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

.github/workflows/ci.yml

@@ -55,7 +55,7 @@ jobs:
               # 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' || '' }}
+              run: pytest -v tests ${{ matrix.aiida-core-version == '2.3' && '--cov=aiidalab_qe' || '' }} --skip-slow
 
             - name: Upload coverage reports to Codecov
               uses: codecov/codecov-action@v4

README.md

@@ -70,17 +70,18 @@ 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](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](https://www.max-centre.eu/) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
+* [MARVEL National Centre for Competency in Research](https://nccr-marvel.ch/) funded by the [Swiss National Science Foundation](https://www.snf.ch/en).
+* [BIG-MAP project](https://www.big-map.eu) funded by the Horizon 2020 research and innovation programme (Grant No. 957189).
+* [MARKETPLACE project](https://www.the-marketplace-project.eu/) funded by Horizon 2020 under the H2020-NMBP-25-2017 call (Grant No. 760173).
+* [MaX European Centre of Excellence](https://www.max-centre.eu/) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
+* [DOME 4.0 project](https://dome40.eu/) funded by the EU Horizon 2020 Research and Innovation Programme (Grant No. 953163)
 
-<div style="text-align:left">
+
+<div style="display: flex; flex-wrap: wrap; justify-content: space-around; align-items: center; gap: 50px; text-align: center;">
  <img src="miscellaneous/logos/MARVEL.png" alt="MARVEL" height="75px">
  <img src="miscellaneous/logos/MaX.png" alt="MaX" height="75px">
  <img src="miscellaneous/logos/MarketPlace.png" alt="MarketPlace" height="75px">
-</div>
-<div style="text-align:left">
  <img src="miscellaneous/logos/bigmap_logo.png" alt="BIG-MAP" height="75px">
  <img src="miscellaneous/logos/EU_flag.png" alt="EU" height="75px">
+ <img src="miscellaneous/logos/DOME_4.0.png" alt="DOME 4.0" height="75px">
 </div>

docs/source/conf.py

@@ -13,7 +13,7 @@
 
 # -- Project information -----------------------------------------------------
 
-version = "v24.10.0a2"
+version = "v24.10.0a4"
 release = f"{version}-dev"
 project = "Quantum ESPRESSO App"
 copyright_first_year = "2023"

docs/source/howto/xas.rst

@@ -167,6 +167,19 @@ Finally, click on the "Download CSV" button to the upper left of the plot area t
     * The normalised & weighted spectrum. (with respect to ratio of site multiplicity to total multiplicity)
     * The normalised & un-weighted spectrum.
 
+Additional Note on Charged Systems
+----------------------------------
+Computing XANES spectra for systems where a charge has been applied (in this case using the `Total charge` advanced setting) is possible using the tools
+available in the QE App, however such workflows should always be tested by the user against experimental data if possible.
+
+When running XAS workflows for systems where a total charge has been applied, it is suggested to use the following settings for the total charge to ensure the corresponding
+core-hole treatment is applied correctly:
+
+* "xch_fixed" or "xch_smear": Set the total charge as required for the system's charged ground-state.
+* "full": **Increase** the total charge by 1 *relative* to the system's charged ground-state (e.g. set total charge = 2 in the advanced settings tab if the charge is normally 1).
+
+Note that for neutral systems (total charge = 0), the QE App will handle these settings automatically.
+
 Summary
 -------
 

docs/source/index.rst

@@ -161,19 +161,19 @@ We acknowledge the `AiiDAlab`_ team for the development of the Quantum ESPRESSO
 
 We also 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 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).
+- `BIG-MAP project <https://www.big-map.eu>`_ funded by the Horizon 2020 research and innovation programme (Grant No. 957189).
+- `MARVEL National Centre for Competency in Research <http://nccr-marvel.ch>`_ funded by the `Swiss National Science Foundation <http://www.snf.ch/en>`_.
+- `MARKETPLACE project <https://www.the-marketplace-project.eu/>`_ funded by Horizon 2020 under the H2020-NMBP-25-2017 call (Grant No. 760173).
+- `MaX European Centre of Excellence <http://www.max-centre.eu/>`_ funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
+- `DOME 4.0 project <https://dome40.eu/>`_ funded by the EU Horizon 2020 Research and Innovation Programme (Grant No. 953163).
 
