aiidalab_widgets_base package

Subpackages

• aiidalab_widgets_base.data package
  • Module contents
    • FunctionalGroupSelectorWidget
      • FunctionalGroupSelectorWidget.anchoring_atom
      • FunctionalGroupSelectorWidget.rotate()
    • LigandSelectorWidget
• aiidalab_widgets_base.static package
  • Subpackages
    • aiidalab_widgets_base.static.styles package
      • Module contents
  • Module contents
• aiidalab_widgets_base.utils package
  • Submodules
  • aiidalab_widgets_base.utils.exceptions module
    • ListOrTuppleError
  • aiidalab_widgets_base.utils.loaders module
    • load_css()
  • Module contents
    • MessageLevel
      • MessageLevel.ERROR
      • MessageLevel.INFO
      • MessageLevel.SUCCESS
      • MessageLevel.WARNING
    • PinholeCamera
      • PinholeCamera.inverse_matrix
      • PinholeCamera.screen_to_vector()
    • StatusHTML
      • StatusHTML.new_line
    • ase2spglib()
    • find_ranges()
    • get_ase_from_file()
    • get_formula()
    • list_to_string_range()
    • predefine_settings()
    • string_range_to_list()
    • valid_arguments()
    • wrap_message()

Submodules

aiidalab_widgets_base.bug_report module

Provide more user friendly error messages and automated reporting.

Authors:

• Carl Simon Adorf <simon.adorf@epfl.ch>

aiidalab_widgets_base.bug_report.find_installed_packages(python_bin: str | None = None) → dict[str, str]

Return all currently installed packages.

aiidalab_widgets_base.bug_report.get_environment_fingerprint(encoding='utf-8')

aiidalab_widgets_base.bug_report.install_create_github_issue_exception_handler(output, url, labels=None)

Install a GitHub bug report exception handler.

After installing this handler, kernel exception will show a generic error message to the user, with the option to file an automatic bug report at the given URL.

This is an example of how to use this function:

Example:

output = ipw.Output()
install_create_github_issue_exception_handler(
    output,
    url='https://github.com/aiidalab/aiidalab-qe/issues/new',
    labels=('bug', 'automated-report'))

with output:
    display(welcome_message, app_with_work_chain_selector, footer)

aiidalab_widgets_base.bug_report.parse_environment_fingerprint(fingerprint, encoding='utf-8')

decode the environment fingerprint and return the data as a dictionary.

aiidalab_widgets_base.computational_resources module

class aiidalab_widgets_base.computational_resources.AiidaCodeSetup(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class that allows to setup AiiDA code

code_setup

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

message

A trait for unicode strings.

on_setup_code(_=None)

Setup an AiiDA code.

on_setup_code_success(function)

refresh()

class aiidalab_widgets_base.computational_resources.AiidaComputerSetup(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Inform AiiDA about a computer.

property all_values_provided

computer_configure

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

computer_setup

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

message

A trait for unicode strings.

on_setup_computer(_=None)

Create a new computer.

on_setup_computer_success(function)

property some_values_provided

test(_=None)

class aiidalab_widgets_base.computational_resources.ComputationalResourcesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Code selection widget. Attributes:

value(code UUID): Trait that points to the selected UUID of the code instance. It can be set either to an AiiDA code UUID or to a code label. It is linked to the value trait of the self.code_select_dropdown widget.

codes(Dict): Trait that contains a dictionary (label => Code UUID) for all codes found in the AiiDA database for the selected plugin. It is linked to the ‘options’ trait of the self.code_select_dropdown widget.

allow_hidden_codes(Bool): Trait that defines whether to show hidden codes or not.

allow_disabled_computers(Bool): Trait that defines whether to show codes on disabled computers.

allow_disabled_computers

A boolean (True, False) trait.

allow_hidden_codes

A boolean (True, False) trait.

codes

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

refresh(_=None)

Refresh available codes.

The job of this function is to look in AiiDA database, find available codes and put them in the code_select_dropdown widget.

value

A trait for unicode strings.

class aiidalab_widgets_base.computational_resources.ComputerDropdownWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget to select a configured computer.

