Fix/remove deprecations

.github/workflows/ci.yml

@@ -14,7 +14,6 @@ concurrency:
 jobs:
 
     pre-commit:
-    # Adapted from: https://github.com/CasperWA/voila-optimade-client
 
         runs-on: ubuntu-latest
 
@@ -32,11 +31,7 @@ jobs:
                       **/pyproject.toml
                       **/requirements*.txt
 
-            - name: Install dependencies
-              run: python -m pip install pre-commit~=2.20
-
-            - name: Run pre-commit
-              run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+            - uses: pre-commit/[email protected]
 
 
     test-package:

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
 
         steps:
 
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
 
             - name: Set up Python 3.10
               uses: actions/setup-python@v2

pyproject.toml

@@ -4,3 +4,42 @@ requires = [
     "wheel"
 ]
 build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    'error',
+    'ignore:Creating AiiDA configuration:UserWarning:aiida',
+    # For some reason we get this error, perhaps because we do
+    # not unload the AiiDA profile? Let's ignore this for now.
+    # E pytest.PytestUnraisableExceptionWarning: Exception ignored in: <function Popen.__del__>
+    # E Traceback (most recent call last):
+    # E   File "/opt/conda/lib/python3.9/subprocess.py", line 1052, in __del__
+    # E     _warn("subprocess %s is still running" % self.pid,
+    # E ResourceWarning: subprocess 382685 is still running
+    'ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning:_pytest',
+    # TODO: This comes from a transitive dependency of optimade_client
+    # Remove this when this issue is addressed:
+    # https://github.com/CasperWA/ipywidgets-extended/issues/85
+    'ignore::DeprecationWarning:ipywidgets_extended',
+    # TODO: StructureManagerWidget pass arguments by kwargs to StructureDataViewer and will be deprecated.
+    # E           DeprecationWarning: Passing unrecognized arguments to super(StructureManagerWidget).__init__(configuration_tabs=['Cell', 'Selection', 'Appearance', 'Download']).
+    # E           object.__init__() takes exactly one argument (the instance to initialize)
+    # E           This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.
+    'ignore::DeprecationWarning:ipywidgets',
+    'ignore::DeprecationWarning:ase.atoms',
+    # TODO: bandsplot_widget has an issue in schema validation
+    # >       result._update_view()
+    #
+    # tests/test_plugins_bands.py:12:
+    # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
+    # src/aiidalab_qe/plugins/bands/result.py:40: in _update_view
+    #     _bands_plot_view = BandsPlotWidget(
+    # ../../.local/lib/python3.9/site-packages/widget_bandsplot/bandsplot.py:112: in __init__
+    #     validate(instance=i, schema=BANDS_SCHEMA)
+    # /opt/conda/lib/python3.9/site-packages/jsonschema/validators.py:928: in validate
+    #     cls = validator_for(schema)
+    'ignore::DeprecationWarning:jsonschema',
+    # TODO: use uuid instead of node object in WorkChainViewer.
+    # Otherwise, the `Instance '<DbNode at 0x7f2f1bd885b0>' is not persistent within this Session` exception is raised.
+    'ignore::pytest.PytestUnhandledThreadExceptionWarning:_pytest',
+]

setup.cfg

@@ -27,7 +27,7 @@ install_requires =
     aiida-core~=2.2,<3
     Jinja2~=3.0
     aiida-quantumespresso~=4.3.0
-    aiidalab-widgets-base~=2.0.2
+    aiidalab-widgets-base==2.1.0a0
     filelock~=3.8
     importlib-resources~=5.2
     widget-bandsplot~=0.5.1

src/aiidalab_qe/app/configuration/advanced.py

@@ -39,6 +39,7 @@ class AdvancedSettings(Panel):
 
