Merge branch 'main' into bands_projwfn

.github/workflows/ci.yml

@@ -20,9 +20,8 @@ jobs:
 
         strategy:
             matrix:
-                tag: [latest]
-                python-version: ['3.9', '3.10']
-                aiida-core-version: [2.3, 2.5]
+                python-version: ['3.9', '3.11']
+                aiida-core-version: ['2.3', '2.6']
             fail-fast: false
 
         runs-on: ubuntu-latest
@@ -45,15 +44,18 @@ jobs:
                   python-version: ${{ matrix.python-version }}
 
             - name: Install uv
-              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.2.13/uv-installer.sh | sh
+              uses: astral-sh/setup-uv@v1
+              with:
+                  version: 0.4.7
 
             - name: Install package
               run: uv pip install --system -e .[dev] aiida-core==${{ matrix.aiida-core-version }}
 
             - name: Run pytest
-              run: pytest -v tests --cov=aiidalab_qe
-              env:
-                  TAG: ${{ matrix.tag }}
+              # Only collect code coverage with aiida-core=2.3, to speed up tests
+              # with higher aiida versions that for some reason run slower, see:
+              # https://github.com/aiidalab/aiidalab-qe/issues/766
+              run: pytest -v tests ${{ matrix.aiida-core-version == '2.3' && '--cov=aiidalab_qe' || '' }}
 
             - name: Upload coverage reports to Codecov
               uses: codecov/codecov-action@v4

.gitignore

@@ -7,7 +7,7 @@
 build/
 export/
 .do-not-setup-on-localhost
-
+.mypy_cache/
 
 # Sphinx documentation
 docs/html

.pre-commit-config.yaml

@@ -24,28 +24,16 @@ repos:
       hooks:
           - id: check-github-workflows
 
-    - repo: https://github.com/nbQA-dev/nbQA
-      rev: 1.8.5
-      hooks:
-          - id: nbqa-pyupgrade
-            args: [--py38-plus]
-          - id: nbqa-isort
-            args: [--profile=black]
-          - id: nbqa-ruff
-            # suppress E402
-            args: [--ignore=E402]
-
     - repo: https://github.com/kynan/nbstripout
       rev: 0.7.1
       hooks:
           - id: nbstripout
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      # Ruff version.
-      rev: v0.5.0
+      rev: v0.6.1
       hooks:
-        # Run the linter.
           - id: ruff
+            types_or: [python, pyi, jupyter]
             args: [--fix]
-        # Run the formatter.
           - id: ruff-format
+            types_or: [python, pyi, jupyter]

Dockerfile

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
-ARG FULL_STACK_VER=2024.1021
-ARG UV_VER=0.2.27
+ARG FULL_STACK_VER=2024.1022
+ARG UV_VER=0.4.7
 ARG QE_VER=7.2
 ARG QE_DIR=/opt/conda/envs/quantum-espresso-${QE_VER}
 
@@ -86,7 +86,7 @@ COPY --from=qe_conda_env ${QE_DIR} ${QE_DIR}
 
 USER root
 COPY ./before-notebook.d/* /usr/local/bin/before-notebook.d/
-RUN fix-permissions "${CONDA_DIR}"
+
 # Remove content of $HOME
 # '-mindepth=1' ensures that we do not remove the home directory itself.
 RUN find /home/${NB_USER}/ -mindepth 1 -delete

README.md

@@ -5,8 +5,8 @@
 
 ## About
 
-This is a early-development implementation of an AiiDAlab application for Quantum ESPRESSO workflow.
-The app allows the execution of a workflow with Quantum ESPRESSO that includes the selection of an input structure, its relaxation, and the bands structure calculation.
+This is an AiiDAlab application for Quantum ESPRESSO workflows.
+The app allows the execution of a workflow with Quantum ESPRESSO that includes the selection of an input structure, its relaxation, the bands structure calculation, and more!
 