Attributes:

value(computer UUID): Trait that points to the selected Computer instance. It can be set to an AiiDA Computer UUID. It is linked to the ‘value’ trait of self._dropdown widget. computers(Dict): Trait that contains a dictionary (label => Computer UUID) for all computers found in the AiiDA database. It is linked to the ‘options’ trait of self._dropdown widget. allow_select_disabled(Bool): Trait that defines whether to show disabled computers.

allow_select_disabled

A boolean (True, False) trait.

computers

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

refresh(_=None)

Refresh the list of configured computers.

select_by_label(label)

Select computer by computer label.

value

A trait for unicode strings.

class aiidalab_widgets_base.computational_resources.ResourceSetupBaseWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

The widget that allows to setup a computer and code. This is the building block of the ComputationalResourcesDatabaseWidget which will be directly used by the user.

message

A trait for unicode strings.

reset()

Reset the widget.

ssh_auth = None

success

A boolean (True, False) trait.

class aiidalab_widgets_base.computational_resources.SshComputerSetup(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Setup a passwordless access to a computer.

SSH_POSSIBLE_RESPONSES = ['[Pp]assword:', 'Now try logging into', 'All keys were skipped because they already exist on the remote system', 'Are you sure you want to continue connecting (yes/no)?', 'ERROR: No identities found', 'Could not resolve hostname', 'Connection refused', <class 'pexpect.exceptions.EOF'>]

key_pair_prepare()

Prepare key pair for the ssh connection.

message

A trait for unicode strings.

password_message

A trait for unicode strings.

ssh_config

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

ssh_connection_state

Use a Enum class as model for the data type description. Note that if no default-value is provided, the first enum-value is used as default-value.

# -- SINCE: Python 3.4 (or install backport: pip install enum34)
import enum
from traitlets import HasTraits, UseEnum


class Color(enum.Enum):
    red = 1  # -- IMPLICIT: default_value
    blue = 2
    green = 3


class MyEntity(HasTraits):
    color = UseEnum(Color, default_value=Color.blue)


entity = MyEntity(color=Color.red)
entity.color = Color.green  # USE: Enum-value (preferred)
entity.color = "green"  # USE: name (as string)
entity.color = "Color.green"  # USE: scoped-name (as string)
entity.color = 3  # USE: number (as int)
assert entity.color is Color.green

thread_ssh_copy_id()

Copy public key on the remote computer, on a separate thread.

class aiidalab_widgets_base.computational_resources.SshConnectionState(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

connection_refused = 6

do_you_want_to_continue = 3

end_of_file = 7

enter_password = 0

keys_already_present = 2

no_keys = 4

success = 1

unknown_hostname = 5

waiting_for_input = -1

class aiidalab_widgets_base.computational_resources.TemplateVariable(widget, lines)

Bases: tuple

lines

Alias for field number 1

widget

Alias for field number 0

class aiidalab_widgets_base.computational_resources.TemplateVariableLine(key, str, vars)

Bases: tuple

key

Alias for field number 0

str

Alias for field number 1

vars

Alias for field number 2

class aiidalab_widgets_base.computational_resources.TemplateVariablesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

fill()

Use template and current widgets value to fill the template and update the filled_template.

filled_templates

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

metadata

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

reset()

Reset the widget.

templates

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

aiidalab_widgets_base.databases module

Widgets that allow to query online databases.

class aiidalab_widgets_base.databases.CodQueryWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Query structures in Crystallography Open Database (COD) Useful class members: :ivar structure(Atoms): trait that contains the selected structure, None if structure is not selected.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.databases.ComputationalResourcesDatabaseWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Extract the setup of a known computer from the AiiDA code registry.

LAYOUT = {'width': '400px'}

STYLE = {'description_width': '180px'}

code_setup

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

computer_configure

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

computer_setup

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

configured

A boolean (True, False) trait.

database_source

A trait for unicode strings.

reset(_=None)

Reset widget and traits

class aiidalab_widgets_base.databases.OptimadeQueryWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

AiiDAlab-specific OPTIMADE Query widget

Useful as a widget to integrate with the aiidalab_widgets_base.structures.StructureManagerWidget, embedded into applications.

NOTE: embedded for OptimadeQueryFilterWidget was introduced in optimade-client version 2020.11.5.

Parameters:

• embedded (bool) – Whether or not to show extra database and provider information. When set to True, the extra information will be hidden, this is useful in situations where the widget is used in a Tab or similar, e.g., for the class aiidalab_widgets_base.structures.StructureManagerWidget.

