Merge pull request #136 from aiidalab/release/1.0.0b11

Release/1.0.0b11

.readthedocs.yml

@@ -0,0 +1,7 @@
+build:
+  image: latest
+python:
+  version: 3.7
+  pip_install: true
+  extra_requirements:
+  - "docs"

.travis.yml

@@ -7,8 +7,9 @@ before_install:
   - pip install -U wheel setuptools coveralls
 
 install:
-- pip install .[testing,pre-commit]
+- pip install .[pre-commit,docs]
 - reentry scan -r aiida
 
 script:
   - pre-commit install; pre-commit run --all-files || ( git status --short; git diff ; exit 1 );
+  - cd docs && make

README.md

@@ -1,6 +1,6 @@
-# aiidalab-widgets-base 
+[![Documentation Status](https://readthedocs.org/projects/aiidalab-widgets-base/badge/?version=latest)](https://aiidalab-widgets-base.readthedocs.io/en/latest/?badge=latest)
 
-Reusable widgets for applications in the AiiDA lab.
+# Base widgets for AiiDAlab
 
 ## Installation
 
@@ -9,50 +9,22 @@ Install the `aiidalab_widgets_base` python package via:
 pip install aiidalab-widgets-base 
 ```
 
-Install the corresponding `aiidalab-widgets-base` AiiDA lab application
+Install the corresponding `aiidalab-widgets-base` AiiDAlab application
 via the app manager as usual.
 
 ### Optional dependencies
 
 * The `SmilesWidget` widget requires the [OpenBabel](http://openbabel.org/) library.
 
+## Documentation
+The documentation can be found on the [following web page](https://aiidalab-widgets-base.readthedocs.io).
+
 ## Usage
 
 Using the widgets usually just involves importing and displaying them.
 For demos, have a look at the jupyter notebooks (`.ipynb` extension) in
 this folder.
 
-### Structures
-
-Uploading structures
-```python
-from aiidalab_widgets_base import StructureUploadWidget
-from IPython.display import display
-
-widget = StructureUploadWidget()
-# Enforce node format to be CifData:
-# widget = StructureUploadWidget(node_class='CifData')
-display(widget)
-```
-
-![Demo](https://image.ibb.co/fjnHco/structure.gif "Using the StructureUploadWidget.")
-
-### Codes
-
-Selecting codes
-```python
-from aiidalab_widgets_base import CodeDropdown
-from IPython.display import display
-
-# Select from installed codes for 'zeopp.network' input plugin
-dropdown = CodeDropdown(input_plugin='zeopp.network')
-display(dropdown)
-
-dropdown.selected_code  # returns selected code
-```
-
-![Demo](https://image.ibb.co/gSFFf8/codes.gif "Using the CodeDropDown.")
-
 ## License
 
 MIT

aiidalab_widgets_base/__init__.py

@@ -1,4 +1,4 @@
-"""Reusable widgets for AiiDA lab applications."""
+"""Reusable widgets for AiiDAlab applications."""
 # pylint: disable=unused-import,wrong-import-position
 from aiida import load_profile
 load_profile()
@@ -7,7 +7,7 @@
 from .computers import SshComputerSetup, valid_sshcomputer_args
 from .computers import AiidaComputerSetup, valid_aiidacomputer_args
 from .computers import ComputerDropdown
-from .databases import CodQueryWidget
+from .databases import CodQueryWidget, OptimadeQueryWidget
 from .export import ExportButtonWidget
 from .process import ProgressBarWidget, ProcessFollowerWidget, ProcessInputsWidget, ProcessOutputsWidget
 from .process import ProcessCallStackWidget, RunningCalcJobOutputWidget, SubmitButtonWidget, ProcessReportWidget
@@ -18,4 +18,4 @@
 from .structures_multi import MultiStructureUploadWidget
 from .viewers import viewer
 
-__version__ = "1.0.0b10"
+__version__ = "1.0.0b11"

aiidalab_widgets_base/codes.py

@@ -22,19 +22,20 @@ def valid_aiidacode_args(arguments):
 class CodeDropdown(ipw.VBox):
     """Code selection widget.
     Attributes:
-        selected_code(Unicode or Code): Trait that points to the selected Code instance.
-            It can be set either to an AiiDA Code instance or to a code label (will
-            automatically be replaced by the corresponding Code instance).
-            It is linked to the 'value' trait of the `self.dropdown` widget.
 
-        codes(Dict): Trait that contains a dictionary (label => Code instance) for all
-            codes found in the AiiDA database for the selected plugin. It is linked
-            to the 'options' trait of the `self.dropdown` widget.
+    selected_code(Unicode or Code): Trait that points to the selected Code instance.
+    It can be set either to an AiiDA Code instance or to a code label (will automatically
+    be replaced by the corresponding Code instance). It is linked to the 'value' trait of
+    the `self.dropdown` widget.
 
-        allow_hidden_codes(Bool): Trait that defines whether to show hidden codes or not.
+    codes(Dict): Trait that contains a dictionary (label => Code instance) for all
+    codes found in the AiiDA database for the selected plugin. It is linked
+    to the 'options' trait of the `self.dropdown` widget.
 
-        allow_disabled_computers(Bool): Trait that defines whether to show codes on disabled
-            computers.
+    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.
     """
     selected_code = Union([Unicode(), Instance(Code)], allow_none=True)
     codes = Dict(allow_none=True)

aiidalab_widgets_base/databases.py

@@ -3,6 +3,9 @@
 from traitlets import Instance, default
 from ase import Atoms
 
