Merge branch 'main' into pre-commit-ci-update-config

.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

@@ -1,5 +1,5 @@
 # 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_DIR=/opt/conda/envs/quantum-espresso-${QE_VER}
@@ -49,6 +49,7 @@ RUN --mount=from=uv,source=/uv,target=/bin/uv \
 # - Install QE codes and pseudopotentials
 # - Archive home folder
 FROM build_deps AS home_build
+ARG UV_CACHE_DIR
 ARG QE_DIR
 ARG HQ_VER
 ARG HQ_COMPUTER
@@ -89,7 +90,9 @@ RUN --mount=from=qe_conda_env,source=${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 app calculation history'"
    ]
   },
   {
@@ -104,11 +42,66 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from aiidalab_qe.app.utils.search_jobs import QueryInterface\n",
+    "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",
+    "title = ipw.HTML(\n",
+    "    \"<h1> Calculation history</h1>\", layout=ipw.Layout(margin=\"0 0 15px 0\")\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=[title, guide_toggle, info_container])\n",
+    "controls"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "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 +110,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "calculation_history.table"
+    "calculation_history.load_table()"
    ]
   }
  ],

docs/source/_static/logo.png

@@ -0,0 +1 @@
+../../../src/aiidalab_qe/app/static/images/logo.png

docs/source/_static/logo_dark.png

@@ -0,0 +1 @@
+../../../src/aiidalab_qe/app/static/images/logo_dark.png

docs/source/conf.py

@@ -13,7 +13,7 @@
 
 # -- Project information -----------------------------------------------------
 
-version = "v24.10.0a4"
+version = "v24.10.0a7"
 release = f"{version}-dev"
 project = "Quantum ESPRESSO App"
 copyright_first_year = "2023"

docs/source/development/guides.rst

@@ -49,3 +49,24 @@ Developers have two options when using the ``InAppGuide`` widget:
 A decent amount of ``InAppGuide(identifier=<identifier>)`` instances have been placed strategically throughout the app.
 Developers may suggest additional core guide sections via GitHub pull requests.
 For plugin developers, additional instances of either flavor are recommended to be added in any component of the plugin in conjunction with dedicated plugin-specific guides.
+
+Plugin guides
+-------------
+
+Plugin developers can enhance user experience while using the app by introducing custom guides.
+To do so, add the following key/value entry in your plugin's ``__init__.py`` file:
+
+.. code:: python
+
+    my_plugin = {
+        ...
+        "guides": <path-to-guide>,
+    }
+
+where ``path-to-guide`` is the path (``Path`` object or absolute string path) to the directory containing the guide HTML files.
+On app start, the guide manager will scan the plugin entry points for the ``guides`` key and load the guides accordingly.
+
+Guide order
+-----------
+
+When naming your guide HTML documents, prefix the file name with ``#_``. The number ``#`` will determine the order in which the guides are displayed in the list.