Merge branch 'main' into python-3.10.11

Author: danielhollas

.github/workflows/build.yml

@@ -27,7 +27,7 @@ jobs:
         timeout-minutes: 120
 
         outputs:
-            images: ${{ steps.bake_metadata.outputs.images }}
+            images: ${{ steps.set-output.outputs.result }}
 
         # Make sure we fail if any command in a piped command sequence fails
         defaults:
@@ -77,15 +77,32 @@ jobs:
                       build.json
                       .github/workflows/env.hcl
 
-            - name: Set output image names
-              id: bake_metadata
-              # bake-action metadata output has gotten too big, so we first write it
-              # to a file. See https://github.com/aiidalab/aiidalab-docker-stack/issues/491
-              run: |
-                  cat << EOF > bake_metadata.json
-                  ${{ steps.build-upload.outputs.metadata }}
-                  EOF
-                  images=$(.github/workflows/extract-image-names.sh bake_metadata.json)
-                  echo "images=${images}" >> "${GITHUB_OUTPUT}"
-                  # Pretty-print for GHA logs
-                  echo "$images" | jq
+            - name: Set output variables
+              id: set-output
+              uses: actions/github-script@v7
+              with:
+                  # We need to produce the following JSON string from the bake action output,
+                  # which is then used in follow-up steps to uniquelly identify the built
+                  # images by their digests, and not by their tags. See e.g. test.yml
+                  # {
+                  #   "BASE_IMAGE": "ghcr.io/aiidalab/base@sha256:bc53c...",
+                  #   "BASE_WITH_SERVICES_IMAGE":"ghcr.io/aiidalab/base-with-services@sha256:0df1...",
+                  #   "FULL_STACK_IMAGE":"ghcr.io/aiidalab/full-stack@sha256:dd04...",
+                  #   "LAB_IMAGE":"ghcr.io/aiidalab/lab@sha256:e8c7b3a662660ad20fef7...",
+                  # }
+                  script: |
+                      const bake_output = JSON.parse(process.env.BAKE_METADATA, 'utf-8');
+                      images = {};
+                      for (const key in bake_output) {
+                          const image = bake_output[key];
+                          // turn e.g. 'full-stack' to 'FULL_STACK_IMAGE' key
+                          const image_envvar = `${key.toUpperCase().replace(/-/g, "_")}_IMAGE`;
+                          // create full canonical path to the image using its digest, i.e.
+                          // ghcr.io/aiidalab/base@sha256:cdad93278a...
+                          const image_digest = `${image["image.name"]}@${image["containerimage.digest"]}`;
+                          images[image_envvar] = image_digest;
+                      }
+                      console.log(images);
+                      return images;
+              env:
+                  BAKE_METADATA: ${{ steps.build-upload.outputs.metadata }}

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

@@ -18,14 +18,14 @@ repos:
             args: [--preserve-quotes]
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.9.2
+      rev: v0.11.4
       hooks:
           - id: ruff-format
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
     - repo: https://github.com/python-jsonschema/check-jsonschema
-      rev: "0.31.0"
+      rev: "0.32.1"
       hooks:
           - id: check-dependabot
           - id: check-github-workflows

.pre-commit-config.yaml

@@ -10,7 +10,7 @@
       "default": "3.9.13"
     },
     "AIIDA_VERSION": {
-      "default": "2.6.3"
+      "default": "2.7.1"
     },
     "AIIDALAB_VERSION": {
       "default": "24.09.0"

build.json

@@ -1,5 +1,5 @@
 [bumpver]
-current_version = "v2025.1026"
+current_version = "v2025.1027"
 version_pattern = "vYYYY.BUILD[-TAG]"
 commit_message = "Bump version {old_version} -> {new_version}."
 commit = true

bumpver.toml

@@ -11,7 +11,7 @@ USER root
 # rsync: needed to support the new AiiDA backup command
 # povray: rendering engine used in aiidalab-widgets-base
 # bc: needed to compute the resources for computer setup
-ENV EXTRA_APT_PACKAGES "curl povray rsync build-essential bc"
+ENV EXTRA_APT_PACKAGES="curl povray rsync build-essential bc"
 
 # For ARM64 we need to install erlang as it is not available on conda-forge
 # (this is needed later as rabbitmq dependency in base-with-services image,
@@ -41,7 +41,7 @@ RUN echo "notebook==$(jupyter-notebook --version)" >> /opt/requirements.txt
 RUN cat /opt/requirements.txt | xargs -I{} conda config --system --add pinned_packages {}
 
 # Configure pip to use the same requirements file as constraints file.
-ENV PIP_CONSTRAINT /opt/requirements.txt
+ENV PIP_CONSTRAINT=/opt/requirements.txt
 # Ensure that pip installs packages to '~/.local/lib/python3.X/site-packages/' by default
 # by implicitly passing the '--user' option to 'pip install'
 # Otherwise, pip would install into /opt/conda and such packages would be lost
@@ -80,12 +80,12 @@ COPY config-quick-setup.yaml .
 COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
 
