Fix remaining issues

Author: edan-bainglass

src/aiidalab_qe/app/configuration/__init__.py

@@ -9,6 +9,11 @@
 
 from aiidalab_qe.app.parameters import DEFAULT_PARAMETERS
 from aiidalab_qe.app.utils import get_entry_items
+from aiidalab_qe.app.utils.plugin_manager import (
+    DEFAULT_PLUGIN_CONFIG_SOURCE,
+    PluginManager,
+    is_package_installed,
+)
 from aiidalab_qe.common.infobox import InAppGuide
 from aiidalab_qe.common.panel import (
     ConfigurationSettingsModel,
@@ -106,7 +111,6 @@ def _render(self):
             description="Plugin store",
             link="plugin_manager.ipynb",
             icon="puzzle-piece",  # More intuitive icon
-            button_style="primary",  # Keeps it prominent
             tooltip="Browse and install additional plugins from the Plugin Store",
         )
 
@@ -211,12 +215,6 @@ def _update_state(self, _=None):
             self.state = self.State.INIT
 
     def _fetch_not_installed_property(self, plugin_config_source=None):
-        from aiidalab_qe.app.utils.plugin_manager import (
-            DEFAULT_PLUGIN_CONFIG_SOURCE,
-            PluginManager,
-            is_package_installed,
-        )
-
         self.not_installed_property_children = []
 
         plugin_config_source = plugin_config_source or DEFAULT_PLUGIN_CONFIG_SOURCE

src/aiidalab_qe/app/result/components/viewer/viewer.py

@@ -92,7 +92,4 @@ def _fetch_plugin_results(self, viewer_model: WorkChainResultsViewerModel):
             panel = entry["panel"]
             model = entry["model"]()
             viewer_model.add_model(identifier, model)
-            self.panels[identifier] = panel(
-                identifier=identifier,
-                model=model,
-            )
+            self.panels[identifier] = panel(model=model)

src/aiidalab_qe/app/submission/__init__.py

@@ -83,16 +83,16 @@ def _render(self):
         super()._render()
 
         self.process_label = ipw.Text(
-            description="Label:",
-            layout=ipw.Layout(width="auto", indent="0px"),
+            description="Label",
+            layout=ipw.Layout(width="auto"),
         )
         ipw.link(
             (self._model, "process_label"),
             (self.process_label, "value"),
         )
         self.process_description = ipw.Textarea(
             description="Description",
-            layout=ipw.Layout(width="auto", indent="0px"),
+            layout=ipw.Layout(width="auto"),
         )
         ipw.link(
             (self._model, "process_description"),

src/aiidalab_qe/app/submission/global_settings/model.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import numpy as np
 import traitlets as tl
 
 from aiida import orm
@@ -208,6 +209,9 @@ def _get_properties(self) -> list[str]:
         return self.input_parameters.get("workchain", {}).get("properties", [])
 
     def _check_blockers(self):
+        if not self.input_parameters:
+            return
+
         warning_in_blockers = (
             """
              <b>Please note</b> that, if this blocker is shown for an already finished workflow,
@@ -252,7 +256,8 @@ def _check_blockers(self):
             if not code_model.is_ready:
                 continue
             if not issubclass(
-                code_model.code_widget_class, QEAppComputationalResourcesWidget
+                code_model.code_widget_class,
+                QEAppComputationalResourcesWidget,
             ):
                 yield (
                     f"Error: hi, plugin developer, please use the QEAppComputationalResourcesWidget from aiidalab_qe.common.widgets for code {identifier}."
@@ -306,8 +311,6 @@ def _estimate_min_cpus(
         `int`
             The estimated minimum number of CPUs required.
         """
-        import numpy as np
-
         return int(
             np.ceil(
                 num_cpus0

src/aiidalab_qe/app/submission/global_settings/setting.py

@@ -63,6 +63,7 @@ def render(self):
     def build_global_codes(self, codes: PluginCodes):
         for identifier, code_models in codes.items():
             for _, code_model in code_models.items():
+                self.register_code(code_model)
                 base_code_model = self._model.add_global_model(identifier, code_model)
                 if base_code_model is not None:
                     base_code_model.observe(
@@ -73,15 +74,26 @@ def build_global_codes(self, codes: PluginCodes):
                         self._on_code_selection_change,
                         "selected",
                     )
+                    self.register_code(base_code_model)
+                    if base_code_model.default_calc_job_plugin == "quantumespresso.pw":
+                        base_code_model.observe(
+                            self._on_pw_code_resource_change,
+                            [
+                                "num_cpus",
+                                "num_nodes",
+                                "ntasks_per_node",
+                                "cpus_per_task",
+                                "max_wallclock_seconds",
+                            ],
+                        )
         self._model.update_global_codes()
 
     def reset(self):
         self._model.set_selected_codes()
 
     def _on_input_parameters_change(self, _):
         self._model.update_active_codes()
-        if self._model.input_parameters:
-            self._model.update_blockers()
+        self._model.update_blockers()
 
     def _on_input_structure_change(self, _):
         self._model.check_resources()
@@ -107,17 +119,6 @@ def _render_code_widget(
         code_widget: QEAppComputationalResourcesWidget,
     ):
         super()._render_code_widget(code_model, code_widget)
-        if code_model.default_calc_job_plugin == "quantumespresso.pw":
-            code_model.observe(
-                self._on_pw_code_resource_change,
-                [
-                    "num_cpus",
-                    "num_nodes",
-                    "ntasks_per_node",
-                    "cpus_per_task",
-                    "max_wallclock_seconds",
-                ],
-            )
 
         def toggle_widget(_=None, model=code_model, widget=code_widget):
             widget = self.code_widgets[model.name]

src/aiidalab_qe/app/submission/model.py

@@ -230,9 +230,8 @@ def _get_properties(self) -> list[str]:
     def _create_builder(self, parameters) -> ProcessBuilderNamespace:
         builder = QeAppWorkChain.get_builder_from_protocol(
             structure=self.input_structure,
-            parameters=shallow_copy_nested_dict(
-                parameters
-            ),  # use shallow copy to avoid workflow mute these parameters.
+            # Use shallow copy to avoid parameter mutation by the workflow
+            parameters=shallow_copy_nested_dict(parameters),
         )
 
         codes = parameters["codes"]["global"]["codes"]

src/aiidalab_qe/app/utils/plugin_manager.py

@@ -396,8 +396,8 @@ def _build_ui(self) -> None:
 