• title (str) – Title used for Tab header if employed in aiidalab_widgets_base.structures.StructureManagerWidget.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

aiidalab_widgets_base.dicts module

aiidalab_widgets_base.elns module

class aiidalab_widgets_base.elns.ElnConfigureWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

check_connection(_=None)

display_eln_config(value=None)

Display ELN configuration specific to the selected type of ELN.

erase_current_eln_from_configuration(_=None)

get_config()

save_eln_configuration(_=None)

set_current_eln_as_default(_=None)

update_eln_configuration(eln_instance, eln_config)

update_list_of_elns()

write_to_config(config)

class aiidalab_widgets_base.elns.ElnExportWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

handle_output(_=None)

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

send_to_eln(_=None)

class aiidalab_widgets_base.elns.ElnImportWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

aiidalab_widgets_base.elns.connect_to_eln(eln_instance=None, **kwargs)

aiidalab_widgets_base.export module

Widgets to manage AiiDA export.

class aiidalab_widgets_base.export.ExportButtonWidget(*args: t.Any, **kwargs: t.Any)

Bases: Button

Export Node button.

export_aiida_subgraph(change=None)

Perform export when the button is pressed

aiidalab_widgets_base.loaders module

class aiidalab_widgets_base.loaders.LoadingWidget(*args: t.Any, **kwargs: t.Any)

Bases: HBox

Widget for displaying a loading spinner.

aiidalab_widgets_base.misc module

Some useful classes used acrross the repository.

class aiidalab_widgets_base.misc.CopyToClipboardButton(*args: t.Any, **kwargs: t.Any)

Bases: Button

Button to copy text to clipboard.

copy_to_clipboard(change=None)

Copy text to clipboard.

value

A trait for unicode strings.

class aiidalab_widgets_base.misc.ReversePolishNotation(operators, additional_operands=None)

Bases: object

Class defining operations for RPN conversion

convert(expr)

Convert expression to postfix.

execute(expression)

Execute the provided expression.

haslessorequalpriority(opa, opb)

Priority of the different operators

is_operator(opx)

Identifies operators

static iscloseparenthesis(operator)

Identifies closed paretheses.

static isopenparenthesis(operator)

Identifies open paretheses.

static parse_infix_notation(condition)

Convert a string containing the expression into a list of operators and operands.

aiidalab_widgets_base.nodes module

Widgets to work with AiiDA nodes.

class aiidalab_widgets_base.nodes.AiidaNodeTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: Node

class aiidalab_widgets_base.nodes.AiidaOutputsTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: Node

disabled

A boolean (True, False) trait.

icon

A trait for unicode strings.

class aiidalab_widgets_base.nodes.AiidaProcessNodeTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: AiidaNodeTreeNode

class aiidalab_widgets_base.nodes.CalcFunctionTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: AiidaProcessNodeTreeNode

icon

A trait for unicode strings.

class aiidalab_widgets_base.nodes.CalcJobTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: AiidaProcessNodeTreeNode

icon

A trait for unicode strings.

class aiidalab_widgets_base.nodes.NodesTreeWidget(*args: t.Any, **kwargs: t.Any)

Bases: Output

A tree widget for the structured representation of a nodes graph.

NODE_TYPE = {<class 'aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode'>: <class 'aiidalab_widgets_base.nodes.CalcFunctionTreeNode'>, <class 'aiida.orm.nodes.process.calculation.calcjob.CalcJobNode'>: <class 'aiidalab_widgets_base.nodes.CalcJobTreeNode'>, <class 'aiida.orm.nodes.process.workflow.workchain.WorkChainNode'>: <class 'aiidalab_widgets_base.nodes.WorkChainProcessTreeNode'>}

PROCESS_STATE_STYLE = {ProcessState.EXCEPTED: 'danger', ProcessState.FINISHED: 'success', ProcessState.KILLED: 'warning', ProcessState.RUNNING: 'info', ProcessState.WAITING: 'info'}

PROCESS_STATE_STYLE_DEFAULT = 'default'

find_node(pk, namespaces=None)

Find a node by its pk and namespaces. If node is an output node, it is identified by the parent pk and namespaces, otherwise by the pk.

nodes

An instance of a Python tuple.

selected_nodes

An instance of a Python tuple.

update(_=None)

Refresh nodes based on the latest state of the root process and its children.

class aiidalab_widgets_base.nodes.UnknownTypeTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: AiidaNodeTreeNode

icon

A trait for unicode strings.

class aiidalab_widgets_base.nodes.WorkChainProcessTreeNode(*args: t.Any, **kwargs: t.Any)

Bases: AiidaProcessNodeTreeNode

icon

A trait for unicode strings.

aiidalab_widgets_base.process module

Widgets to work with processes.

