/download/v${RMQ_VERSION}/rabbitmq-server-generic-unix-${RMQ_VERSION}.tar.xz && \

.docker/aiida-core-with-services/s6-assets/s6-rc.d/rabbitmq/data/check

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+rabbitmq-diagnostics ping
+
+if [ $? -ne 0 ]; then
+    exit 1
+fi
+
+rabbitmq-diagnostics check_running
+
+if [ $? -ne 0 ]; then
+    exit 1
+fi
+
+exit 0

.docker/aiida-core-with-services/s6-assets/s6-rc.d/rabbitmq/notification-fd

@@ -0,0 +1 @@
+3

.docker/aiida-core-with-services/s6-assets/s6-rc.d/rabbitmq/run

@@ -2,5 +2,14 @@
 
 with-contenv
 
-foreground { s6-echo "Calling /etc/init/rabbitmq.sh" }
-rabbitmq-server
+foreground { s6-echo "Starting RMQ server and notifying back when the service is ready" }
+
+
+# For the container that includes the services, aiida-prepare.sh script is called as soon as the RabbitMQ startup script has
+# been launched, but it can take a while for the RMQ service to come up. If ``verdi presto`` is called straight away
+# it is possible it tries to connect to the service before that and it will configure the profile without a broker.
+# Here we use s6-notifyoncheck to do the polling healthy check of the readyness of RMQ service.
+#
+# -w 500: 500 ms between two invocations of ./data/check
+
+s6-notifyoncheck -w 500 rabbitmq-server

.docker/docker-bake.hcl

@@ -43,7 +43,6 @@ target "aiida-core-base" {
   platforms = "${PLATFORMS}"
   args = {
     "PYTHON_VERSION" = "${PYTHON_VERSION}"
-    "MAMBA_VERSION" = "1.5.2"
   }
 }
 target "aiida-core-with-services" {

.docker/tests/test_aiida.py

@@ -1,4 +1,5 @@
 import json
+import re
 
 import pytest
 from packaging.version import parse
@@ -32,8 +33,10 @@ def test_verdi_status(aiida_exec, container_user):
     assert '✔ broker:' in output
     assert 'Daemon is running' in output
 
-    # check that we have suppressed the warnings
-    assert 'Warning' not in output
+    # Check that we have suppressed the warnings coming from using an install from repo and newer RabbitMQ version.
+    # Make sure to match only lines that start with ``Warning:`` because otherwise deprecation warnings from other
+    # packages that we cannot control may fail the test.
+    assert not re.match('^Warning:.*', output)
 
 
 def test_computer_setup_success(aiida_exec, container_user):

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

@@ -28,7 +28,7 @@ runs:
   - name: Install uv installer
     run: curl --proto '=https' --tlsv1.2 -LsSf https://${{ env.UV_URL }} | sh
     env:
-      UV_VERSION: 0.2.5
+      UV_VERSION: 0.2.9
       UV_URL: github.com/astral-sh/uv/releases/download/$UV_VERSION/uv-installer.sh
     shell: bash
 

.github/config/profile.yaml

@@ -4,7 +4,7 @@ first_name: Giuseppe
 last_name: Verdi
 institution: Khedivial
 db_backend: core.psql_dos
-db_engine: postgresql_psycopg2
+db_engine: postgresql_psycopg
 db_host: localhost
 db_port: 5432
 db_name: test_aiida

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+# Maintain dependencies for GitHub Actions
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: monthly
+  groups:
+    gha-dependencies:
+      patterns:
+      - '*'

.github/workflows/ci-code.yml

@@ -40,7 +40,7 @@ jobs:
 
     - name: Create commit comment
       if: failure() && steps.check_reqs.outputs.error
-      uses: peter-evans/commit-comment@v1
+      uses: peter-evans/commit-comment@v3
       with:
         path: pyproject.toml
         body: |
@@ -139,17 +139,7 @@ jobs:
     - name: Run test suite
       env:
         AIIDA_WARN_v3: 0
-      run: pytest -m 'presto' --cov aiida
-
-    - name: Upload coverage report
-      if: github.repository == 'aiidateam/aiida-core'
-      uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        name: aiida-pytests-presto
-        flags: presto
-        file: ./coverage.xml
-        fail_ci_if_error: false  # don't fail job, if coverage upload fails
+      run: pytest -m 'presto'
 
 
   verdi:
@@ -165,6 +155,7 @@ jobs:
       uses: ./.github/actions/install-aiida-core
       with:
         python-version: '3.12'
+        from-requirements: 'false'
 