     # protocol interface
     protocol = tl.Unicode(allow_none=True)
+    # TODO: (unckpz) the DbNode persistence issue will be raised if using AiiDA Node as the trait.
     input_structure = tl.Instance(orm.StructureData, allow_none=True)
     spin_type = tl.Unicode()
     electronic_type = tl.Unicode()

src/aiidalab_qe/app/result/workchain_viewer.py

@@ -111,11 +111,11 @@ def toggle_camera():
             **kwargs,
         )
         self._process_monitor = ProcessMonitor(
-            process=self.node,
             callbacks=[
                 self._update_view,
             ],
         )
+        self._process_monitor.value = self.node.uuid
 
     def _update_view(self):
         with self.hold_trait_notifications():

src/aiidalab_qe/common/widgets.py

@@ -245,7 +245,7 @@ def _observe_value(self, change):
 class CalcJobOutputFollower(traitlets.HasTraits):
     calcjob_uuid = traitlets.Unicode(allow_none=True)
     filename = traitlets.Unicode(allow_none=True)
-    output = traitlets.List(trait=traitlets.Unicode)
+    output = traitlets.List(trait=traitlets.Unicode())
     lineno = traitlets.Int()
 
     def __init__(self, **kwargs):
@@ -430,8 +430,8 @@ class AddingTagsEditor(ipw.VBox):
     """Editor for adding tags to atoms."""
 
     structure = traitlets.Instance(ase.Atoms, allow_none=True)
-    selection = traitlets.List(traitlets.Int, allow_none=True)
-    input_selection = traitlets.List(traitlets.Int, allow_none=True)
+    selection = traitlets.List(traitlets.Int(), allow_none=True)
+    input_selection = traitlets.List(traitlets.Int(), allow_none=True)
     structure_node = traitlets.Instance(orm_Data, allow_none=True, read_only=True)
 
     def __init__(self, title=""):

tests/conftest.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import io
 import pathlib
 import tempfile
@@ -301,15 +303,10 @@ def app(pw_code, dos_code, projwfc_code):
     app.submit_step.pw_code.refresh()
     app.submit_step.codes["dos"].refresh()
     app.submit_step.codes["projwfc"].refresh()
-    app.submit_step.pw_code.value = (
-        app.submit_step.pw_code.code_select_dropdown.options[pw_code.full_label]
-    )
-    app.submit_step.codes["dos"].value = app.submit_step.codes[
-        "dos"
-    ].code_select_dropdown.options[dos_code.full_label]
-    app.submit_step.codes["projwfc"].value = app.submit_step.codes[
-        "projwfc"
-    ].code_select_dropdown.options[projwfc_code.full_label]
+
+    app.submit_step.pw_code.value = pw_code.uuid
+    app.submit_step.codes["dos"].value = dos_code.uuid
+    app.submit_step.codes["projwfc"].value = projwfc_code.uuid
 
     yield app
 
@@ -558,12 +555,15 @@ def _generate_bands_workchain(structure):
 
 @pytest.fixture
 def generate_qeapp_workchain(
-    app, generate_workchain, generate_pdos_workchain, generate_bands_workchain
+    app,
+    generate_workchain,
+    generate_pdos_workchain,
+    generate_bands_workchain,
 ):
     """Generate an instance of the WorkChain."""
 
     def _generate_qeapp_workchain(
-        structure=None,
+        structure: orm.StructureData | None = None,
         relax_type="positions_cell",
         run_bands=True,
         run_pdos=True,
@@ -580,17 +580,13 @@ def _generate_qeapp_workchain(
         s1 = app.structure_step
         if structure is None:
             from_example = s1.manager.children[0].children[3]
+            # TODO: (unkpcz) using options to set value in test is cranky, instead, use fixture which will make the test more static and robust.
             from_example.children[0].value = from_example.children[0].options[1][1]
         else:
             structure.store()
             aiida_database = s1.manager.children[0].children[2]
             aiida_database.search()
-            key = [
-                key
-                for key in aiida_database.results.options
-                if key.startswith(f"PK: {structure.pk}")
-            ][0]
-            aiida_database.results.value = aiida_database.results.options[key]
+            aiida_database.results.value = structure
         s1.confirm()
         structure = s1.confirmed_structure
         # step 2 configure

tests/test_plugins_bands.py

@@ -4,7 +4,6 @@ def test_result(generate_qeapp_workchain):
     from aiidalab_qe.plugins.bands.result import Result, export_bands_data
 
     wkchain = generate_qeapp_workchain()
-    #
     data = export_bands_data(wkchain.node.outputs.bands)
     assert data is not None
     # generate structure for scf calculation

tests/test_result.py

@@ -76,5 +76,5 @@ def test_summary_view(generate_qeapp_workchain):
         "Initial Magnetic Moments": "",
     }
     for key, value in parameters.items():
-        td = parsed.find("td", text=key).find_next_sibling("td")
+        td = parsed.find("td", string=key).find_next_sibling("td")
         assert td.text == value