class aiidalab_widgets_base.process.ProcessFollowerWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

A Widget that follows a process until finished.

follow(detach=False)

Initiate following the process with or without blocking.

on_completed(function)

Run functions after a process has been completed.

process

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

update()

class aiidalab_widgets_base.process.ProcessMonitor(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

Monitor a process and execute callback functions at specified intervals.

join()

value

A trait for unicode strings.

class aiidalab_widgets_base.process.ProcessNodesTreeWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

A tree widget for the structured representation of a process graph.

selected_nodes

An instance of a Python tuple.

update(_=None)

value

A trait for unicode strings.

class aiidalab_widgets_base.process.SubmitButtonWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Submit button class that creates submit button jupyter widget.

on_btn_submit_press(_=None)

When submit button is pressed.

on_click(function)

on_submitted(function)

Run functions after a process has been submitted successfully.

process

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

aiidalab_widgets_base.structures module

Module to provide functionality to import structures.

class aiidalab_widgets_base.structures.BasicCellEditor(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget that allows for the basic cell editing.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.structures.BasicStructureEditor(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget that allows for the basic structure (molecule and position of periodic structure in cell) editing.

property action_vector

Define the action vector.

add(_=None, atoms=None, selection=None)

Add atoms.

align(_=None, atoms=None, selection=None)

Rotate atoms to align action vector with XYZ vector.

camera_orientation

An instance of a Python list.

copy_sel(_=None, atoms=None, selection=None)

Copy selected atoms and shift by 1.0 A along X-axis.

def_axis_p1(_=None)

Define the first point of axis.

def_axis_p2(_=None)

Define the second point of axis.

def_perpendicular_to_screen(_=None)

Define a normalized vector perpendicular to the screen.

def_point(_=None)

Define the action point.

input_selection

An instance of a Python list.

mirror(_=None, norm=None, point=None, atoms=None, selection=None)

Mirror atoms on the plane perpendicular to the action vector.

mirror_3p(_=None)

Mirror atoms on the plane containing action vector and action point.

mod_element(_=None, atoms=None, selection=None)

Modify selected atoms into the given element.

remove(_=None, atoms=None, selection=None)

Remove selected atoms.

rotate(_=None, atoms=None, selection=None)

Rotate atoms around selected point in space and vector.

sel2com()

Get center of mass of the selection.

selection

An instance of a Python list.

str2vec(string)

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

translate_dr(_=None, atoms=None, selection=None)

Translate by dr along the selected vector.

translate_dxdydz(_=None, atoms=None, selection=None)

Translate by the selected XYZ delta.

translate_to_xyz(_=None, atoms=None, selection=None)

Translate to the selected XYZ position.

vec2str(vector)

class aiidalab_widgets_base.structures.SmilesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Convert SMILES into 3D structure.

SPINNER = '<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>'

static canonicalize_smiles(smiles: str) → str

Canonicalize the SMILES code.

Raises:

ValueError – if SMILES is invalid or if canonicalization fails

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.structures.StructureBrowserWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class to query for structures stored in the AiiDA database.

Parameters:

• title (string) – Title of the widget displayed on a tab in StructureManagerWidget

• query_types (tuple) – A tuple of Data node types that are searched (default: StructureData, CifData)

preprocess()

Search structures in AiiDA database and add formula extra to them.

search(_=None)

Launch the search of structures in AiiDA database.

structure

A trait type representing a Union type.

class aiidalab_widgets_base.structures.StructureExamplesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class to provide example structures for selection.

static get_example_structures(examples)

Get the list of example structures.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.structures.StructureManagerWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Upload a structure and store it in AiiDA database.

Attributes:

structure(Atoms): trait that contains the selected structure. ‘None’ if no structure is selected. structure_node(StructureData, CifData): trait that contains AiiDA structure object node_class(str): trait that contains structure_node type (as string).

SUPPORTED_DATA_FORMATS = {'CifData': 'core.cif', 'StructureData': 'core.structure'}

input_structure

A trait type representing a Union type.

node_class

A trait for unicode strings.

store_structure(_=None)

Stores the structure in AiiDA database.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

structure_node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

undo(_=None)

Undo modifications.

class aiidalab_widgets_base.structures.StructureUploadWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class that allows to upload structures from user’s computer.

structure

A trait type representing a Union type.

aiidalab_widgets_base.viewers module

class aiidalab_widgets_base.viewers.AiidaNodeViewWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.viewers.DictViewer(*args: t.Any, **kwargs: t.Any)

Bases: VBox

value

Viewer class for Dict object.

