Mig/2.1

.github/workflows/di.yml

@@ -7,35 +7,42 @@ on:
     workflow_dispatch:
     schedule:
         - cron: 41 3 * * *
+    pull_request:
 
 jobs:
 
     test-app:
 
-        runs-on: ubuntu-latest
-        timeout-minutes: 10
-
         strategy:
             matrix:
-                tag: [latest, stable]
-                browser: [chrome, firefox]
+                tag: [latest]
+                browser: [Chrome, Firefox]
+                python-version: ['3.8', '3.10']
             fail-fast: false
 
+        runs-on: ubuntu-latest
+        timeout-minutes: 60
+
         steps:
 
             - name: Check out app
               uses: actions/checkout@v2
 
-            - name: Test app
-              uses: aiidalab/aiidalab-test-app-action@v2
+            - name: Cache Python dependencies
+              uses: actions/cache@v1
               with:
-                  image: aiidalab/aiidalab-docker-stack:${{ matrix.tag }}
-                  browser: ${{ matrix.browser }}
-                  name: quantum-espresso
+                  path: ~/.cache/pip
+                  key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+                  restore-keys: pip-${{ matrix.python-version }}-tests
 
-            - name: Upload screenshots as artifacts
-              uses: actions/upload-artifact@v2
-              if: ${{ always() }}
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
               with:
-                  name: Screenshots-${{ matrix.tag }}-${{ matrix.browser }}
-                  path: screenshots/
+                  python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies for test
+              run: |
+                  pip install -U -r requirements_test.txt
+
+            - name: Run pytest
+              run: TAG=${{ matrix.tag }} JUPYTER_TOKEN=$(openssl rand -hex 32) pytest --driver ${{ matrix.browser }}

aiidalab_qe/setup_codes.py

@@ -67,6 +67,7 @@ def _setup_code(code_name, computer_name="localhost"):
     try:
         load_code(f"{code_name}-{QE_VERSION}@localhost")
     except NotExistent:
+        # TODO replace with API setup after aiida-core 2.1 support
         run(
             [
                 "verdi",
@@ -82,7 +83,7 @@ def _setup_code(code_name, computer_name="localhost"):
                 "--computer",
                 computer_name,
                 "--prepend-text",
-                f"conda activate {CONDA_ENV_PREFIX}\nexport OMP_NUM_THREADS=1",
+                f'eval "$(conda shell.posix hook)"\nconda activate {CONDA_ENV_PREFIX}\nexport OMP_NUM_THREADS=1',
                 "--remote-abs-path",
                 CONDA_ENV_PREFIX.joinpath("bin", f"{code_name}.x"),
             ],

aiidalab_qe/steps.py

@@ -11,7 +11,7 @@
 import traitlets
 from aiida.common import NotExistent
 from aiida.engine import ProcessBuilderNamespace, ProcessState, submit
-from aiida.orm import ProcessNode, WorkChainNode, load_code
+from aiida.orm import WorkChainNode, load_code, load_node
 from aiida.plugins import DataFactory
 from aiida_quantumespresso.common.types import ElectronicType, RelaxType, SpinType
 from aiida_quantumespresso.workflows.pw.base import PwBaseWorkChain
@@ -614,9 +614,9 @@ def _identify_submission_blockers(self):
             and len(
                 set(
                     (
-                        self.pw_code.value.computer.pk,
-                        self.dos_code.value.computer.pk,
-                        self.projwfc_code.value.computer.pk,
+                        load_code(self.pw_code.value).computer.pk,
+                        load_code(self.dos_code.value).computer.pk,
+                        load_code(self.projwfc_code.value).computer.pk,
                     )
                 )
             )
@@ -667,7 +667,7 @@ def _auto_select_code(self, change):
                 try:
                     code_widget = getattr(self, code)
                     code_widget.refresh()
-                    code_widget.value = load_code(DEFAULT_PARAMETERS[code])
+                    code_widget.value = load_code(DEFAULT_PARAMETERS[code]).uuid
                 except NotExistent:
                     pass
 
@@ -689,9 +689,10 @@ def _show_alert_message(self, message, alert_class="info"):
     def _update_resources(self, change):
         if change["new"] and (
             change["old"] is None
-            or change["new"].computer.pk != change["old"].computer.pk
+            or load_code(change["new"]).computer.pk
+            != load_code(change["old"]).computer.pk
         ):
-            self.set_resource_defaults(change["new"].computer)
+            self.set_resource_defaults(load_code(change["new"]).computer)
 
     def set_resource_defaults(self, computer=None):
 
@@ -728,7 +729,7 @@ def _check_resources(self):
             return  # No code selected, nothing to do.
 
         num_cpus = self.resources_config.num_cpus.value
-        on_localhost = self.pw_code.value.computer.get_hostname() == "localhost"
+        on_localhost = load_node(self.pw_code.value).computer.hostname == "localhost"
         if self.pw_code.value and on_localhost and num_cpus > 1:
             self._show_alert_message(
                 "The selected code would be executed on the local host, but "
@@ -788,9 +789,9 @@ def get_input_parameters(self):
             run_pdos=self.workchain_settings.pdos_run.value,
             protocol=self.workchain_settings.workchain_protocol.value,
             # Codes
-            pw_code=self.pw_code.value.uuid,
-            dos_code=self.dos_code.value.uuid,
-            projwfc_code=self.projwfc_code.value.uuid,
+            pw_code=self.pw_code.value,
+            dos_code=self.dos_code.value,
+            projwfc_code=self.projwfc_code.value,
             # Advanced settings
             pseudo_family=self.pseudo_family_selector.value,
         )
@@ -808,18 +809,18 @@ def set_selected_codes(self, parameters):
         """Set the inputs in the GUI based on a set of parameters."""
 