 # Configure AiiDA.
-ENV SETUP_DEFAULT_AIIDA_PROFILE true
-ENV AIIDA_PROFILE_NAME default
-ENV AIIDA_USER_EMAIL aiida@localhost
-ENV AIIDA_USER_FIRST_NAME Giuseppe
-ENV AIIDA_USER_LAST_NAME Verdi
-ENV AIIDA_USER_INSTITUTION Khedivial
+ENV SETUP_DEFAULT_AIIDA_PROFILE=true
+ENV AIIDA_PROFILE_NAME=default
+ENV AIIDA_USER_EMAIL=aiida@localhost
+ENV AIIDA_USER_FIRST_NAME=Giuseppe
+ENV AIIDA_USER_LAST_NAME=Verdi
+ENV AIIDA_USER_INSTITUTION=Khedivial
 
 # Install the load-singlesshagent.sh script as described here:
 # https://aiida.readthedocs.io/projects/aiida-core/en/v2.0.0/howto/ssh.html#starting-the-ssh-agent

stack/base/Dockerfile

@@ -1,5 +1,4 @@
 ---
-db_engine: postgresql_psycopg2
 db_backend: core.psql_dos
 db_host: database
 db_port: 5432

stack/base/config-quick-setup.yaml

@@ -1,5 +1,5 @@
 # syntax=docker/dockerfile:1
-FROM base-with-services as base
+FROM base-with-services AS base
 
 FROM lab
 

stack/full-stack/Dockerfile

@@ -51,9 +51,9 @@ COPY --chown=${NB_UID}:${NB_GID} gears.svg ${CONDA_DIR}/share/jupyter/nbextensio
 COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
 
 # Configure AiiDAlab environment.
-ENV AIIDALAB_HOME /home/${NB_USER}
-ENV AIIDALAB_APPS ${AIIDALAB_HOME}/apps
-ENV AIIDALAB_DEFAULT_GIT_BRANCH master
+ENV AIIDALAB_HOME=/home/${NB_USER}
+ENV AIIDALAB_APPS=${AIIDALAB_HOME}/apps
+ENV AIIDALAB_DEFAULT_GIT_BRANCH=master
 
 # Specify which apps to install in addition to the home app. The
 # AIIDALAB_DEFAULT_APPS variable should be a whitespace-delimited variable
@@ -66,10 +66,10 @@ ENV AIIDALAB_DEFAULT_GIT_BRANCH master
 # Please note that multiple entries must be whitespace delimited.
 # Please see `aiidalab install --help` for more information.
 # ENV AIIDALAB_DEFAULT_APPS "aiidalab-widgets-base~=1.0"
-ENV AIIDALAB_DEFAULT_APPS ""
+ENV AIIDALAB_DEFAULT_APPS=""
 
 # Specify default factory reset (not set):
-ENV AIIDALAB_FACTORY_RESET ""
+ENV AIIDALAB_FACTORY_RESET=""
 
 USER ${NB_USER}
 
@@ -88,17 +88,17 @@ RUN  mkdir -p /home/${NB_USER}/apps
 # Instead, here we configure Jupyter to kill all kernels that have been alive for
 # more than 12 hours. We also close all inactive terminals after 10 minutes.
 # NOTE2: show_banner=False disables the banner for upgrading to Notebook 7.
-ENV NOTEBOOK_ARGS \
-     "--NotebookApp.default_url='/apps/apps/home/start.ipynb'" \
-     "--NotebookApp.show_banner=False" \
-     "--ContentsManager.allow_hidden=True" \
-     "--MappingKernelManager.buffer_offline_messages=True" \
-     "--MappingKernelManager.cull_busy=True" \
-     "--MappingKernelManager.cull_connected=True" \
-     "--MappingKernelManager.cull_idle_timeout=64800" \
-     "--MappingKernelManager.cull_interval=300" \
-     "--TerminalManager.cull_inactive_timeout=3600" \
-     "--TerminalManager.cull_interval=300"
+ENV NOTEBOOK_ARGS=\
+"--NotebookApp.default_url=/apps/apps/home/start.ipynb "\
+"--NotebookApp.show_banner=False "\
+"--ContentsManager.allow_hidden=True "\
+"--MappingKernelManager.buffer_offline_messages=True "\
+"--MappingKernelManager.cull_busy=True "\
+"--MappingKernelManager.cull_connected=True "\
+"--MappingKernelManager.cull_idle_timeout=64800 "\
+"--MappingKernelManager.cull_interval=300 "\
+"--TerminalManager.cull_inactive_timeout=3600 "\
+"--TerminalManager.cull_interval=300"
 
 # Set up the logo of notebook interface
 ARG PYTHON_MINOR_VERSION