+from optimade_client.query_filter import OptimadeQueryFilterWidget
+from optimade_client.query_provider import OptimadeQueryProviderWidget
+
 from aiida.tools.dbimporters.plugins.cod import CodDbImporter
 
 
@@ -110,3 +113,49 @@ def _on_select_structure(self, change):
     @default('structure')
     def _default_structure(self):  # pylint: disable=no-self-use
         return None
+
+
+class OptimadeQueryWidget(ipw.VBox):
+    """AiiDAlab-specific OPTIMADE Query widget
+
+    Useful as a widget to integrate with the
+    :class:`aiidalab_widgets_base.structures.StructureManagerWidget`,
+    embedded into applications.
+
+    :param embedded: 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`.
+    :type embedded: bool
+    :param title: Title used for Tab header if employed in
+        :class:`aiidalab_widgets_base.structures.StructureManagerWidget`.
+    :type title: str
+    """
+
+    structure = Instance(Atoms, allow_none=True)
+
+    def __init__(
+            self,
+            embedded: bool = True,
+            title: str = None,
+            **kwargs,
+    ) -> None:
+        providers = OptimadeQueryProviderWidget(embedded=embedded)
+        filters = OptimadeQueryFilterWidget()
+
+        ipw.dlink((providers, 'database'), (filters, 'database'))
+
+        filters.observe(self._update_structure, names='structure')
+
+        self.title = title if title is not None else 'OPTIMADE'
+        layout = kwargs.pop('layout') if 'layout' in kwargs else {'width': 'auto', 'height': 'auto'}
+
+        super().__init__(
+            children=(providers, filters),
+            layout=layout,
+            **kwargs,
+        )
+
+    def _update_structure(self, change: dict) -> None:
+        """New structure chosen"""
+        self.structure = change['new'].as_ase if change['new'] else None

aiidalab_widgets_base/process.py

@@ -4,13 +4,14 @@
 import os
 from inspect import isclass
 from time import sleep
+import warnings
 import pandas as pd
 import ipywidgets as ipw
 from IPython.display import HTML, Javascript, clear_output, display
 from traitlets import Instance, Int, List, Unicode, Union, observe, validate
 
 # AiiDA imports.
-from aiida.engine import submit, Process
+from aiida.engine import submit, Process, ProcessBuilder
 from aiida.orm import CalcFunctionNode, CalcJobNode, Node, ProcessNode, WorkChainNode, WorkFunctionNode, load_node
 from aiida.cmdline.utils.common import get_calcjob_report, get_workchain_report, get_process_function_report
 from aiida.cmdline.utils.ascii_vis import format_call_graph
@@ -39,18 +40,22 @@ class SubmitButtonWidget(ipw.VBox):
     """Submit button class that creates submit button jupyter widget."""
     process = Instance(ProcessNode, allow_none=True)
 
-    def __init__(self,
-                 process_class,
-                 input_dictionary_function,
-                 description="Submit",
-                 disable_after_submit=True,
-                 append_output=False,
-                 **kwargs):
+    def __init__(  # pylint: disable=too-many-arguments
+            self,
+            process_class,
+            inputs_generator=None,
+            input_dictionary_function=None,
+            description="Submit",
+            disable_after_submit=True,
+            append_output=False,
+            **kwargs):
         """Submit Button widget.
 
         process_class (Process): Process class to submit.
 
-        input_dictionary_function (func): Function that generates input parameters dictionary.
+        inputs_generator (func): Function that returns inputs dictionary or inputs builder.
+
+        input_dictionary_function (DEPRECATED): Function that generates input parameters dictionary.
 
         description (str): Description written on the submission button.
 
@@ -63,14 +68,26 @@ def __init__(self,
         if isclass(process_class) and issubclass(process_class, Process):
             self._process_class = process_class
         else:
-            raise ValueError("process_class argument must be a sublcass of {}, got {}".format(Process, process_class))
-
-        if callable(input_dictionary_function):
-            self.input_dictionary_function = input_dictionary_function
+            raise ValueError(f"process_class argument must be a sublcass of {Process}, got {process_class}")
+
+        # Handling the deprecation.
+        if inputs_generator is None and input_dictionary_function is None:
+            raise ValueError("The `inputs_generator` argument must be provided.")
+        if inputs_generator and input_dictionary_function:
+            raise ValueError("You provided both: `inputs_generator` and `input_dictionary_function` "
+                             "arguments. Please provide `inpust_generator` only.")
+        if input_dictionary_function:
+            inputs_generator = input_dictionary_function
+            warnings.warn(("The `input_dictionary_function` argument is deprecated and "
+                           "will be removed in the release 1.1 of the aiidalab-widgets-base package. "
+                           "Please use the `inputs_generator` argument instead."), DeprecationWarning)
