Migrate the app to AiiDA 2.x (#22)

.github/workflows/di.yml

@@ -14,7 +14,7 @@ jobs:
 
         strategy:
             matrix:
-                tag: [stable, latest]
+                tag: [edge, latest]
                 browser: [chrome, firefox]
             fail-fast: false
 
@@ -26,7 +26,7 @@ jobs:
             - name: Test app
               uses: aiidalab/aiidalab-test-app-action@v2
               with:
-                  image: aiidalab/aiidalab-docker-stack:${{ matrix.tag }}
+                  image: aiidalab/full-stack:${{ matrix.tag }}
                   browser: ${{ matrix.browser }}
                   name: empa-molecules
 

empa_molecules/steps.py

@@ -1,6 +1,6 @@
 import aiidalab_widgets_base as awb
 import ipywidgets as ipw
-import traitlets
+import traitlets as tr
 from aiida import engine, orm, plugins
 
 from .widgets import NodeViewWidget
@@ -12,7 +12,7 @@
 class StructureSelectionStep(ipw.VBox, awb.WizardAppWidgetStep):
     """Integrated widget for the selection of structures from different sources."""
 
-    confirmed_structure = traitlets.Instance(StructureData, allow_none=True)
+    confirmed_structure = tr.Instance(StructureData, allow_none=True)
 
     def __init__(self, description=None, **kwargs):
         self.manager = awb.StructureManagerWidget(
@@ -57,7 +57,7 @@ def __init__(self, description=None, **kwargs):
             **kwargs
         )
 
-    @traitlets.default("state")
+    @tr.default("state")
     def _default_state(self):
         return self.State.READY
 
@@ -73,12 +73,12 @@ def _update_state(self, _=None):
             else:
                 self.state = self.State.SUCCESS
 
-    @traitlets.observe("confirmed_structure")
+    @tr.observe("confirmed_structure")
     def _observe_confirmed_structure(self, _):
         with self.hold_trait_notifications():
             self._update_state()
 
-    @traitlets.observe("state")
+    @tr.observe("state")
     def _observe_state(self, change):
         with self.hold_trait_notifications():
             state = change["new"]
@@ -100,8 +100,8 @@ def reset(self):  # unconfirm
 class ConfigureGaussianCalculationStep(ipw.VBox, awb.WizardAppWidgetStep):
     """Widget to prepare gaussian inputs."""
 
-    inputs = traitlets.Dict()
-    input_structure = traitlets.Instance(StructureData, allow_none=True)
+    inputs = tr.Dict()
+    input_structure = tr.Instance(StructureData, allow_none=True)
 
     def __init__(self, **kwargs):
         self.dft_functional = ipw.Dropdown(
@@ -200,7 +200,7 @@ def confirm(self, _=None):
         }
         self.state = self.State.SUCCESS
 
-    @traitlets.default("state")
+    @tr.default("state")
     def _default_state(self):
         return self.State.INIT
 
@@ -210,23 +210,23 @@ class SubmitGaussianCalculationStep(ipw.VBox, awb.WizardAppWidgetStep):
 
     # We use traitlets to connect the different steps.
     # Note that we can use dlinked transformations, they do not need to be of the same type.
-    inputs = traitlets.Dict()
-    process = traitlets.Instance(orm.ProcessNode, allow_none=True)
+    inputs = tr.Dict()
+    value = tr.Unicode(allow_none=True)
 
     def __init__(self, **kwargs):
         self.configuration_label = ipw.HTML("Specify computational resources.")
 
         # Codes.
         self.gaussian_code_dropdown = awb.ComputationalResourcesWidget(
-            description="Gaussian", input_plugin="gaussian"
+            description="Gaussian", default_calc_job_plugin="gaussian"
         )
         self.gaussian_code_dropdown.observe(self._update_state, ["value"])
         self.cubegen_code_dropdown = awb.ComputationalResourcesWidget(
-            description="Cubegen", input_plugin="gaussian.cubegen"
+            description="Cubegen", default_calc_job_plugin="gaussian.cubegen"
         )
         self.cubegen_code_dropdown.observe(self._update_state, ["value"])
         self.formchk_code_dropdown = awb.ComputationalResourcesWidget(
-            description="Formchk", input_plugin="gaussian.formchk"
+            description="Formchk", default_calc_job_plugin="gaussian.formchk"
         )
         self.formchk_code_dropdown.observe(self._update_state, ["value"])
 
