Remove warnings in unit tests (#509)

* Ignore remaining warnings, turn warnings into errors
* Ignore DeprecationWarning from jupyter_core

Co-authored-by: Jusong Yu <jusong.yeu@gmail.com>

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
                       **/pyproject.toml
                       **/requirements*.txt
 
-            - uses: pre-commit/action@v2.0.0
+            - uses: pre-commit/action@v3.0.0
 
     test-notebooks:
 

.github/workflows/publish.yml

@@ -19,7 +19,7 @@ jobs:
 
         steps:
 
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
 
             - name: Set up Python 3.10
               uses: actions/setup-python@v2

aiidalab_widgets_base/data/__init__.py

@@ -34,7 +34,10 @@ def __init__(self, value=0, description="Select functional group", **kwargs):
         self.style = {"description_width": "initial"}
         self.layout = {"width": "initial"}
         super().__init__(
-            value=value, description=description, options=FUNCTIONAL_GROUPS, **kwargs
+            value=value,
+            description=description,
+            options=tuple((key, value) for key, value in FUNCTIONAL_GROUPS.items()),
+            **kwargs,
         )
 
     def rotate(self, align_to=(0, 0, 1), remove_anchor=False):

aiidalab_widgets_base/nodes.py

@@ -320,7 +320,7 @@ class OpenAiidaNodeInAppWidget(ipw.VBox):
 
     def __init__(self, path_to_root="../", **kwargs):
         self.path_to_root = path_to_root
-        self.tab = ipw.Tab(style={"description_width": "initial"})
+        self.tab = ipw.Tab()
         self.tab_selection = ipw.RadioButtons(
             options=[],
             description="",

aiidalab_widgets_base/process.py

@@ -414,7 +414,6 @@ def __init__(self, title="Progress Bar", **kwargs):
             value=0,
             min=0,
             max=2,
-            step=1,
             description="Progress:",
             bar_style="warning",  # 'success', 'info', 'warning', 'danger' or ''
             orientation="horizontal",
@@ -537,7 +536,7 @@ def __init__(self, title="Running Job Output", **kwargs):
         self.title = title
         self.selection = ipw.Dropdown(
             description="Select calculation:",
-            options={p.id: p for p in get_running_calcs(self.process)},
+            options=tuple((p.id, p) for p in get_running_calcs(self.process)),
             style={"description_width": "initial"},
         )
         self.output = CalcJobOutputWidget()
@@ -550,9 +549,9 @@ def update(self):
             return
         with self.hold_trait_notifications():
             old_label = self.selection.label
-            self.selection.options = {
-                str(p.id): p for p in get_running_calcs(self.process)
-            }
+            self.selection.options = tuple(
+                (str(p.id), p) for p in get_running_calcs(self.process)
+            )
             # If the selection remains the same.
             if old_label in self.selection.options:
                 self.label = old_label  # After changing options trait, the label and value traits might change as well.

aiidalab_widgets_base/structures.py

@@ -5,7 +5,6 @@
 import io
 import pathlib
 import tempfile
-from collections import OrderedDict
 
 import ase
 import ipywidgets as ipw
@@ -98,7 +97,10 @@ def __init__(
 
         # Store format selector.
         data_format = ipw.RadioButtons(
-            options=self.SUPPORTED_DATA_FORMATS, description="Data type:"
+            options=tuple(
+                (key, value) for key, value in self.SUPPORTED_DATA_FORMATS.items()
+            ),
+            description="Data type:",
         )
         tl.link((data_format, "label"), (self, "node_class"))
 
@@ -658,17 +660,15 @@ def search(self, _=None):
         matches = {n[0] for n in qbuild.iterall()}
         matches = sorted(matches, reverse=True, key=lambda n: n.ctime)
 
-        options = OrderedDict()
-        options[f"Select a Structure ({len(matches)} found)"] = False
-
+        options = [(f"Select a Structure ({len(matches)} found)", False)]
         for mch in matches:
             label = f"PK: {mch.pk}"
             label += " | " + mch.ctime.strftime("%Y-%m-%d %H:%M")
             label += " | " + mch.base.extras.get("formula", "")
             label += " | " + mch.node_type.split(".")[-2]
             label += " | " + mch.label
             label += " | " + mch.description
-            options[label] = mch
+            options.append((label, mch))
 
         self.results.options = options
 

aiidalab_widgets_base/viewers.py

@@ -34,32 +34,22 @@ def registration_decorator(widget):
     return registration_decorator
 
 
-def viewer(obj, downloadable=True, **kwargs):
+def viewer(obj, **kwargs):
     """Display AiiDA data types in Jupyter notebooks.
 
