Merge branch 'main' into fix_605_hide_kill_button

.pre-commit-config.yaml

@@ -20,12 +20,12 @@ repos:
             exclude: tests
 
     - repo: https://github.com/sirosen/check-jsonschema
-      rev: 0.27.3
+      rev: 0.28.1
       hooks:
           - id: check-github-workflows
 
     - repo: https://github.com/nbQA-dev/nbQA
-      rev: 1.7.1
+      rev: 1.8.5
       hooks:
           - id: nbqa-pyupgrade
             args: [--py38-plus]
@@ -36,13 +36,13 @@ repos:
             args: [--ignore=E402]
 
     - repo: https://github.com/kynan/nbstripout
-      rev: 0.6.1
+      rev: 0.7.1
       hooks:
           - id: nbstripout
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
       # Ruff version.
-      rev: v0.1.11
+      rev: v0.3.4
       hooks:
         # Run the linter.
           - id: ruff

docs/source/conf.py

@@ -18,7 +18,7 @@
 
 # -- Project information -----------------------------------------------------
 
-version = "v24.04.0a2"
+version = "v24.04.0a3"
 release = f"{version}-dev"
 project = "Quantum ESPRESSO App"
 copyright_first_year = "2023"

docs/source/development/plugin.rst

@@ -98,14 +98,15 @@ Beside, you need to override the the following methods:
             }
 
         def set_panel_value(self, input_dict):
-            """Set a dictionary with the input parameters for the plugin."""
+            """Set the value of the widgets in the panel from the input dictionary.
+            This method is called when the user wants to reload the panel from the previous calculation,
+            or reset the panel to the default values."""
             self.scale.value = input_dict.get("scale", 0.05)
             self.npoint.value = input_dict.get("npoint", 5)
 
         def reset(self):
             """Reset the input fields."""
-            self.scale.value = 0.05
-            self.npoint.value = 5
+            self.set_panel_value({"scale": 0.05, "npoint": 5})
 
 Result
 -----------------------

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = aiidalab_qe
-version = 24.4.0a2
+version = 24.4.0a3
 description = Package for the AiiDAlab QE app
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -66,7 +66,7 @@ categories =
     quantum
 
 [bumpver]
-current_version = "v24.04.0a2"
+current_version = "v24.04.0a3"
 version_pattern = "v0Y.0M.PATCH[PYTAGNUM]"
 commit_message = "Bump version {old_version} -> {new_version}"
 commit = True

src/aiidalab_qe/__init__.py

@@ -1,6 +1,7 @@
 """Package for the AiiDAlab QE app version.
 Plugin (workflow) version will be read from the plugin's __init__.py file.
 """
+
 from aiidalab_qe.version import __version__
 
 __all__ = [

src/aiidalab_qe/__main__.py

@@ -1,5 +1,4 @@
-"""For running the app from the command line used for post_install script.
-"""
+"""For running the app from the command line used for post_install script."""
 
 from pathlib import Path
 

src/aiidalab_qe/app/configuration/__init__.py

@@ -3,6 +3,7 @@
 
 Authors: AiiDAlab team
 """
+
 from __future__ import annotations
 
 import ipywidgets as ipw

src/aiidalab_qe/app/configuration/advanced.py

@@ -3,6 +3,7 @@
 
 Authors: AiiDAlab team
 """
+
 import os
 
 import ipywidgets as ipw
@@ -267,40 +268,40 @@ def get_panel_value(self):
         parameters["pseudo_family"] = self.pseudo_family_selector.value
         if self.pseudo_setter.pseudos:
             parameters["pw"]["pseudos"] = self.pseudo_setter.pseudos
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "ecutwfc"
-            ] = self.pseudo_setter.ecutwfc
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "ecutrho"
-            ] = self.pseudo_setter.ecutrho
+            parameters["pw"]["parameters"]["SYSTEM"]["ecutwfc"] = (
+                self.pseudo_setter.ecutwfc
+            )
+            parameters["pw"]["parameters"]["SYSTEM"]["ecutrho"] = (
+                self.pseudo_setter.ecutrho
+            )
         # if override is not ticked, use the default value
         parameters["pw"]["parameters"]["SYSTEM"]["tot_charge"] = self.total_charge.value
 
         if self.van_der_waals.value in ["none", "ts-vdw"]:
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "vdw_corr"
-            ] = self.van_der_waals.value
+            parameters["pw"]["parameters"]["SYSTEM"]["vdw_corr"] = (
+                self.van_der_waals.value
+            )
         else:
             parameters["pw"]["parameters"]["SYSTEM"]["vdw_corr"] = "dft-d3"
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "dftd3_version"
-            ] = self.dftd3_version[self.van_der_waals.value]
+            parameters["pw"]["parameters"]["SYSTEM"]["dftd3_version"] = (
+                self.dftd3_version[self.van_der_waals.value]
+            )
 
