Merge branch 'main' into dependabot/pip/docs/jinja2-3.1.5

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+---
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+    release:
+        types: [published]
+
+permissions:
+    contents: read
+
+jobs:
+    deploy:
+
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v3
+              with:
+                  python-version: 3.x
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install build
+            - name: Build package
+              run: python -m build
+            - name: Publish package
+              uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+              with:
+                  user: __token__
+                  password: ${{ secrets.PYPI_API_TOKEN }}

.readthedocs.yaml

@@ -5,6 +5,9 @@
 # Required
 version: 2
 
+sphinx:
+    configuration: docs/source/conf.py
+
 # Set the OS, Python version and other tools you might need
 build:
     os: ubuntu-22.04

Dockerfile

@@ -1,7 +1,7 @@
 # syntax=docker/dockerfile:1
-ARG FULL_STACK_VER=2024.1023
+ARG FULL_STACK_VER=2025.1025
 ARG UV_VER=0.4.7
-ARG QE_VER=7.2
+ARG QE_VER=7.4
 ARG QE_DIR=/opt/conda/envs/quantum-espresso-${QE_VER}
 ARG HQ_VER=0.19.0
 
@@ -49,6 +49,7 @@ RUN --mount=from=uv,source=/uv,target=/bin/uv \
 # - Install QE codes and pseudopotentials
 # - Archive home folder
 FROM build_deps AS home_build
+ARG UV_CACHE_DIR
 ARG QE_DIR
 ARG HQ_VER
 ARG HQ_COMPUTER
@@ -89,7 +90,9 @@ RUN --mount=from=qe_conda_env,source=${QE_DIR},target=${QE_DIR} \
     verdi daemon stop && \
     mamba run -n aiida-core-services pg_ctl stop && \
     touch /home/${NB_USER}/.FLAG_HOME_INITIALIZED && \
-    cd /home/${NB_USER} && tar -cf /opt/conda/home.tar .
+    # NOTE: The work folder is empty but if included clashes with the work folder in a Renku
+    # session whose permissions cannot be changed.
+    cd /home/${NB_USER} && tar -cf /opt/conda/home.tar --exclude work .
 
 # STAGE 3 - Final stage
 # - Install python dependencies

before-notebook.d/00_untar-home.sh

@@ -15,10 +15,11 @@ if [ ! -e $home/.FLAG_HOME_INITIALIZED ]; then
   fi
 
   echo "Extracting $HOME_TAR to $home"
-  # NOTE: a tar error when deployed to k8s but at the momment not cause any issue
-  # tar: .: Cannot utime: Operation not permitted
-  # tar: .: Cannot change mode to rwxr-s---: Operation not permitted
-  tar -xf $HOME_TAR -C "$home"
+  # NOTE: the added flags to tar are to address some errors that occur in k8s
+  # tar: .: Cannot utime: Operation not permitted -> --touch solves this problem
+  # tar: .: Cannot change mode to rwxr-s---: Operation not permitted -> --no-overwrite-dir solves this problem
+  # this only refers to the metadata and permissions of existing directories, not their contents
+  tar -xf $HOME_TAR -C "$home" --no-overwrite-dir --touch
 else
   echo "$home folder is not empty!"
   ls -lrta "$home"

before-notebook.d/43_start-hq.sh

@@ -10,34 +10,51 @@ set -x
 # But for developers, please update your cgroup version to v2.
 # See: https://kubernetes.io/docs/concepts/architecture/cgroups/#using-cgroupv2
 
-# computer memory from runtime
-MEMORY_LIMIT=$(cat /sys/fs/cgroup/memory.max)
+# Default to cgroupv1 paths
+CPU_QUOTA_PATH="/sys/fs/cgroup/cpu/cpu.cfs_quota_us"
+CPU_PERIOD_PATH="/sys/fs/cgroup/cpu/cpu.cfs_period_us"
+MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory/memory.limit_in_bytes"
 
-if [ "$MEMORY_LIMIT" = "max" ]; then
-  MEMORY_LIMIT=4096
-  echo "No memory limit set, use 4GiB"
-else
-  MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
-  echo "Memory Limit: ${MEMORY_LIMIT} MiB"
+# Fallback if cgroupv2 paths exist
+if [ -f /sys/fs/cgroup/cpu.max ]; then
+  CPU_QUOTA_PATH="/sys/fs/cgroup/cpu.max"
+  CPU_PERIOD_PATH="/sys/fs/cgroup/cpu.max"
+fi
+
+if [ -f /sys/fs/cgroup/memory.max ]; then
+  MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory.max"
 fi
 