 **The app is currently in an early development stage!**
 
@@ -41,6 +41,16 @@ Then, you can run the integration tests with:
 pytest --driver Chrome tests_integration
 ```
 
+### Published Docker images
+
+Supported tags released on [Github Container Registry](https://ghcr.io/aiidalab):
+
+- `edge` – the latest commit on the default branch (`main`)
+- `latest` – the latest stable release
+- `$version` – the version of a specific release (ex. `2022.1001`)
+
+Pull requests into the default branch are further released on ghcr.io with the `pr-###` tag to simplify the testing of development versions.
+
 ## For maintainers
 
 To create a new release, clone the repository, install development dependencies with `pip install '.[dev]'`, and then execute `bumpver update`.
@@ -61,9 +71,9 @@ Additional notes:
 ## Acknowledgements
 We acknowledge support from:
 * the European Union\'s Horizon 2020 research and innovation programme (Grant No. 957189, [project BIG-MAP](https://www.big-map.eu)).
-* the [MARVEL National Centre for Competency in Research](<http://nccr-marvel.ch>) funded by the [Swiss National Science Foundation](<http://www.snf.ch/en>).
+* the [MARVEL National Centre for Competency in Research](https://nccr-marvel.ch/) funded by the [Swiss National Science Foundation](https://www.snf.ch/en).
 * the MARKETPLACE project funded by [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) under the H2020-NMBP-25-2017 call (Grant No. 760173).
-* the [MaX European Centre of Excellence](<http://www.max-centre.eu/>) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
+* the [MaX European Centre of Excellence](https://www.max-centre.eu/) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
 
 <div style="text-align:left">
  <img src="miscellaneous/logos/MARVEL.png" alt="MARVEL" height="75px">

delete.ipynb

@@ -18,18 +18,19 @@
     "import urllib.parse as urlparse\n",
     "\n",
     "import ipywidgets as widgets\n",
+    "from IPython.display import Markdown, display\n",
+    "\n",
     "from aiida import load_profile\n",
     "from aiida.orm import load_node\n",
     "from aiida.tools import delete_nodes\n",
-    "from IPython.display import Markdown, display\n",
     "\n",
     "# Load AiiDA profile\n",
     "load_profile()\n",
     "\n",
     "# Parse the primary key from the Jupyter notebook URL\n",
-    "url = urlparse.urlsplit(jupyter_notebook_url) # noqa F821\n",
+    "url = urlparse.urlsplit(jupyter_notebook_url)  # noqa F821\n",
     "query = urlparse.parse_qs(url.query)\n",
-    "pk = int(query['pk'][0])\n",
+    "pk = int(query[\"pk\"][0])\n",
     "\n",
     "\n",
     "def display_node_details(pk):\n",
@@ -41,7 +42,7 @@
     "        print(f\"Description: {node.description}\")\n",
     "        print(f\"Creation Time: {node.ctime}\")\n",
     "    except Exception as e:\n",
-    "        print(f\"Error loading node: {str(e)}\")\n",
+    "        print(f\"Error loading node: {e!s}\")\n",
     "        return False\n",
     "    return True\n",
     "\n",
@@ -50,31 +51,36 @@
     "    if dry_run:\n",
     "        _, was_deleted = delete_nodes([pk], dry_run=True)\n",
     "        if was_deleted:\n",
-    "            print(f'Dry run: Node {pk} can be deleted.')\n",
+    "            print(f\"Dry run: Node {pk} can be deleted.\")\n",
     "        return\n",
-    "    \n",
+    "\n",
     "    _, was_deleted = delete_nodes([pk], dry_run=False)\n",
     "    if was_deleted:\n",
-    "        print(f'Node {pk} deleted successfully.')\n",
+    "        print(f\"Node {pk} deleted successfully.\")\n",
     "\n",
     "\n",
-    "def confirm_deletion(b):\n",
-    "    if delete_confirmation.value.lower() in ['y', 'yes']:\n",