Parameters:

• parameter (Dict) – Dict object to be viewed

• downloadable (bool) – If True, add link/button to download the content of the object

class aiidalab_widgets_base.viewers.FolderDataViewer(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Viewer class for FolderData object.

Parameters:

• folder (FolderData) – FolderData object to be viewed

• downloadable (bool) – If True, add link/button to download the content of the selected file in the folder

change_file_view(_=None)

download(_=None)

Download selected file.

class aiidalab_widgets_base.viewers.NglViewerRepresentation(*args: t.Any, **kwargs: t.Any)

Bases: HBox

This class represents the parameters for displaying a structure in NGLViewer.

It is utilized in the structure viewer, where multiple representations can be defined, each specifying how to visually represent a particular subset of atoms.

add_myself_to_atoms_object(structure: Atoms | None)

Add representation array to the structure object. If the array already exists, update it.

atoms_in_representation(structure: Atoms | None = None)

Return an array of booleans indicating which atoms are present in the representation.

delete_myself(_)

nglview_parameters(indices)

Return the parameters dictionary of a representation.

sync_myself_to_array_from_atoms_object(structure: Atoms | None)

Update representation from the structure object.

viewer_class = None

class aiidalab_widgets_base.viewers.ProcessNodeViewerWidget(*args: t.Any, **kwargs: t.Any)

Bases: HTML

class aiidalab_widgets_base.viewers.StructureDataViewer(*args: t.Any, **kwargs: t.Any)

Bases: _StructureDataBaseViewer

Viewer class for AiiDA structure objects.

Attributes:

structure (Atoms, StructureData, CifData): Trait that contains a structure object, which was initially provided to the viewer. It can be either directly set to an ASE Atoms object or to AiiDA structure object containing get_ase() method.

displayed_structure (Atoms): Trait that contains a structure object that is currently displayed (supercell, for example). The trait is generated automatically and can’t be set outside of the class.

create_selection_info()

Create information to be displayed with selected atoms

d_from(operand)

displayed_structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

name_operator(operand)

Defining the name operator which will handle atom kind names.

not_operator(operand)

Reverting the selected atoms.

pk

An int trait.

structure

A trait type representing a Union type.

aiidalab_widgets_base.viewers.register_viewer_widget(key)

Register widget as a viewer for the given key.

aiidalab_widgets_base.viewers.viewer(obj, **kwargs)

Display AiiDA data types in Jupyter notebooks.

Returns the object itself if the viewer wasn’t found.

aiidalab_widgets_base.wizard module

The wizard application allows the implication of a Wizard-like GUI.

Authors:

• Carl Simon Adorf <simon.adorf@epfl.ch>

exception aiidalab_widgets_base.wizard.AtLeastTwoStepsWizardError(steps)

Bases: ValueError

Using WizardAppWidget only makes sense if the number of setps is at least two.

class aiidalab_widgets_base.wizard.WizardAppWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

ICONS = {State.ACTIVE: '⌛', State.CONFIGURED: '●', State.FAIL: '×', State.INIT: '○', State.READY: '◎', State.SUCCESS: '✓'}

ICON_SEPARATOR = '\u2000'

can_reset()

reset(step=0)

Reset the app up to the given step.

For example, with step=0 (the default), the whole app is reset. With step=1, all but the first step are reset.

selected_index

An int trait.

property show_header

class aiidalab_widgets_base.wizard.WizardAppWidgetStep(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

One step of a WizardAppWidget.

class State(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

Each step is always in one specific state.

The state is used to determine:

1. how the step is visually presented to the user, and

2. whether the next step is accessible (i.e. reached the SUCCESS state).

App developers are encouraged to use the step states to couple application logic and interface. In general, all widget changes should trigger a re-evaluation of the step state, and states also determine whether certain widgets are enabled or disabled.

A step can be in one of the following states:

INIT: The initial state, usually all widgets disabled. READY: The step (widget) is ready for user input (some or all widgets enabled). CONFIGURED: The step is in a consistent configuration awaiting confirmation. ACTIVE: The step is carrying out a runtime operation. SUCCESS: A configuration has been confirmed / a runtime operation successfully finished. FAIL: A runtime operation has failed in an unrecoverable way.

Not all steps must implement all states, for example:

• the first step does not need an INIT state

• a step without runtime process should not have an ACTIVE or FAIL state

• a “review & confirm” step does not require a READY state.