 .. raw:: html
 
-   <div style="text-align:left">
+   <div style="display: flex; flex-wrap: wrap; justify-content: space-around; align-items: center; gap: 50px; text-align: center;">
     <img src="../_static/logos/MARVEL.png" alt="MARVEL" height="75px">
     <img src="../_static/logos/MaX.png" alt="MaX" height="75px">
     <img src="../_static/logos/MarketPlace.png" alt="MarketPlace" height="75px">
-   </div>
-   <div style="text-align:left">
     <img src="../_static/logos/bigmap_logo.png" alt="BIG-MAP" height="75px">
     <img src="../_static/logos/EU_flag.png" alt="EU" height="75px">
+    <img src="../_static/logos/DOME_4.0.png" alt="DOME 4.0" height="75px">
    </div>

qe.ipynb

@@ -73,8 +73,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import urllib.parse as urlparse\n",
-    "\n",
     "from aiidalab_qe.app.main import App\n",
     "from aiidalab_widgets_base.bug_report import (\n",
     "    install_create_github_issue_exception_handler,\n",
@@ -86,17 +84,23 @@
     "    labels=(\"bug\", \"automated-report\"),\n",
     ")\n",
     "\n",
+    "app = App(qe_auto_setup=True)\n",
+    "\n",
+    "view.main.children = [app]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import urllib.parse as urlparse\n",
+    "\n",
     "url = urlparse.urlsplit(jupyter_notebook_url)  # noqa F821\n",
     "query = urlparse.parse_qs(url.query)\n",
-    "\n",
-    "app = App(qe_auto_setup=True)\n",
-    "# if a pk is provided in the query string, set it as the process of the app\n",
     "if \"pk\" in query:\n",
-    "    pk = query[\"pk\"][0]\n",
-    "    app.process = pk\n",
-    "\n",
-    "view.main.children = [app]\n",
-    "view.app = app"
+    "    app.process = query[\"pk\"][0]"
    ]
   },
   {
@@ -111,7 +115,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -126,11 +130,6 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.9.13"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "d4d1e4263499bec80672ea0156c357c1ee493ec2b1c70f0acce89fc37c4a6abe"
-   }
   }
  },
  "nbformat": 4,

setup.cfg

@@ -1,11 +1,11 @@
 [metadata]
 name = aiidalab_qe
-version = 24.10.0a2
+version = 24.10.0a4
 description = Package for the AiiDAlab QE app
 long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/aiidalab/aiidalab-qe
-author = Carl Simon Adorf, Aliaksandr Yakutovich, Marnik Bercx, Jusong Yu
+author = AiiDAlab team
 author_email = [email protected]
 license = MIT
 license_file = LICENSE
@@ -16,7 +16,7 @@ classifiers =
     Programming Language :: Python :: 3 :: Only
 project_urls =
     Bug Tracker = https://github.com/aiidalab/aiidalab-qe/issues
-    Documentation = https://github.com/aiidalab/aiidalab-qe#readme
+    Documentation = https://aiidalab-qe.readthedocs.io/
     Logo = https://raw.githubusercontent.com/aiidalab/aiidalab-qe/master/miscellaneous/logos/QE.jpg
 
 [options]
@@ -57,21 +57,21 @@ aiidalab_qe.plugins.xas = pseudo_toc.yaml
 aiidalab_qe.properties =
     bands = aiidalab_qe.plugins.bands:bands
     pdos = aiidalab_qe.plugins.pdos:pdos
-    xps = aiidalab_qe.plugins.xps:xps
     electronic_structure = aiidalab_qe.plugins.electronic_structure:electronic_structure
+    xps = aiidalab_qe.plugins.xps:xps
     xas = aiidalab_qe.plugins.xas:xas
 
 aiida.workflows =
     aiidalab_qe.bands_workchain = aiidalab_qe.plugins.bands.bands_workchain:BandsWorkChain
 
 [aiidalab]
 title = Quantum ESPRESSO
-description = Perform Quantum ESPRESSO calculations
+description = The Quantum ESPRESSO (QE) app is a web-based interface within AiiDAlab that allows users to perform first-principles calculations and analyze material properties (e.g., band structures) directly from their browser.
 categories =
     quantum
 
 [bumpver]
-current_version = "v24.10.0a2"
+current_version = "v24.10.0a4"
 version_pattern = "v0Y.0M.PATCH[PYTAGNUM]"
 commit_message = "Bump version {old_version} -> {new_version}"
 commit = True