-# Compute number of cpus allocated to the container
-CPU_LIMIT=$(awk '{print $1}' /sys/fs/cgroup/cpu.max)
-CPU_PERIOD=$(awk '{print $2}' /sys/fs/cgroup/cpu.max)
+# Compute memory limit
+if [ -f "$MEMORY_LIMIT_PATH" ]; then
+  MEMORY_LIMIT=$(cat "$MEMORY_LIMIT_PATH")
+  if [ "$MEMORY_LIMIT" = "max" ] || [ "$MEMORY_LIMIT" -eq -1 ]; then
+    MEMORY_LIMIT=4096
+  else
+    MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
+  fi
+else
+  MEMORY_LIMIT=4096
+fi
+echo "Memory Limit: ${MEMORY_LIMIT} MiB"
 
-if [ "$CPU_PERIOD" -ne 0 ]; then
-  CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
-  echo "Number of CPUs allocated: $CPU_NUMBER"
+# Compute CPU limit
+if [ -f "$CPU_QUOTA_PATH" ] && [ -f "$CPU_PERIOD_PATH" ]; then
+  CPU_LIMIT=$(cat "$CPU_QUOTA_PATH")
+  CPU_PERIOD=$(cat "$CPU_PERIOD_PATH")
 
-  # for HQ setting round to integer number of CPUs, the left are for system tasks
-  CPU_LIMIT=$(echo "scale=0; $CPU_LIMIT / $CPU_PERIOD" | bc)
+  if [ "$CPU_LIMIT" != "max" ] && [ "$CPU_PERIOD" -ne 0 ]; then
+    CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
+    CPU_LIMIT=$(echo "$CPU_NUMBER / 1" | bc)  # Round down to integer
+  else
+    CPU_LIMIT=$(nproc)
+  fi
 else
-  # if no limit (with local OCI without setting cpu limit, use all CPUs)
   CPU_LIMIT=$(nproc)
-  echo "No CPU limit set"
 fi
+echo "Number of CPUs allocated: $CPU_LIMIT"
 
-# Start hq server with a worker
+# Start HQ server and worker
 run-one-constantly hq server start 1>$HOME/.hq-stdout 2>$HOME/.hq-stderr &
 run-one-constantly hq worker start --cpus=${CPU_LIMIT} --resource "mem=sum(${MEMORY_LIMIT})" --no-detect-resources &
 