-    :param downloadable: If True, add link/button to download the content of displayed AiiDA object.
-    :type downloadable: bool
-
     Returns the object itself if the viewer wasn't found."""
     if not isinstance(obj, orm.Node):  # only working with AiiDA nodes
         warnings.warn(
             f"This viewer works only with AiiDA objects, got {type(obj)}", stacklevel=2
         )
         return obj
 
-    try:
+    if obj.node_type in AIIDA_VIEWER_MAPPING:
         _viewer = AIIDA_VIEWER_MAPPING[obj.node_type]
-    except KeyError as exc:
-        if obj.node_type in str(exc):
-            warnings.warn(
-                f"Did not find an appropriate viewer for the {type(obj)} object. Returning the object "
-                "itself.",
-                stacklevel=2,
-            )
-            return obj
-        raise
+        return _viewer(obj, **kwargs)
     else:
-        return _viewer(obj, downloadable=downloadable, **kwargs)
+        # No viewer registered for this type, return object itself
+        return obj
 
 
 class AiidaNodeViewWidget(ipw.VBox):
@@ -294,12 +284,11 @@ def change_supercell(_=None):
 
         # 3. Camera switcher
         camera_type = ipw.ToggleButtons(
-            options={"Orthographic": "orthographic", "Perspective": "perspective"},
+            options=[("Orthographic", "orthographic"), ("Perspective", "perspective")],
             description="Camera type:",
             value=self._viewer.camera,
             layout={"align_self": "flex-start"},
             style={"button_width": "115.5px"},
-            orientation="vertical",
         )
 
         def change_camera(change):
@@ -482,7 +471,7 @@ def _download_tab(self):
         )
 
         # 4. Render a high quality image
-        self.render_btn = ipw.Button(description="Render", icon="fa-paint-brush")
+        self.render_btn = ipw.Button(description="Render", icon="paint-brush")
         self.render_btn.on_click(self._render_structure)
         self.render_box = ipw.VBox(
             children=[ipw.Label("Render an image with POVRAY:"), self.render_btn]

pyproject.toml

@@ -4,3 +4,27 @@ requires = [
     "wheel"
 ]
 build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    'error',
+    'ignore::DeprecationWarning:bokeh.core.property.primitive',
+    'ignore:Creating AiiDA configuration:UserWarning:aiida',
+    'ignore:crystal system:UserWarning:ase.io.cif',
+    'ignore::DeprecationWarning:ase.atoms',
+    # 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:metadata.*trait.*<traitlets.traitlets.Unicode object:DeprecationWarning:traitlets',
+    # 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',
+    'ignore::DeprecationWarning:jupyter_client',
+    'ignore::DeprecationWarning:selenium',
+    'ignore::DeprecationWarning:pytest_selenium',
+]

tests/test_databases.py

@@ -1,19 +1,23 @@
 import ase
 
+import aiidalab_widgets_base as awb
+
 
 def test_cod_query_widget():
     """Test the COD query widget."""
-    from aiidalab_widgets_base import CodQueryWidget
 
-    widget = CodQueryWidget()
+    widget = awb.CodQueryWidget()
 
     # Enter the query string.
     widget.inp_elements.value = "Ni Ti"
 
     # Run the query.
     widget._on_click_query()
 
-    # Select on of the results.
+    # Select one of the results.
+    # TODO: Select a different structure to get rid of the ASE warning:
+    # "ase/io/cif.py:401: UserWarning: crystal system 'cubic' is not interpreted
+    # for space group 'Pm-3m'. This may result in wrong setting!"
     widget.drop_structure.label = "NiTi (id: 1100132)"
 
     # Check that the structure was loaded.
@@ -23,9 +27,8 @@ def test_cod_query_widget():
 
 def test_optimade_query_widget():
     """Test the OPTIMADE query widget."""
-    from aiidalab_widgets_base import OptimadeQueryWidget
 
-    widget = OptimadeQueryWidget()
+    widget = awb.OptimadeQueryWidget()
 
     # At the present state I cannot check much. Most of the variables are locals of the  __init__ method.
 
@@ -34,14 +37,15 @@ def test_optimade_query_widget():
 
 def test_computational_resources_database_widget():
     """Test the structure browser widget."""
-    from aiidalab_widgets_base.databases import ComputationalResourcesDatabaseWidget
 
     # Initiate the widget with no arguments.
-    widget = ComputationalResourcesDatabaseWidget()
+    widget = awb.databases.ComputationalResourcesDatabaseWidget()
     assert "merlin.psi.ch" in widget.database
 
     # Initialize the widget with default_calc_job_plugin="cp2k"
-    widget = ComputationalResourcesDatabaseWidget(default_calc_job_plugin="cp2k")
+    widget = awb.databases.ComputationalResourcesDatabaseWidget(
+        default_calc_job_plugin="cp2k"
+    )
     assert (
         "merlin.psi.ch" not in widget.database
     )  # Merlin does not have CP2K installed.

tests/test_process.py

@@ -32,7 +32,6 @@ def return_inputs():
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_inputs_widget(generate_calc_job_node):
     """Test ProcessInputWidget with a simple `CalcJobNode`"""
-    from aiidalab_widgets_base.process import ProcessInputsWidget
 
     process = generate_calc_job_node(
         inputs={
@@ -44,9 +43,9 @@ def test_process_inputs_widget(generate_calc_job_node):
     )
 
     # Test the widget can be instantiated with empty inputs
-    process_input_widget = ProcessInputsWidget()
+    process_input_widget = awb.ProcessInputsWidget()
 