             # Build plugin description details
             details = f"""
-                <b>Author:</b> {plugin_data.get('author', 'N/A')}<br>
-                <b>Description:</b> {plugin_data.get('description', 'No description available')}<br>
+                <b>Author:</b> {plugin_data.get("author", "N/A")}<br>
+                <b>Description:</b> {plugin_data.get("description", "No description available")}<br>
                 <b>Status:</b> {badge_html}<br>
                 {version_message}
             """

src/aiidalab_qe/common/panel.py

@@ -272,6 +272,27 @@ def __init__(self, model, **kwargs):
         super().__init__(model, **kwargs)
         self.code_widgets = {}
 
+    def register_code(self, code_model: CodeModel):
+        if code_model.default_calc_job_plugin == "quantumespresso.pw":
+            code_model.observe(
+                self._on_code_resource_change,
+                [
+                    "parallelization_override",
+                    "npool",
+                ],
+            )
+        code_model.observe(
+            self._on_code_resource_change,
+            [
+                "selected",
+                "num_cpus",
+                "num_nodes",
+                "ntasks_per_node",
+                "cpus_per_task",
+                "max_wallclock_seconds",
+            ],
+        )
+
     def _on_code_resource_change(self, _):
         pass
 
@@ -346,24 +367,6 @@ def _render_code_widget(
                 (code_model, "npool"),
                 (code_widget.parallelization.npool, "value"),
             )
-            code_model.observe(
-                self._on_code_resource_change,
-                [
-                    "parallelization_override",
-                    "npool",
-                ],
-            )
-        code_model.observe(
-            self._on_code_resource_change,
-            [
-                "selected",
-                "num_cpus",
-                "num_nodes",
-                "ntasks_per_node",
-                "cpus_per_task",
-                "max_wallclock_seconds",
-            ],
-        )
         code_widget.code_selection.code_select_dropdown.observe(
             self._on_code_options_change,
             "options",

src/aiidalab_qe/common/widgets.py

@@ -262,7 +262,7 @@ def _observe_value(self, change):
 class CalcJobOutputFollower(traitlets.HasTraits):
     calcjob_uuid = traitlets.Unicode(allow_none=True)
     filename = traitlets.Unicode(allow_none=True)
-    output = traitlets.List(trait=traitlets.Unicode)
+    output = traitlets.List(trait=traitlets.Unicode())
     lineno = traitlets.Int()
 
     def __init__(self, **kwargs):
@@ -447,8 +447,8 @@ class AddingTagsEditor(ipw.VBox):
     """Editor for adding tags to atoms."""
 
     structure = traitlets.Instance(ase.Atoms, allow_none=True)
-    selection = traitlets.List(traitlets.Int, allow_none=True)
-    input_selection = traitlets.List(traitlets.Int, allow_none=True)
+    selection = traitlets.List(traitlets.Int(), allow_none=True)
+    input_selection = traitlets.List(traitlets.Int(), allow_none=True)
     structure_node = traitlets.Instance(orm_Data, allow_none=True, read_only=True)
 
     def __init__(self, title="", **kwargs):
@@ -693,18 +693,29 @@ def __init__(self, **kwargs):
         the number of nodes and the number of cpus.
         """
         self.code_selection = ComputationalResourcesWidget(
+            description=kwargs.pop("description", None),
+            default_calc_job_plugin=kwargs.pop("default_calc_job_plugin", None),
             include_setup_widget=False,
             fetch_codes=True,  # TODO resolve testing issues when set to `False`
             **kwargs,
         )
         self.code_selection.layout.width = "80%"
 
         self.num_nodes = ipw.BoundedIntText(
-            value=1, step=1, min=1, max=1000, description="Nodes", width="10%"
+            value=1,
+            step=1,
+            min=1,
+            max=1000,
+            description="Nodes",
         )
+
         self.num_cpus = ipw.BoundedIntText(
-            value=1, step=1, min=1, description="CPUs", width="10%"
+            value=1,
+            step=1,
+            min=1,
+            description="CPUs",
         )
+
         self.btn_setup_resource_detail = ipw.ToggleButton(description="More")
         self.btn_setup_resource_detail.observe(self._setup_resource_detail, "value")
         self._setup_resource_detail_output = ipw.Output(layout={"width": "500px"})
@@ -896,7 +907,7 @@ def __init__(self, **kwargs):
             value=1, step=1, min=1, max=128, description="Number of k-pools", **extra
         )
         self.override = ipw.Checkbox(
-            escription="",
+            description="",
             indent=False,
             value=False,
             layout=ipw.Layout(max_width="20px"),
@@ -1285,7 +1296,7 @@ def __init__(self, widget: ipw.ValueWidget, units: str, **kwargs):
 
 class ShakeNBreakEditor(ipw.VBox):
     structure = traitlets.Instance(ase.Atoms, allow_none=True)
-    selection = traitlets.List(traitlets.Int)
+    selection = traitlets.List(traitlets.Int())
     structure_node = traitlets.Instance(orm_Data, allow_none=True, read_only=True)
 
     def __init__(self, title="Editor ShakeNbreak"):