     - name: Run verdi tests
       run: |

.github/workflows/ci-style.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches-ignore: [gh-pages]
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
 
   pre-commit:

.github/workflows/docker-build-test.yml

@@ -41,7 +41,7 @@ jobs:
       uses: docker/setup-buildx-action@v3
 
     - name: Build images
-      uses: docker/bake-action@v4
+      uses: docker/bake-action@v5
       with:
         # Load to Docker engine for testing
         load: true

.github/workflows/docker-build.yml

@@ -54,7 +54,7 @@ jobs:
 
     - name: Build and upload to ghcr.io 📤
       id: build
-      uses: docker/bake-action@v4
+      uses: docker/bake-action@v5
       with:
         push: true
         workdir: .docker/

.github/workflows/docker-publish.yml

@@ -59,6 +59,12 @@ jobs:
         vars=$(cat build.json | jq -c '[.variable | to_entries[] | {"key": .key, "value": .value.default}] | from_entries')
         echo "vars=$vars" | tee -a "${GITHUB_OUTPUT}"
 
+    - id: get-version
+      if: ${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
+      run: |
+        tag="${{ github.ref_name }}"
+        echo "AIIDA_VERSION=${tag#v}" >> $GITHUB_OUTPUT
+
     - name: Docker meta
       id: meta
       uses: docker/metadata-action@v5
@@ -69,7 +75,7 @@ jobs:
           type=ref,event=pr
           type=ref,event=branch,enable=${{ github.ref_name != 'main' }}
           type=edge,enable={{is_default_branch}}
-          type=raw,value=aiida-${{ env.AIIDA_VERSION }},enable=${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
+          type=raw,value=aiida-${{ steps.get-version.outputs.AIIDA_VERSION }},enable=${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
           type=raw,value=python-${{ env.PYTHON_VERSION }},enable=${{ github.ref_type == 'tag' && startsWith(github.ref_name, 'v') }}
           type=raw,value=postgresql-${{ env.PGSQL_VERSION }},enable=${{ github.ref_type == 'tag' && startsWith(github.ref_name, 'v') }}
           type=match,pattern=v(\d{4}\.\d{4}(-.+)?),group=1

.github/workflows/docs-build.yml

@@ -7,6 +7,9 @@ on:
     branches-ignore: [gh-pages]
     paths: [docs/**]
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
 
   docs-linkcheck:

.github/workflows/extract-docker-image-names.sh

@@ -9,38 +9,35 @@ set -euo pipefail
 # The input to this script is a JSON string passed via BAKE_METADATA env variable
 # Here's example input (trimmed to relevant bits):
 # BAKE_METADATA: {
-#    "base": {
+#    "aiida-core-base": {
+#      # ...
 #      "containerimage.descriptor": {
 #        "mediaType": "application/vnd.docker.distribution.manifest.v2+json",
 #        "digest": "sha256:8e57a52b924b67567314b8ed3c968859cad99ea13521e60bbef40457e16f391d",
 #        "size": 6170,
 #      },
 #      "containerimage.digest": "sha256:8e57a52b924b67567314b8ed3c968859cad99ea13521e60bbef40457e16f391d",
-#      "image.name": "ghcr.io/aiidalab/base"
-#    },
-#    "aiida-core-base": {
 #      "image.name": "ghcr.io/aiidateam/aiida-core-base"
-#       "containerimage.digest": "sha256:6753a809b5b2675bf4c22408e07c1df155907a465b33c369ef93ebcb1c4fec26",
-#       "...": ""
-#    }
-#    "aiida-core-with-services": {
-#      "image.name": "ghcr.io/aiidateam/aiida-core-with-services"
-#      "containerimage.digest": "sha256:85ee91f61be1ea601591c785db038e5899d68d5fb89e07d66d9efbe8f352ee48",
-#      "...": ""
-#    }
+#    },
 #    "aiida-core-dev": {
-#      "image.name": "ghcr.io/aiidateam/aiida-core-with-services"
 #      "containerimage.digest": "sha256:4d9be090da287fcdf2d4658bb82f78bad791ccd15dac9af594fb8306abe47e97",
+#      "...": ...
+#      "image.name": "ghcr.io/aiidateam/aiida-core-dev"
+#    },
+#    "aiida-core-with-services": {
 #      "...": ""
-#    }
+#      "containerimage.digest": "sha256:85ee91f61be1ea601591c785db038e5899d68d5fb89e07d66d9efbe8f352ee48",
+#      "image.name": "ghcr.io/aiidateam/aiida-core-with-services"
+#    },
+#    "some-other-key": ...
 #  }
 #
 # Example output (real output is on one line):
 #
 # images={
-#   "AIIDA_CORE_BASE_IMAGE": "ghcr.io/aiidateam/aiida-core-base@sha256:8e57a52b924b67567314b8ed3c968859cad99ea13521e60bbef40457e16f391d",
-#   "AIIDA_CORE_WITH_SERVICES_IMAGE": "ghcr.io/aiidateam/aiida-core-with-services@sha256:6753a809b5b2675bf4c22408e07c1df155907a465b33c369ef93ebcb1c4fec26",
-#   "AIIDA_CORE_DEV_IMAGE": "ghcr.io/aiidateam/aiida-core-dev@sha256:85ee91f61be1ea601591c785db038e5899d68d5fb89e07d66d9efbe8f352ee48",
+#   "AIIDA_CORE_BASE_IMAGE": "ghcr.io/aiidateam/aiida-core-base@sha256:4c402a8bfd635650ad691674f8f29e7ddec5fa656fb425452067950415ee447f",
+#   "AIIDA_CORE_DEV_IMAGE": "ghcr.io/aiidateam/aiida-core-dev@sha256:f94c06e47f801e751f9829010b31532039b210aad2649d43205e16c08371b2ed",
+#   "AIIDA_CORE_WITH_SERVICES_IMAGE": "ghcr.io/aiidateam/aiida-core-with-services@sha256:bd8272f2a331af7eac3e83c44cc16d23b2e5f601a20ab4a865402659b758515e"
 # }
 #
 # This json output is later turned to environment variables using fromJson() GHA builtin
@@ -52,5 +49,7 @@ if [[ -z ${BAKE_METADATA-} ]];then
     exit 1
 fi
 