+    "def confirm_deletion(_):\n",
+    "    if delete_confirmation.value.lower() in (\"y\", \"yes\"):\n",
     "        delete_node(pk, dry_run=False)\n",
     "    else:\n",
-    "        print('Deletion aborted.')\n",
+    "        print(\"Deletion aborted.\")\n",
     "\n",
     "\n",
-    "def find_linked_qeapp_jobs(root_node_pk, process_label='QeAppWorkChain'):\n",
+    "def find_linked_qeapp_jobs(root_node_pk, process_label=\"QeAppWorkChain\"):\n",
     "    \"\"\"Query all linked node with process_label = QeAppWorkChain.\"\"\"\n",
     "    from aiida.orm import Node, QueryBuilder\n",
     "    from aiida.orm.nodes.process.workflow.workchain import WorkChainNode\n",
+    "\n",
     "    qb = QueryBuilder()\n",
-    "    qb.append(WorkChainNode, filters={'id': root_node_pk}, tag='root')\n",
-    "    qb.append(Node, with_incoming='root', tag='calcjob')\n",
+    "    qb.append(WorkChainNode, filters={\"id\": root_node_pk}, tag=\"root\")\n",
+    "    qb.append(Node, with_incoming=\"root\", tag=\"calcjob\")\n",
     "    # There are seems a bug with `with_ancestors` in the QueryBuilder, so we have to use `with_incoming` instead.\n",
-    "    # For the moment, it's safe to use `with_incoming` since we check it very time we delete a QEApp \n",
-    "    qb.append(WorkChainNode, filters={'attributes.process_label': 'QeAppWorkChain'}, with_incoming='calcjob')\n",
+    "    # For the moment, it's safe to use `with_incoming` since we check it very time we delete a QEApp\n",
+    "    qb.append(\n",
+    "        WorkChainNode,\n",
+    "        filters={\"attributes.process_label\": process_label},\n",
+    "        with_incoming=\"calcjob\",\n",
+    "    )\n",
     "    results = qb.all()\n",
     "    if len(results) == 0:\n",
     "        return None\n",
@@ -96,12 +102,16 @@
     "    else:\n",
     "        # Ask for confirmation\n",
     "        nodes, _ = delete_nodes([pk], dry_run=True)\n",
-    "        display(Markdown(f'**YOU ARE ABOUT TO DELETE `{len(nodes)}` NODES! THIS CANNOT BE UNDONE!**'))\n",
+    "        display(\n",
+    "            Markdown(\n",
+    "                f\"**YOU ARE ABOUT TO DELETE `{len(nodes)}` NODES! THIS CANNOT BE UNDONE!**\"\n",
+    "            )\n",
+    "        )\n",
     "        delete_confirmation = widgets.Text(\n",
-    "            value='',\n",
+    "            value=\"\",\n",
     "            placeholder='Type \"yes\" to confirm',\n",
-    "            description='Confirm:',\n",
-    "            disabled=False\n",
+    "            description=\"Confirm:\",\n",
+    "            disabled=False,\n",
     "        )\n",
     "        confirm_button = widgets.Button(description=\"Delete Node\")\n",
     "        confirm_button.on_click(confirm_deletion)\n",

docs/requirements.txt

@@ -70,7 +70,7 @@ sphinxcontrib-serializinghtml==1.1.5
     # via sphinx
 typing-extensions==4.8.0
     # via pydata-sphinx-theme
-urllib3==2.0.7
+urllib3==2.2.2
     # via requests
 zipp==3.19.1
     # via importlib-metadata

docs/source/conf.py

@@ -9,13 +9,8 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
 import time
 
-# sys.path.insert(0, os.path.abspath('.'))
-
 # -- Project information -----------------------------------------------------
 
 version = "v24.10.0a1"
@@ -30,9 +25,7 @@
     if current_year == copyright_first_year
     else f"{copyright_first_year}-{current_year}"
 )
-copyright = "{}, {}. All rights reserved".format(
-    copyright_year_string, copyright_owners
-)
+copyright = f"{copyright_year_string}, {copyright_owners}. All rights reserved"  # noqa: A001
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.