• a step without configuration options (e.g. pure “review & confirm” step)

Important: The next step is only accessible if the current step is within the SUCCESS state!

ACTIVE = 3

CONFIGURED = 1

FAIL = -1

INIT = 0

READY = 2

SUCCESS = 4

auto_advance

A boolean (True, False) trait.

can_reset()

state

Use a Enum class as model for the data type description. Note that if no default-value is provided, the first enum-value is used as default-value.

# -- SINCE: Python 3.4 (or install backport: pip install enum34)
import enum
from traitlets import HasTraits, UseEnum


class Color(enum.Enum):
    red = 1  # -- IMPLICIT: default_value
    blue = 2
    green = 3


class MyEntity(HasTraits):
    color = UseEnum(Color, default_value=Color.blue)


entity = MyEntity(color=Color.red)
entity.color = Color.green  # USE: Enum-value (preferred)
entity.color = "green"  # USE: name (as string)
entity.color = "Color.green"  # USE: scoped-name (as string)
entity.color = 3  # USE: number (as int)
assert entity.color is Color.green

Module contents

Reusable widgets for AiiDAlab applications.

class aiidalab_widgets_base.AiidaNodeViewWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.BasicCellEditor(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget that allows for the basic cell editing.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.BasicStructureEditor(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget that allows for the basic structure (molecule and position of periodic structure in cell) editing.

property action_vector

Define the action vector.

add(_=None, atoms=None, selection=None)

Add atoms.

align(_=None, atoms=None, selection=None)

Rotate atoms to align action vector with XYZ vector.

camera_orientation

An instance of a Python list.

copy_sel(_=None, atoms=None, selection=None)

Copy selected atoms and shift by 1.0 A along X-axis.

def_axis_p1(_=None)

Define the first point of axis.

def_axis_p2(_=None)

Define the second point of axis.

def_perpendicular_to_screen(_=None)

Define a normalized vector perpendicular to the screen.

def_point(_=None)

Define the action point.

input_selection

An instance of a Python list.

mirror(_=None, norm=None, point=None, atoms=None, selection=None)

Mirror atoms on the plane perpendicular to the action vector.

mirror_3p(_=None)

Mirror atoms on the plane containing action vector and action point.

mod_element(_=None, atoms=None, selection=None)

Modify selected atoms into the given element.

remove(_=None, atoms=None, selection=None)

Remove selected atoms.

rotate(_=None, atoms=None, selection=None)

Rotate atoms around selected point in space and vector.

sel2com()

Get center of mass of the selection.

selection

An instance of a Python list.

str2vec(string)

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

translate_dr(_=None, atoms=None, selection=None)

Translate by dr along the selected vector.

translate_dxdydz(_=None, atoms=None, selection=None)

Translate by the selected XYZ delta.

translate_to_xyz(_=None, atoms=None, selection=None)

Translate to the selected XYZ position.

vec2str(vector)

class aiidalab_widgets_base.CodQueryWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Query structures in Crystallography Open Database (COD) Useful class members: :ivar structure(Atoms): trait that contains the selected structure, None if structure is not selected.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.ComputationalResourcesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Code selection widget. Attributes:

value(code UUID): Trait that points to the selected UUID of the code instance. It can be set either to an AiiDA code UUID or to a code label. It is linked to the value trait of the self.code_select_dropdown widget.

codes(Dict): Trait that contains a dictionary (label => Code UUID) for all codes found in the AiiDA database for the selected plugin. It is linked to the ‘options’ trait of the self.code_select_dropdown widget.

allow_hidden_codes(Bool): Trait that defines whether to show hidden codes or not.

allow_disabled_computers(Bool): Trait that defines whether to show codes on disabled computers.

allow_disabled_computers

A boolean (True, False) trait.

allow_hidden_codes

A boolean (True, False) trait.

codes

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

refresh(_=None)

Refresh available codes.

The job of this function is to look in AiiDA database, find available codes and put them in the code_select_dropdown widget.

value

A trait for unicode strings.

class aiidalab_widgets_base.ComputerDropdownWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget to select a configured computer.

Attributes:

value(computer UUID): Trait that points to the selected Computer instance. It can be set to an AiiDA Computer UUID. It is linked to the ‘value’ trait of self._dropdown widget. computers(Dict): Trait that contains a dictionary (label => Computer UUID) for all computers found in the AiiDA database. It is linked to the ‘options’ trait of self._dropdown widget. allow_select_disabled(Bool): Trait that defines whether to show disabled computers.

allow_select_disabled

A boolean (True, False) trait.

computers

An instance of a Python dict.