+
+        # Checking if the inputs generator is
+        if callable(inputs_generator):
+            self.inputs_generator = inputs_generator
         else:
-            raise ValueError(
-                "input_dictionary_function argument must be a function that returns input dictionary, got {}".format(
-                    input_dictionary_function))
+            raise ValueError("The `inputs_generator` argument must be a function that "
+                             f"returns input dictionary, got {inputs_generator}")
 
         self.disable_after_submit = disable_after_submit
         self.append_output = append_output
@@ -91,24 +108,28 @@ def on_btn_submit_press(self, _=None):
         if not self.append_output:
             self.submit_out.value = ''
 
-        input_dict = self.input_dictionary_function()
-        if input_dict is None:
+        inputs = self.inputs_generator()
+        if inputs is None:
             if self.append_output:
-                self.submit_out.value += "SubmitButtonWidget: did not recieve input dictionary.<br>"
+                self.submit_out.value += "SubmitButtonWidget: did not recieve the process inputs.<br>"
             else:
-                self.submit_out.value = "SubmitButtonWidget: did not recieve input dictionary."
+                self.submit_out.value = "SubmitButtonWidget: did not recieve the process inputs."
         else:
-            self.btn_submit.disabled = self.disable_after_submit
-            self.process = submit(self._process_class, **input_dict)
+            if self.disable_after_submit:
+                self.btn_submit.disabled = True
+            if isinstance(inputs, ProcessBuilder):
+                self.process = submit(inputs)
+            else:
+                self.process = submit(self._process_class, **inputs)
 
             if self.append_output:
-                self.submit_out.value += """Submitted process {0}. Click
-                <a href={1}aiidalab-widgets-base/process.ipynb?id={2} target="_blank">here</a>
-                to follow.<br>""".format(self.process, self.path_to_root, self.process.pk)
+                self.submit_out.value += f"""Submitted process {self.process}. Click
+                <a href={self.path_to_root}aiidalab-widgets-base/process.ipynb?id={self.process.pk}
+                target="_blank">here</a> to follow.<br>"""
             else:
-                self.submit_out.value = """Submitted process {0}. Click
-                <a href={1}aiidalab-widgets-base/process.ipynb?id={2} target="_blank">here</a>
-                to follow.""".format(self.process, self.path_to_root, self.process.pk)
+                self.submit_out.value = f"""Submitted process {self.process}. Click
+                <a href={self.path_to_root}aiidalab-widgets-base/process.ipynb?id={self.process.pk}
+                target="_blank">here</a> to follow."""
 
             for func in self._run_after_submitted:
                 func(self.process)

aiidalab_widgets_base/structures.py

@@ -8,17 +8,19 @@
 import ipywidgets as ipw
 from traitlets import Instance, Int, List, Unicode, Union, dlink, link, default, observe
 
-from sklearn.decomposition import PCA
-
 # ASE imports
 import ase
 from ase import Atom, Atoms
 from ase.data import chemical_symbols, covalent_radii
 
-# AiiDA and AiiDA lab imports
+# AiiDA imports
 from aiida.engine import calcfunction
 from aiida.orm import CalcFunctionNode, CalcJobNode, Data, QueryBuilder, Node, WorkChainNode
 from aiida.plugins import DataFactory
+
+from sklearn.decomposition import PCA
+
+# Local imports
 from .utils import get_ase_from_file
 from .viewers import StructureDataViewer
 from .data import LigandSelectorWidget
@@ -106,7 +108,7 @@ def __init__(self, importers, viewer=None, editors=None, storable=True, node_cla
             ipw.HBox(store_and_description + [self.structure_label, self.structure_description])
         ]
 
-        structure_editors = self._struture_editors(editors)
+        structure_editors = self._structure_editors(editors)
         if structure_editors:
             structure_editors = ipw.VBox([btn_undo, structure_editors])
             accordion = ipw.Accordion([structure_editors])
@@ -137,7 +139,7 @@ def _structure_importers(self, importers):
             dlink((importer, 'structure'), (self, 'input_structure'))
         return importers_tab
 
-    def _struture_editors(self, editors):
+    def _structure_editors(self, editors):
         """Preparing structure editors."""
         if editors and len(editors) == 1:
             link((editors[0], 'structure'), (self, 'structure'))
@@ -150,7 +152,7 @@ def _struture_editors(self, editors):
         # If more than one editor was defined.
         if editors:
             editors_tab = ipw.Tab()
-            editors_tab.children = [i for i in editors]
+            editors_tab.children = tuple(editors)
             for i, editor in enumerate(editors):
                 editors_tab.set_title(i, editor.title)
                 link((editor, 'structure'), (self, 'structure'))

docs/.gitignore

@@ -0,0 +1 @@
+build/