-    process_input_widget = ProcessInputsWidget(process=process)
+    process_input_widget = awb.ProcessInputsWidget(process=process)
     input_dropdown = process_input_widget._inputs
 
     assert "parameters" in [key for key, _ in input_dropdown.options]
@@ -64,13 +63,11 @@ def test_process_inputs_widget(generate_calc_job_node):
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_outputs_widget(multiply_add_completed_workchain):
     """Test ProcessOutputWidget with a simple `WorkChainNode`"""
-    from aiidalab_widgets_base.process import ProcessOutputsWidget
-
     # Test the widget can be instantiated with empty inputs
-    widget = ProcessOutputsWidget()
+    widget = awb.ProcessOutputsWidget()
 
     # Test the widget can be instantiated with a process
-    widget = ProcessOutputsWidget(process=multiply_add_completed_workchain)
+    widget = awb.ProcessOutputsWidget(process=multiply_add_completed_workchain)
 
     # Simulate output selection.
     widget.show_selected_output(change={"new": "result"})
@@ -79,17 +76,15 @@ def test_process_outputs_widget(multiply_add_completed_workchain):
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_follower_widget(multiply_add_process_builder_ready, daemon_client):
     """Test ProcessFollowerWidget with a simple `WorkChainNode`"""
-    from aiidalab_widgets_base.process import ProcessFollowerWidget
-
     # Test the widget can be instantiated with empty inputs
-    widget = ProcessFollowerWidget()
+    widget = awb.ProcessFollowerWidget()
 
     if daemon_client.is_daemon_running:
         daemon_client.stop_daemon(wait=True)
     process = engine.submit(multiply_add_process_builder_ready)
 
     # Test the widget can be instantiated with a process
-    widget = ProcessFollowerWidget(process=process)
+    widget = awb.ProcessFollowerWidget(process=process)
 
     daemon_client.start_daemon()
 
@@ -104,18 +99,16 @@ def test_process_report_widget(
     multiply_add_process_builder_ready, daemon_client, await_for_process_completeness
 ):
     """Test ProcessReportWidget with a simple `WorkChainNode`"""
-    from aiidalab_widgets_base.process import ProcessReportWidget
-
     # Test the widget can be instantiated with empty inputs
-    ProcessReportWidget()
+    awb.ProcessReportWidget()
 
     # Stopping the daemon and submitting the process.
     if daemon_client.is_daemon_running:
         daemon_client.stop_daemon(wait=True)
     process = engine.submit(multiply_add_process_builder_ready)
 
     # Test the widget can be instantiated with a process
-    widget = ProcessReportWidget(process=process)
+    widget = awb.ProcessReportWidget(process=process)
     assert (
         widget.value == "No log messages recorded for this entry"
     )  # No report produced yet.
@@ -218,26 +211,22 @@ def test_running_calcjob_output_widget(generate_calc_job_node):
         }
     )
 
-    # Test the widget can be instantiated with a process
-    RunningCalcJobOutputWidget(calculation=process)
+    widget = RunningCalcJobOutputWidget()
+    widget.process = process
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_list_widget(multiply_add_completed_workchain):
     """Test ProcessListWidget with a simple `WorkChainNode`"""
-    from aiidalab_widgets_base.process import ProcessListWidget
-
-    ProcessListWidget()
+    awb.ProcessListWidget()
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_monitor(
     multiply_add_process_builder_ready, daemon_client, await_for_process_completeness
 ):
     """Test ProcessMonitor with a simple `WorkChainNode`"""
-    from aiidalab_widgets_base.process import ProcessMonitor
-
-    ProcessMonitor()
+    awb.ProcessMonitor()
 
     # Stopping the daemon and submitting the process.
     if daemon_client.is_daemon_running:
@@ -250,7 +239,7 @@ def f():
         nonlocal test_variable
         test_variable = True
 
-    widget = ProcessMonitor(value=process.uuid, callbacks=[f])
+    widget = awb.ProcessMonitor(value=process.uuid, callbacks=[f])
 
     # Starting the daemon and waiting for the process to complete.
     daemon_client.start_daemon()
@@ -265,7 +254,4 @@ def f():
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_process_nodes_tree_widget(multiply_add_completed_workchain):
     """Test ProcessNodesTreeWidget with a simple `WorkChainNode`"""
-
-    from aiidalab_widgets_base.process import ProcessNodesTreeWidget
-
-    ProcessNodesTreeWidget(value=multiply_add_completed_workchain.uuid)
+    awb.ProcessNodesTreeWidget(value=multiply_add_completed_workchain.uuid)

tests/test_viewers.py

@@ -10,8 +10,6 @@ def test_pbc_structure_data_viewer(structure_data_object):
 
     import ase
 
-    from aiidalab_widgets_base import viewers
-
     # Prepare a structure with periodicity xy
     ase_input = ase.Atoms(
         symbols="Li2",
@@ -59,7 +57,7 @@ def test_several_data_viewers(
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")
-def test_structure_data_viwer(structure_data_object):
+def test_structure_data_viewer(structure_data_object):
     v = viewers.viewer(structure_data_object)
     assert isinstance(v, viewers.StructureDataViewer)