One or more traits can be passed to the constructor to validate the keys and/or values of the dict. If you need more detailed validation, you may use a custom validator method.

Changed in version 5.0: Added key_trait for validating dict keys.

Changed in version 5.0: Deprecated ambiguous trait, traits args in favor of value_trait, per_key_traits.

refresh(_=None)

Refresh the list of configured computers.

select_by_label(label)

Select computer by computer label.

value

A trait for unicode strings.

class aiidalab_widgets_base.ElnConfigureWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

check_connection(_=None)

display_eln_config(value=None)

Display ELN configuration specific to the selected type of ELN.

erase_current_eln_from_configuration(_=None)

get_config()

save_eln_configuration(_=None)

set_current_eln_as_default(_=None)

update_eln_configuration(eln_instance, eln_config)

update_list_of_elns()

write_to_config(config)

class aiidalab_widgets_base.ElnExportWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

handle_output(_=None)

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

send_to_eln(_=None)

class aiidalab_widgets_base.ElnImportWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.ExportButtonWidget(*args: t.Any, **kwargs: t.Any)

Bases: Button

Export Node button.

export_aiida_subgraph(change=None)

Perform export when the button is pressed

class aiidalab_widgets_base.LoadingWidget(*args: t.Any, **kwargs: t.Any)

Bases: HBox

Widget for displaying a loading spinner.

class aiidalab_widgets_base.NodesTreeWidget(*args: t.Any, **kwargs: t.Any)

Bases: Output

A tree widget for the structured representation of a nodes graph.

NODE_TYPE = {<class 'aiida.orm.nodes.process.calculation.calcfunction.CalcFunctionNode'>: <class 'aiidalab_widgets_base.nodes.CalcFunctionTreeNode'>, <class 'aiida.orm.nodes.process.calculation.calcjob.CalcJobNode'>: <class 'aiidalab_widgets_base.nodes.CalcJobTreeNode'>, <class 'aiida.orm.nodes.process.workflow.workchain.WorkChainNode'>: <class 'aiidalab_widgets_base.nodes.WorkChainProcessTreeNode'>}

PROCESS_STATE_STYLE = {ProcessState.EXCEPTED: 'danger', ProcessState.FINISHED: 'success', ProcessState.KILLED: 'warning', ProcessState.RUNNING: 'info', ProcessState.WAITING: 'info'}

PROCESS_STATE_STYLE_DEFAULT = 'default'

find_node(pk, namespaces=None)

Find a node by its pk and namespaces. If node is an output node, it is identified by the parent pk and namespaces, otherwise by the pk.

nodes

An instance of a Python tuple.

selected_nodes

An instance of a Python tuple.

update(_=None)

Refresh nodes based on the latest state of the root process and its children.

class aiidalab_widgets_base.OptimadeQueryWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

AiiDAlab-specific OPTIMADE Query widget

Useful as a widget to integrate with the aiidalab_widgets_base.structures.StructureManagerWidget, embedded into applications.

NOTE: embedded for OptimadeQueryFilterWidget was introduced in optimade-client version 2020.11.5.

Parameters:

• embedded (bool) – Whether or not to show extra database and provider information. When set to True, the extra information will be hidden, this is useful in situations where the widget is used in a Tab or similar, e.g., for the class aiidalab_widgets_base.structures.StructureManagerWidget.

• title (str) – Title used for Tab header if employed in aiidalab_widgets_base.structures.StructureManagerWidget.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.ProcessFollowerWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

A Widget that follows a process until finished.

follow(detach=False)

Initiate following the process with or without blocking.

on_completed(function)

Run functions after a process has been completed.

process

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

update()

class aiidalab_widgets_base.ProcessMonitor(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

Monitor a process and execute callback functions at specified intervals.

join()

log_widget: ipw.Output | None

value

A trait for unicode strings.

class aiidalab_widgets_base.ProcessNodesTreeWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

A tree widget for the structured representation of a process graph.

selected_nodes

An instance of a Python tuple.

update(_=None)

value

A trait for unicode strings.

class aiidalab_widgets_base.SmilesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Convert SMILES into 3D structure.

SPINNER = '<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>'

static canonicalize_smiles(smiles: str) → str

Canonicalize the SMILES code.