@@ -255,10 +255,14 @@ def __init__(self, **kwargs):
         self.observe(self._update_state, ["inputs"])
 
         self.btn_submit_mol_opt = awb.SubmitButtonWidget(
-            GaussianSpinWorkChain, input_dictionary_function=self.prepare_spin_calc
+            GaussianSpinWorkChain, inputs_generator=self.prepare_spin_calc
         )
         self.btn_submit_mol_opt.btn_submit.disabled = True
-        traitlets.dlink((self.btn_submit_mol_opt, "process"), (self, "process"))
+        tr.dlink(
+            (self.btn_submit_mol_opt, "process"),
+            (self, "value"),
+            transform=lambda x: x.uuid if x else None,
+        )
 
         super().__init__(
             [
@@ -316,9 +320,9 @@ def prepare_spin_calc(self):
             builder[key] = value
 
         # Codes.
-        builder.gaussian_code = self.gaussian_code_dropdown.value
-        builder.formchk_code = self.formchk_code_dropdown.value
-        builder.cubegen_code = self.cubegen_code_dropdown.value
+        builder.gaussian_code = orm.load_code(self.gaussian_code_dropdown.value)
+        builder.formchk_code = orm.load_code(self.formchk_code_dropdown.value)
+        builder.cubegen_code = orm.load_code(self.cubegen_code_dropdown.value)
 
         # Resources.
         builder.options = orm.Dict(
@@ -338,11 +342,12 @@ def prepare_spin_calc(self):
 
 
 class ViewGaussianWorkChainStatusAndResultsStep(ipw.VBox, awb.WizardAppWidgetStep):
-    process = traitlets.Instance(orm.ProcessNode, allow_none=True)
+    value = tr.Unicode(allow_none=True)
 
     def __init__(self, **kwargs):
+        self.process = None
         self.process_tree = awb.ProcessNodesTreeWidget()
-        ipw.dlink((self, "process"), (self.process_tree, "process"))
+        ipw.dlink((self, "value"), (self.process_tree, "value"))
 
         self.node_view = NodeViewWidget(layout={"width": "auto", "height": "auto"})
         ipw.dlink(
@@ -360,7 +365,7 @@ def __init__(self, **kwargs):
                 self._update_state,
             ],
         )
-        ipw.dlink((self, "process"), (self.process_monitor, "process"))
+        ipw.dlink((self, "value"), (self.process_monitor, "value"))
 
         super().__init__([self.process_status], **kwargs)
 
@@ -369,7 +374,7 @@ def can_reset(self):
         return self.state is not self.State.ACTIVE
 
     def reset(self):
-        self.process = None
+        self.value = None
 
     def _update_state(self):
         if self.process is None:
@@ -390,6 +395,10 @@ def _update_state(self):
             elif process_state is engine.ProcessState.FINISHED:
                 self.state = self.State.SUCCESS
 
-    @traitlets.observe("process")
+    @tr.observe("value")
     def _observe_process(self, change):
+        if self.value is None:
+            self.process = None
+        else:
+            self.process = orm.load_node(self.value)
         self._update_state()

empa_molecules/templates/search.j2

@@ -14,7 +14,7 @@
 {% for row in rows %}
 
 <tr>
-    <td> <a target="_blank" href="./spin_calculation.ipynb?pk={{ row['pk'] }}"> {{ row['pk'] }}</a> </td>
+    <td> <a target="_blank" href="./spin_calculation.ipynb?uuid={{ row['uuid'] }}"> {{ row['pk'] }}</a> </td>
     <td> {{ row['ctime'] }} </td>
     <td> {{ row['formula'] }} </td>
     <td>{{ row['description'] }} </td>

empa_molecules/version.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """This module contains project version information."""
 