calculation_history.ipynb

@@ -6,73 +6,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import ipywidgets as ipw\n",
-    "\n",
-    "how_to = ipw.HTML(\n",
-    "    \"\"\"\n",
-    "    <style>\n",
-    "        .page-title {\n",
-    "            font-family: Arial, sans-serif;\n",
-    "            font-size: 28px;\n",
-    "            color: #2c3e50;\n",
-    "            margin-top: 0;\n",
-    "            margin-bottom: 20px;\n",
-    "        }\n",
-    "        .how-to-section {\n",
-    "            font-family: Arial, sans-serif;\n",
-    "            background-color: #f9f9f9;\n",
-    "            border: 1px solid #ddd;\n",
-    "            border-radius: 8px;\n",
-    "            padding: 15px 20px;\n",
-    "            margin-bottom: 20px;\n",
-    "            box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1);\n",
-    "        }\n",
-    "        .how-to-section h2 {\n",
-    "            color: #2c3e50;\n",
-    "            font-size: 24px;\n",
-    "            margin-top: 0;\n",
-    "        }\n",
-    "        .how-to-section p {\n",
-    "            font-size: 14px;\n",
-    "            color: #7f8c8d;\n",
-    "            line-height: 1.6;\n",
-    "        }\n",
-    "        .how-to-section ul {\n",
-    "            list-style-type: disc;\n",
-    "            padding-left: 20px;\n",
-    "        }\n",
-    "        .how-to-section ul li {\n",
-    "            font-size: 14px;\n",
-    "            color: #34495e;\n",
-    "            margin-bottom: 8px;\n",
-    "        }\n",
-    "        .how-to-section ul li b {\n",
-    "            color: #2c3e50;\n",
-    "        }\n",
-    "    </style>\n",
-    "    <div class=\"page-title\">Calculation History</div>\n",
-    "    <div class=\"how-to-section\">\n",
-    "        <h2>How to Use This Page</h2>\n",
-    "        <p>\n",
-    "            This page allows you to view and manage your calculation history. Use the table below to \n",
-    "            see all jobs in the database. You can use the following filters to narrow down your search:\n",
-    "        </p>\n",
-    "        <ul>\n",
-    "            <li><b>Label Search Field:</b> Enter a job label to find matching jobs.</li>\n",
-    "            <li><b>Job State Dropdown:</b> Filter jobs based on their state (e.g., finished, running).</li>\n",
-    "            <li><b>Date Range Picker:</b> Select a start and end date to view jobs created within that range.</li>\n",
-    "            <li><b>Properties Filter:</b> Select specific properties associated with jobs.</li>\n",
-    "        </ul>\n",
-    "        <p>\n",
-    "            Each row in the table provides links to inspect, delete or download a job. To delete a job, click the \"Delete\" \n",
-    "            link in the respective row. To view detailed information about a job, click the \"PK\" link. To download the \n",
-    "            input/output files of a job, click the \"Download\" link.\n",
-    "        </p>\n",
-    "    </div>\n",
-    "    \"\"\"\n",
-    ")\n",
-    "\n",
-    "how_to"
+    "%%javascript\n",
+    "IPython.OutputArea.prototype._should_scroll = function(lines) {\n",
+    "    return false;\n",
+    "}\n",
+    "document.title='AiiDAlab QE | View history'"
    ]
   },
   {
@@ -98,17 +36,76 @@
     "load_css(css_path=\"src/aiidalab_qe/app/static/styles\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AiiDAlab Quantum ESPRESSO - Calculation history"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ipywidgets as ipw\n",
+    "from importlib_resources import files\n",
+    "from jinja2 import Environment\n",
+    "\n",
+    "from aiidalab_qe.app.static import templates\n",
+    "from aiidalab_qe.common.infobox import InfoBox\n",
+    "\n",
+    "env = Environment()\n",
+    "guide_template = (\n",
+    "    files(templates).joinpath(\"calculation_history_guide.jinja\").read_text()\n",
+    ")\n",
+    "guide = ipw.HTML(env.from_string(guide_template).render())\n",
+    "\n",
+    "\n",
+    "info_container = InfoBox(layout=ipw.Layout(margin=\"14px 2px 0\"))\n",
+    "guide_toggle = ipw.ToggleButton(\n",
+    "    layout=ipw.Layout(width=\"150px\"),\n",
+    "    button_style=\"\",\n",
+    "    icon=\"book\",\n",
+    "    value=False,\n",
+    "    description=\"Page guide\",\n",
+    "    tooltip=\"Learn how to use the app\",\n",
+    "    disabled=False,\n",
+    ")\n",
+    "\n",
+    "\n",
+    "def _on_guide_toggle(change: dict):\n",
+    "    \"\"\"Toggle the guide section.\"\"\"\n",
+    "    if change[\"new\"]:\n",
+    "        info_container.children = [\n",
+    "            guide,\n",
+    "        ]\n",
+    "        info_container.layout.display = \"flex\"\n",
+    "    else:\n",
+    "        info_container.children = []\n",
+    "        info_container.layout.display = \"none\"\n",
+    "\n",
+    "\n",
+    "guide_toggle.observe(\n",
+    "    _on_guide_toggle,\n",
+    "    \"value\",\n",
+    ")\n",
+    "\n",
+    "controls = ipw.VBox(children=[guide_toggle, info_container])\n",
+    "controls"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from aiidalab_qe.app.utils.search_jobs import QueryInterface\n",
+    "from aiidalab_qe.app.utils.search_jobs import CalculationHistory\n",
     "\n",
-    "calculation_history = QueryInterface()\n",
-    "calculation_history.setup_table()\n",
-    "calculation_history.filters_layout"
+    "calculation_history = CalculationHistory()\n",
+    "calculation_history.main"
    ]
   },
   {
@@ -117,7 +114,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "calculation_history.table"
+    "calculation_history.load_table()"
    ]
   }
  ],