Raises:

ValueError – if SMILES is invalid or if canonicalization fails

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.StructureBrowserWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class to query for structures stored in the AiiDA database.

Parameters:

• title (string) – Title of the widget displayed on a tab in StructureManagerWidget

• query_types (tuple) – A tuple of Data node types that are searched (default: StructureData, CifData)

preprocess()

Search structures in AiiDA database and add formula extra to them.

search(_=None)

Launch the search of structures in AiiDA database.

structure

A trait type representing a Union type.

class aiidalab_widgets_base.StructureExamplesWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class to provide example structures for selection.

static get_example_structures(examples)

Get the list of example structures.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.StructureManagerWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Upload a structure and store it in AiiDA database.

Attributes:

structure(Atoms): trait that contains the selected structure. ‘None’ if no structure is selected. structure_node(StructureData, CifData): trait that contains AiiDA structure object node_class(str): trait that contains structure_node type (as string).

SUPPORTED_DATA_FORMATS = {'CifData': 'core.cif', 'StructureData': 'core.structure'}

input_structure

A trait type representing a Union type.

node_class

A trait for unicode strings.

store_structure(_=None)

Stores the structure in AiiDA database.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

structure_node

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

undo(_=None)

Undo modifications.

class aiidalab_widgets_base.StructureUploadWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Class that allows to upload structures from user’s computer.

structure

A trait type representing a Union type.

class aiidalab_widgets_base.SubmitButtonWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Submit button class that creates submit button jupyter widget.

on_btn_submit_press(_=None)

When submit button is pressed.

on_click(function)

on_submitted(function)

Run functions after a process has been submitted successfully.

process

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

class aiidalab_widgets_base.WizardAppWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

ICONS = {State.ACTIVE: '⌛', State.CONFIGURED: '●', State.FAIL: '×', State.INIT: '○', State.READY: '◎', State.SUCCESS: '✓'}

ICON_SEPARATOR = '\u2000'

can_reset()

reset(step=0)

Reset the app up to the given step.

For example, with step=0 (the default), the whole app is reset. With step=1, all but the first step are reset.

selected_index

An int trait.

property show_header

class aiidalab_widgets_base.WizardAppWidgetStep(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

One step of a WizardAppWidget.

class State(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

Each step is always in one specific state.

The state is used to determine:

1. how the step is visually presented to the user, and

2. whether the next step is accessible (i.e. reached the SUCCESS state).

App developers are encouraged to use the step states to couple application logic and interface. In general, all widget changes should trigger a re-evaluation of the step state, and states also determine whether certain widgets are enabled or disabled.

A step can be in one of the following states:

INIT: The initial state, usually all widgets disabled. READY: The step (widget) is ready for user input (some or all widgets enabled). CONFIGURED: The step is in a consistent configuration awaiting confirmation. ACTIVE: The step is carrying out a runtime operation. SUCCESS: A configuration has been confirmed / a runtime operation successfully finished. FAIL: A runtime operation has failed in an unrecoverable way.

Not all steps must implement all states, for example:

• the first step does not need an INIT state

• a step without runtime process should not have an ACTIVE or FAIL state

• a “review & confirm” step does not require a READY state.

• a step without configuration options (e.g. pure “review & confirm” step)

Important: The next step is only accessible if the current step is within the SUCCESS state!

ACTIVE = 3

CONFIGURED = 1

FAIL = -1

INIT = 0

READY = 2

SUCCESS = 4

auto_advance

A boolean (True, False) trait.

can_reset()

state

Use a Enum class as model for the data type description. Note that if no default-value is provided, the first enum-value is used as default-value.

# -- SINCE: Python 3.4 (or install backport: pip install enum34)
import enum
from traitlets import HasTraits, UseEnum


class Color(enum.Enum):
    red = 1  # -- IMPLICIT: default_value
    blue = 2
    green = 3


class MyEntity(HasTraits):
    color = UseEnum(Color, default_value=Color.blue)


entity = MyEntity(color=Color.red)
entity.color = Color.green  # USE: Enum-value (preferred)
entity.color = "green"  # USE: name (as string)
entity.color = "Color.green"  # USE: scoped-name (as string)
entity.color = 3  # USE: number (as int)
assert entity.color is Color.green

aiidalab_widgets_base.register_viewer_widget(key)

Register widget as a viewer for the given key.

aiidalab_widgets_base.viewer(obj, **kwargs)

Display AiiDA data types in Jupyter notebooks.

Returns the object itself if the viewer wasn’t found.