         # there are two choose, use link or parent
         if self.spin_type == "collinear":
-            parameters[
-                "initial_magnetic_moments"
-            ] = self.magnetization.get_magnetization()
+            parameters["initial_magnetic_moments"] = (
+                self.magnetization.get_magnetization()
+            )
         parameters["kpoints_distance"] = self.value.get("kpoints_distance")
         if self.electronic_type == "metal":
             # smearing type setting
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "smearing"
-            ] = self.smearing.smearing_value
+            parameters["pw"]["parameters"]["SYSTEM"]["smearing"] = (
+                self.smearing.smearing_value
+            )
             # smearing degauss setting
-            parameters["pw"]["parameters"]["SYSTEM"][
-                "degauss"
-            ] = self.smearing.degauss_value
+            parameters["pw"]["parameters"]["SYSTEM"]["degauss"] = (
+                self.smearing.degauss_value
+            )
 
         return parameters
 

src/aiidalab_qe/app/configuration/workflow.py

@@ -3,6 +3,7 @@
 
 Authors: AiiDAlab team
 """
+
 import ipywidgets as ipw
 from aiida_quantumespresso.common.types import RelaxType
 

src/aiidalab_qe/app/result/summary_viewer.py

@@ -130,9 +130,9 @@ def generate_report_parameters(qeapp_wc):
         )["bands_kpoints_distance"]
 
     if "pdos" in qeapp_wc.inputs:
-        report[
-            "nscf_kpoints_distance"
-        ] = qeapp_wc.inputs.pdos.nscf.kpoints_distance.value
+        report["nscf_kpoints_distance"] = (
+            qeapp_wc.inputs.pdos.nscf.kpoints_distance.value
+        )
     return report
 
 

src/aiidalab_qe/app/submission/__init__.py

@@ -3,6 +3,7 @@
 
 Authors: AiiDAlab team
 """
+
 from __future__ import annotations
 
 import os
@@ -198,6 +199,8 @@ def _toggle_install_widgets(self, change):
     def _auto_select_code(self, change):
         if change["new"] and not change["old"]:
             for name, code_widget in self.codes.items():
+                if not DEFAULT_PARAMETERS["codes"].get(name):
+                    continue
                 try:
                     code_widget.refresh()
                     code_widget.value = orm.load_code(

src/aiidalab_qe/app/submission/resource.py

@@ -3,6 +3,7 @@
 
 Authors: AiiDAlab team
 """
+
 import ipywidgets as ipw
 
 

src/aiidalab_qe/common/bandpdoswidget.py

@@ -816,8 +816,8 @@ def get_bands_labeling(bandsdata: dict) -> list:
     UNICODE_SYMBOL = {
         "GAMMA": "\u0393",
         "DELTA": "\u0394",
-        "LAMBDA": "\u039B",
-        "SIGMA": "\u03A3",
+        "LAMBDA": "\u039b",
+        "SIGMA": "\u03a3",
         "EPSILON": "\u0395",
     }
     paths = bandsdata.get("paths")

src/aiidalab_qe/common/panel.py

@@ -5,6 +5,7 @@
 
     AiiDAlab Team
 """
+
 import ipywidgets as ipw
 
 DEFAULT_PARAMETERS = {}

src/aiidalab_qe/common/process.py

@@ -1,4 +1,5 @@
 """Widgets related to process management."""
+
 from dataclasses import make_dataclass
 
 import ipywidgets as ipw

src/aiidalab_qe/plugins/bands/result.py

@@ -1,6 +1,5 @@
-"""Bands results view widgets
+"""Bands results view widgets"""
 
-"""
 from aiidalab_qe.common.bandpdoswidget import BandPdosWidget
 from aiidalab_qe.common.panel import ResultPanel
 

src/aiidalab_qe/plugins/bands/setting.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Panel for Bands plugin."""
+
 import ipywidgets as ipw
 
 from aiidalab_qe.common.panel import Panel

src/aiidalab_qe/plugins/pdos/result.py

@@ -1,6 +1,4 @@
-"""PDOS results view widgets
-
-"""
+"""PDOS results view widgets"""
 
 from aiidalab_qe.common.bandpdoswidget import BandPdosWidget
 from aiidalab_qe.common.panel import ResultPanel

src/aiidalab_qe/plugins/pdos/setting.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Panel for Pdos plugin."""
+
 import ipywidgets as ipw
 import traitlets as tl
 from aiida import orm

src/aiidalab_qe/plugins/xas/result.py

@@ -1,6 +1,5 @@
-"""XAS results view widgets
+"""XAS results view widgets"""
 
-"""
 import base64
 import hashlib
 from typing import Callable

src/aiidalab_qe/plugins/xas/setting.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
-"""Panel for XAS plugin.
+"""Panel for XAS plugin."""
 
-"""
 import os
 import tarfile
 from importlib import resources