-images=$(echo "${BAKE_METADATA}" | jq -c '. as $base |[to_entries[] |{"key": (.key|ascii_upcase|sub("-"; "_"; "g") + "_IMAGE"), "value": [(.value."image.name"|split(",")[0]),.value."containerimage.digest"]|join("@")}] |from_entries')
+images=$(echo "${BAKE_METADATA}" |
+jq -c 'to_entries | map(select(.key | startswith("aiida"))) | from_entries' | # filters out every key that does not start with aiida
+jq -c '. as $base |[to_entries[] |{"key": (.key|ascii_upcase|sub("-"; "_"; "g") + "_IMAGE"), "value": [(.value."image.name"|split(",")[0]),.value."containerimage.digest"]|join("@")}] |from_entries')
 echo "images=$images"

.github/workflows/release.yml

@@ -9,6 +9,9 @@ on:
     tags:
     - v[0-9]+.[0-9]+.[0-9]+*
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
 
   check-release-tag:
@@ -33,17 +36,13 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Install system dependencies
-      # note libkrb5-dev is required as a dependency for the gssapi pip install
-      run: |
-        sudo apt update
-        sudo apt install libkrb5-dev ruby ruby-dev
 
     - name: Install aiida-core and pre-commit
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         extras: '[pre-commit]'
+        from-requirements: 'false'
 
     - name: Run pre-commit
       run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/test-install.yml

@@ -81,7 +81,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         channels: conda-forge
 
@@ -148,7 +148,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         channels: conda-forge
 
@@ -229,7 +229,7 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest --cov aiida --verbose tests -m 'not nightly'
+      run: pytest --verbose tests -m 'not nightly'
 
     - name: Freeze test environment
       run: pip freeze | sed '1d' | tee requirements-py-${{ matrix.python-version }}.txt
@@ -274,7 +274,7 @@ jobs:
 #
     - name: Create commit comment
       if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      uses: peter-evans/commit-comment@v1
+      uses: peter-evans/commit-comment@v3
       with:
         token: ${{ secrets.GITHUB_TOKEN }}
         path: pyproject.toml
@@ -306,7 +306,7 @@ jobs:
       if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
       id: create_update_requirements_pr
       continue-on-error: true
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v6
       with:
         branch: update-requirements
         commit-message: Automated update of requirements/ files.
@@ -324,7 +324,7 @@ jobs:
 
     - name: Create PR comment on success
       if: steps.create_update_requirements_pr.outcome == 'Success'
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v4
       with:
         issue-number: ${{ github.event.number }}
         body: |
@@ -333,7 +333,7 @@ jobs:
 
     - name: Create PR comment on failure
       if: steps.create_update_requirements_pr.outcome == 'Failure'
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v4
       with:
         issue-number: ${{ github.event.number }}
         body: |