         # Codes
-        def _load_code(code):
+        def _get_code_uuid(code):
             if code is not None:
                 try:
-                    return load_code(code)
+                    return load_code(code).uuid
                 except NotExistent:
                     return None
 
         with self.hold_trait_notifications():
             # Codes
-            self.pw_code.value = _load_code(parameters["pw_code"])
-            self.dos_code.value = _load_code(parameters["dos_code"])
-            self.projwfc_code.value = _load_code(parameters["projwfc_code"])
+            self.pw_code.value = _get_code_uuid(parameters["pw_code"])
+            self.dos_code.value = _get_code_uuid(parameters["dos_code"])
+            self.projwfc_code.value = _get_code_uuid(parameters["projwfc_code"])
 
     def set_pdos_status(self):
         if self.workchain_settings.pdos_run.value:
@@ -904,11 +905,14 @@ def reset(self):
 
 class ViewQeAppWorkChainStatusAndResultsStep(ipw.VBox, WizardAppWidgetStep):
 
-    process = traitlets.Instance(ProcessNode, allow_none=True)
+    process_uuid = traitlets.Unicode(allow_none=True)
 
     def __init__(self, **kwargs):
         self.process_tree = ProcessNodesTreeWidget()
-        ipw.dlink((self, "process"), (self.process_tree, "process"))
+        ipw.dlink(
+            (self, "process_uuid"),
+            (self.process_tree, "process_uuid"),
+        )
 
         self.node_view = NodeViewWidget(layout={"width": "auto", "height": "auto"})
         ipw.dlink(
@@ -926,7 +930,7 @@ def __init__(self, **kwargs):
                 self._update_state,
             ],
         )
-        ipw.dlink((self, "process"), (self.process_monitor, "process"))
+        ipw.dlink((self, "process_uuid"), (self.process_monitor, "process_uuid"))
 
         super().__init__([self.process_status], **kwargs)
 
@@ -935,13 +939,14 @@ def can_reset(self):
         return self.state is not self.State.ACTIVE
 
     def reset(self):
-        self.process = None
+        self.process_uuid = None
 
     def _update_state(self):
-        if self.process is None:
+        if self.process_uuid is None:
             self.state = self.State.INIT
         else:
-            process_state = self.process.process_state
+            process = load_node(self.process_uuid)
+            process_state = process.process_state
             if process_state in (
                 ProcessState.CREATED,
                 ProcessState.RUNNING,
@@ -950,12 +955,12 @@ def _update_state(self):
                 self.state = self.State.ACTIVE
             elif (
                 process_state in (ProcessState.EXCEPTED, ProcessState.KILLED)
-                or self.process.is_failed
+                or process.is_failed
             ):
                 self.state = self.State.FAIL
-            elif self.process.is_finished_ok:
+            elif process.is_finished_ok:
                 self.state = self.State.SUCCESS
 
-    @traitlets.observe("process")
+    @traitlets.observe("process_uuid")
     def _observe_process(self, change):
         self._update_state()

aiidalab_qe/widgets.py

@@ -14,7 +14,7 @@
 
 import ipywidgets as ipw
 import traitlets
-from aiida.orm import CalcJobNode, Node
+from aiida.orm import CalcJobNode, Node, load_node
 from aiidalab_widgets_base import register_viewer_widget, viewer
 from IPython.display import HTML, Javascript, clear_output, display
 
@@ -242,7 +242,7 @@ def _observe_value(self, change):
 
 class CalcJobOutputFollower(traitlets.HasTraits):
 
-    calcjob = traitlets.Instance(CalcJobNode, allow_none=True)
+    calcjob_uuid = traitlets.Unicode(allow_none=True)
     filename = traitlets.Unicode(allow_none=True)
     output = traitlets.List(trait=traitlets.Unicode)
     lineno = traitlets.Int()
@@ -258,14 +258,11 @@ def __init__(self, **kwargs):
 
         super().__init__(**kwargs)
 
-    @traitlets.observe("calcjob")
+    @traitlets.observe("calcjob_uuid")
     def _observe_calcjob(self, change):
-        try:
-            if change["old"].pk == change["new"].pk:
-                # Old and new process are identical.
-                return
-        except AttributeError:
-            pass
+        calcjob_uuid = change["new"]
+        if change["old"] == calcjob_uuid:
+            return
 
         with self._lock:
             # Stop following
@@ -283,15 +280,15 @@ def _observe_calcjob(self, change):
             # (Re/)start following
             if change["new"]:
                 self._follow_output_thread = Thread(
-                    target=self._follow_output, args=(change["new"],)
+                    target=self._follow_output, args=(calcjob_uuid,)
                 )
                 self._follow_output_thread.start()
 
