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Adapt module and files layout for plugin implementation
This PR is separated and prepared for #428 to avoid mixing changes, especially for moving modules/files without changing any implementations. See #428 (comment) for the design of restructuring the modules. It include following changes: - Move strucute selction to step1 module - Move modules/folders to configuration folder (step2) - Move modules/folders to submission (step3) - Move modules/folders to results (steps) - move modules/widgets to common folder - load registred viewer in __init__ to trigger
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| # trigger registration of the viewer widget: | ||
| from .node_view import CalcJobNodeViewerWidget # noqa: F401 | ||
| from .process import WorkChainSelector | ||
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| __all__ = [ | ||
| "WorkChainSelector", | ||
| ] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| """Results view widgets (MOVE TO OTHER MODULE!) | ||
| Authors: AiiDAlab team | ||
| """ | ||
|
|
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| import ipywidgets as ipw | ||
| import nglview | ||
| import traitlets as tl | ||
| from aiida import orm | ||
| from aiidalab_widgets_base import register_viewer_widget | ||
| from ase import Atoms | ||
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|
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| from .widgets import CalcJobOutputFollower, LogOutputWidget | ||
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| class MinimalStructureViewer(ipw.VBox): | ||
| structure = tl.Union([tl.Instance(Atoms), tl.Instance(orm.Node)], allow_none=True) | ||
| _displayed_structure = tl.Instance(Atoms, allow_none=True, read_only=True) | ||
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| background = tl.Unicode() | ||
| supercell = tl.List(tl.Int()) | ||
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| def __init__(self, structure, *args, **kwargs): | ||
| self._viewer = nglview.NGLWidget() | ||
| self._viewer.camera = "orthographic" | ||
| self._viewer.stage.set_parameters(mouse_preset="pymol") | ||
| ipw.link((self, "background"), (self._viewer, "background")) | ||
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| self.structure = structure | ||
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| super().__init__( | ||
| children=[ | ||
| self._viewer, | ||
| ], | ||
| *args, | ||
| **kwargs, | ||
| ) | ||
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| @tl.default("background") | ||
| def _default_background(self): | ||
| return "#FFFFFF" | ||
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| @tl.default("supercell") | ||
| def _default_supercell(self): | ||
| return [1, 1, 1] | ||
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| @tl.validate("structure") | ||
| def _valid_structure(self, change): # pylint: disable=no-self-use | ||
| """Update structure.""" | ||
| structure = change["value"] | ||
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| if structure is None: | ||
| return None # if no structure provided, the rest of the code can be skipped | ||
|
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| if isinstance(structure, Atoms): | ||
| return structure | ||
| if isinstance(structure, orm.Node): | ||
| return structure.get_ase() | ||
| raise ValueError( | ||
| "Unsupported type {}, structure must be one of the following types: " | ||
| "ASE Atoms object, AiiDA CifData or StructureData." | ||
| ) | ||
|
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| @tl.observe("structure") | ||
| def _update_displayed_structure(self, change): | ||
| """Update displayed_structure trait after the structure trait has been modified.""" | ||
| # Remove the current structure(s) from the viewer. | ||
| if change["new"] is not None: | ||
| self.set_trait("_displayed_structure", change["new"].repeat(self.supercell)) | ||
| else: | ||
| self.set_trait("_displayed_structure", None) | ||
|
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| @tl.observe("_displayed_structure") | ||
| def _update_structure_viewer(self, change): | ||
| """Update the view if displayed_structure trait was modified.""" | ||
| with self.hold_trait_notifications(): | ||
| for ( | ||
| comp_id | ||
| ) in self._viewer._ngl_component_ids: # pylint: disable=protected-access | ||
| self._viewer.remove_component(comp_id) | ||
| self.selection = list() | ||
| if change["new"] is not None: | ||
| self._viewer.add_component(nglview.ASEStructure(change["new"])) | ||
| self._viewer.clear() | ||
| self._viewer.stage.set_parameters(clipDist=0) | ||
| self._viewer.add_representation("unitcell", diffuse="#df0587") | ||
| self._viewer.add_representation("ball+stick", aspectRatio=3.5) | ||
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| class VBoxWithCaption(ipw.VBox): | ||
| def __init__(self, caption, body, *args, **kwargs): | ||
| super().__init__(children=[ipw.HTML(caption), body], *args, **kwargs) | ||
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| @register_viewer_widget("process.calculation.calcjob.CalcJobNode.") | ||
| class CalcJobNodeViewerWidget(ipw.VBox): | ||
| def __init__(self, calcjob, **kwargs): | ||
| self.calcjob = calcjob | ||
| self.output_follower = CalcJobOutputFollower() | ||
| self.log_output = LogOutputWidget() | ||
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| self.output_follower.calcjob_uuid = self.calcjob.uuid | ||
| self.output_follower.observe(self._observe_output_follower_lineno, ["lineno"]) | ||
|
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| super().__init__( | ||
| [ipw.HTML(f"CalcJob: {self.calcjob}"), self.log_output], **kwargs | ||
| ) | ||
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| def _observe_output_follower_lineno(self, _): | ||
| with self.hold_trait_notifications(): | ||
| self.log_output.filename = self.output_follower.filename | ||
| self.log_output.value = "\n".join(self.output_follower.output) |
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