 __version__ = "v23.06.1"

empa_molecules/widgets.py

@@ -34,7 +34,7 @@ def _observe_node(self, change):
 
 class WorkChainSelectorWidget(ipw.HBox):
     # The PK of a 'aiida.workflows:quantumespresso.pw.bands' WorkChainNode.
-    value = traitlets.Int(allow_none=True)
+    value = traitlets.Unicode(allow_none=True)
 
     # When this trait is set to a positive value, the work chains are automatically
     # refreshed every `auto_refresh_interval` seconds.
@@ -59,7 +59,7 @@ def __init__(self, **kwargs):
         ipw.dlink(
             (self.work_chains_selector, "value"),
             (self, "value"),
-            transform=lambda pk: None if pk is self._NO_PROCESS else pk,
+            transform=lambda uuid: None if uuid is self._NO_PROCESS else uuid,
         )
 
         self.refresh_work_chains_button = ipw.Button(description="Refresh")
@@ -82,6 +82,7 @@ def __init__(self, **kwargs):
     @dataclass
     class WorkChainData:
         pk: int
+        uuid: str
         ctime: str
         state: str
         formula: str
@@ -97,12 +98,12 @@ def find_work_chains(cls):
             order_by={"ctime": "desc"},
         )
         projected = builder.get_projected(
-            query_set, projections=["pk", "ctime", "state"]
+            query_set, projections=["pk", "uuid", "ctime", "state"]
         )
 
         for process in projected[1:]:
-            pk = process[0]
-            formula = orm.load_node(pk).inputs.structure.get_formula()
+            uuid = process[0]
+            formula = orm.load_node(uuid).inputs.structure.get_formula()
             yield cls.WorkChainData(formula=formula, *process)
 
     @traitlets.default("busy")
@@ -127,7 +128,7 @@ def refresh_work_chains(self, _=None):
                     self.work_chains_selector.options = [
                         ("New calculation...", self._NO_PROCESS)
                     ] + [
-                        (self.FMT_WORKCHAIN.format(wc=wc), wc.pk)
+                        (self.FMT_WORKCHAIN.format(wc=wc), wc.uuid)
                         for wc in self.find_work_chains()
                     ]
 
@@ -170,7 +171,7 @@ def _observe_value(self, change):
 
         new = self._NO_PROCESS if change["new"] is None else change["new"]
 
-        if new not in {pk for _, pk in self.work_chains_selector.options}:
+        if new not in {uuid for _, uuid in self.work_chains_selector.options}:
             self.refresh_work_chains()
 
         self.work_chains_selector.value = new
@@ -379,8 +380,7 @@ def observe_inp_pks(_=None):
             style=style,
         )
 
-        # ---------
-        # date selection
+        # Date selection
         dt_now = datetime.datetime.now()
         dt_from = dt_now - datetime.timedelta(days=20)
         self.date_start = ipw.Text(
@@ -398,7 +398,6 @@ def observe_inp_pks(_=None):
         )
 
         self.date_text = ipw.HTML(value="<p>Select the date range:</p>", width="150px")
-        # ---------
 
         search_crit = [
             ipw.HBox([inp_pks, pks_wrong_syntax]),
@@ -431,15 +430,15 @@ def search(self):
         # html table header
         column_names = {
             "pk": "PK",
+            "uuid": "UUID",
             "ctime": "Creation Time",
             "formula": "Formula",
             "description": "Descrition",
             "energy": "Energy (eV)",
             "thumbnail": "Thumbnail",
         }
 
-        # query AiiDA database
-
+        # Query AiiDA database
         qb = orm.QueryBuilder()
         qb.append(self.workchain_class, filters=self.prepare_query_filters())
         qb.order_by({self.workchain_class: {"ctime": "desc"}})
@@ -453,6 +452,7 @@ def search(self):
 
             row = {
                 "pk": node.pk,
+                "uuid": node.uuid,
                 "ctime": node.ctime.strftime("%Y-%m-%d %H:%M"),
                 "formula": node.outputs.gs_structure.get_formula(),
                 "description": node.description,

search.ipynb

@@ -48,7 +48,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

setup.cfg

@@ -22,11 +22,10 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    aiida-core~=1.6
-    aiida-gaussian>=1.4.3
-    aiida-nanotech-empa>=0.5.3
-    aiidalab>=21.11.0
-    aiidalab-widgets-base~=1.3
+    aiida-core~=2.2
+    aiida-gaussian~=2.0
+    aiida-nanotech-empa>=1.0.0b3
+    aiidalab-widgets-base~=2.0
 python_requires = >=3.7
 
 [options.extras_require]