-    def _follow_output(self, calcjob):
+    def _follow_output(self, calcjob_uuid):
         """Monitor calcjob and orchestrate pushing and pulling of output."""
-        self._pull_thread = Thread(target=self._pull_output, args=(calcjob,))
+        self._pull_thread = Thread(target=self._pull_output)
         self._pull_thread.start()
-        self._push_thread = Thread(target=self._push_output, args=(calcjob,))
+        self._push_thread = Thread(target=self._push_output, args=(calcjob_uuid,))
         self._push_thread.start()
 
     def _fetch_output(self, calcjob):
@@ -318,9 +315,10 @@ def _fetch_output(self, calcjob):
 
     _EOF = None
 
-    def _push_output(self, calcjob, delay=0.2):
+    def _push_output(self, calcjob_uuid, delay=0.2):
         """Push new log lines onto the queue."""
         lineno = 0
+        calcjob = load_node(calcjob_uuid)
         while True:
             try:
                 lines = self._fetch_output(calcjob)
@@ -335,7 +333,7 @@ def _push_output(self, calcjob, delay=0.2):
                     self._output_queue.put(self._EOF)
                     break  # noqa: B012
 
-    def _pull_output(self, calcjob):
+    def _pull_output(self):
         """Pull new log lines from the queue and update traitlets."""
         while True:
             item = self._output_queue.get()

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 requires = [
-    "setuptools>=42",
+    "setuptools>=65",
     "wheel"
 ]
 build-backend = "setuptools.build_meta"

qe.ipynb

@@ -88,7 +88,7 @@
     "ipw.dlink((configure_qe_app_work_chain_step, 'smearing_settings'), (submit_qe_app_work_chain_step, 'smearing_settings'))\n",
     "ipw.dlink((configure_qe_app_work_chain_step, 'pseudo_family_selector'), (submit_qe_app_work_chain_step, 'pseudo_family_selector'))\n",
     "\n",
-    "ipw.dlink((submit_qe_app_work_chain_step, 'process'), (view_qe_app_work_chain_status_and_results_step, 'process'))\n",
+    "ipw.dlink((submit_qe_app_work_chain_step, 'process'), (view_qe_app_work_chain_status_and_results_step, 'process_uuid'), transform=lambda node: node.uuid if node is not None else None)\n",
     "\n",
     "# Add the application steps to the application\n",
     "app = WizardAppWidget(\n",
@@ -157,7 +157,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -171,7 +171,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.4"
   }
  },
  "nbformat": 4,

requirements_test.txt

@@ -0,0 +1,4 @@
+pytest~=6.0
+pytest-docker~=1.0
+pytest-selenium~=4.0
+webdriver-manager~=3.8

setup.cfg

@@ -22,20 +22,23 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    Jinja2~=2.11.3
-    aiida-core~=1.0
-    aiida-quantumespresso~=3.5
+    Jinja2~=3.0
+    aiida-core~=2.0
+    aiida-quantumespresso~=4.0
     aiidalab-qe-workchain@https://github.com/aiidalab/aiidalab-qe/releases/download/v22.11.1/aiidalab_qe_workchain-22.11.1-py3-none-any.whl
-    aiidalab-widgets-base~=1.4.1
-    filelock~=3.3.0
+    aiidalab-widgets-base@git+https://github.com/aiidalab/aiidalab-widgets-base@fix/uuid-as-traitlets-threading-widget
+    filelock~=3.8
     importlib-resources~=5.2.2
+    numpy~=1.23 # pined for pymatgen
     widget-bandsplot~=0.2.8
-python_requires = >=3.7
+python_requires = >=3.8
 
 [options.extras_require]
 dev =
     bumpver==2022.1119
     pre-commit==2.11.1
+test =
+    requirements-test.txt
 
 [options.package_data]
 aiidalab_qe.parameters = qeapp.yaml

src/aiidalab_qe_workchain/__init__.py

@@ -13,14 +13,14 @@
 PwBandsWorkChain = WorkflowFactory("quantumespresso.pw.bands")
 PdosWorkChain = WorkflowFactory("quantumespresso.pdos")
 
-Bool = DataFactory("bool")
-Float = DataFactory("float")
-Dict = DataFactory("dict")
-Str = DataFactory("str")
-XyData = DataFactory("array.xy")
-StructureData = DataFactory("structure")
-BandsData = DataFactory("array.bands")
-Orbital = DataFactory("orbital")
+Bool = DataFactory("core.bool")
+Float = DataFactory("core.float")
+Dict = DataFactory("core.dict")
+Str = DataFactory("core.str")
+XyData = DataFactory("core.array.xy")
+StructureData = DataFactory("core.structure")
+BandsData = DataFactory("core.array.bands")
+Orbital = DataFactory("core.orbital")
 
 
 class QeAppWorkChain(WorkChain):