Bug fixes and testing

crystal_toolkit/_version.py

@@ -1 +1 @@
-__version__ = "2023.11.03"
+__version__ = "2023.11.4.dev18"

crystal_toolkit/apps/examples/tests/test_bandstructure.py

@@ -32,4 +32,4 @@ def test_bs(dash_duo: DashDuo) -> None:
     # dash_duo.percy_snapshot("example_bsdos_projection_index_2")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/examples/tests/test_basic.py

@@ -22,7 +22,7 @@ def test_hello_scientist(dash_duo: DashDuo):
     dash_duo.percy_snapshot("hello_scientist")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"
 
 
 def test_hello_structure(dash_duo: DashDuo) -> None:
@@ -33,7 +33,7 @@ def test_hello_structure(dash_duo: DashDuo) -> None:
     dash_duo.percy_snapshot("hello_structure")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"
 
 
 def test_hello_structure_interactive(dash_duo: DashDuo) -> None:
@@ -47,4 +47,4 @@ def test_hello_structure_interactive(dash_duo: DashDuo) -> None:
     dash_duo.percy_snapshot("hello_structure_interactive_on_click")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/examples/tests/test_diffraction.py

@@ -31,4 +31,4 @@ def test_diffraction(dash_duo: DashDuo) -> None:
     input_nodes[0].send_keys(Keys.ARROW_UP)
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/examples/tests/test_fermi_surface.py

@@ -2,13 +2,13 @@
 
 from typing import TYPE_CHECKING
 
-from crystal_toolkit.apps.examples.fermi_surface import app
-
 if TYPE_CHECKING:
     from crystal_toolkit.apps.examples.tests.typing import DashDuo
 
 
 def test_diffraction(dash_duo: DashDuo) -> None:
+    from crystal_toolkit.apps.examples.fermi_surface import app
+
     dash_duo.start_server(app)
     dash_duo.clear_storage()
 
@@ -17,4 +17,4 @@ def test_diffraction(dash_duo: DashDuo) -> None:
     assert "dash-graph" in node.get_attribute("class")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/examples/tests/test_structure.py

@@ -36,4 +36,4 @@ def test_structure(dash_duo: DashDuo) -> None:
     sleep(1)
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/tests/test_main.py

@@ -3,13 +3,13 @@
 import time
 from typing import TYPE_CHECKING
 
-from crystal_toolkit.apps.main import app
-
 if TYPE_CHECKING:
     from crystal_toolkit.apps.examples.tests.typing import DashDuo
 
 
 def test_main_app_startup(dash_duo: DashDuo):
+    from crystal_toolkit.apps.main import app
+
     dash_duo.start_server(app)
     # dash_duo.clear_storage()
 
@@ -20,4 +20,4 @@ def test_main_app_startup(dash_duo: DashDuo):
     dash_duo.take_snapshot("main_app_startup-layout")
 
     logs = dash_duo.get_logs()
-    assert logs == [], f"Unexpected browser {logs=}"
+    assert logs is None, f"Unexpected browser {logs=}"

crystal_toolkit/apps/tests/test_pourbaix.py

@@ -2,13 +2,13 @@
 
 from playwright.sync_api import Page
 
-from crystal_toolkit.apps.examples.pourbaix import app
 
-thread = threading.Thread(target=app.run)
-thread.start()
+def test_pourbaix(page: Page):
+    from crystal_toolkit.apps.examples.pourbaix import app
 
+    thread = threading.Thread(target=app.run)
+    thread.start()
 
-def test_pourbaix(page: Page):
     # select 1st structure
     page.locator(".react-select__input-container").click()
     page.get_by_text("Fe₃H (mp-1184287-GGA)", exact=True).click()

crystal_toolkit/apps/tests/test_structure.py

@@ -3,13 +3,13 @@
 
 from playwright.sync_api import Page, expect
 
-from crystal_toolkit.apps.examples.structure import app
 
-thread = threading.Thread(target=app.run)
-thread.start()
+def test_structure(page: Page):
+    from crystal_toolkit.apps.examples.structure import app
 
+    thread = threading.Thread(target=app.run)
+    thread.start()
 
-def test_structure(page: Page):
     expect(page).to_have_title("Crystal Toolkit")
     h1_text = page.text_content("h1")
     assert h1_text == "StructureMoleculeComponent Example"

crystal_toolkit/core/jupyter.py

@@ -6,6 +6,7 @@
 from warnings import warn
 
 from dash import Dash
+from monty.json import jsanitize
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.core.structure import SiteCollection
 
@@ -117,20 +118,20 @@ def _ipython_display_(self):
     # and also check all .parameters .kind.name have no POSITIONAL_ONLY
     # in practice, fairly unlikely this will cause issues without strict checking.
     # TODO: This can be removed once a central registry of renderable objects is implemented.
-    if self.get_scene:
+    if hasattr(self, "get_scene"):
         display_data = {
             "application/vnd.mp.ctk+json": self.get_scene().to_json(),
             "text/plain": repr(self),
         }
-    elif self.get_plot:
+    elif hasattr(self, "get_plot"):
         display_data = {
             "application/vnd.plotly.v1+json": self.get_plot().to_plotly_json(),
-            "application/json": self.as_dict(),
+            "application/json": jsanitize(self.as_dict()),
             "text/plain": repr(self),
         }
     else:
         display_data = {
-            "application/json": self.as_dict(),
+            "application/json": jsanitize(self.as_dict()),
             "text/plain": repr(self),
         }
 

crystal_toolkit/core/legend.py

@@ -257,7 +257,11 @@ def get_color(self, sp: Species | Element, site: Site | None = None) -> str:
         Returns: Color
         """
         # allow manual override by user
-        if site and "display_color" in site.properties:
+        if (
+            site
+            and "display_color" in site.properties
+            and site.properties["display_color"] is not None
+        ):
             color = site.properties["display_color"]
             # TODO: next two lines due to change in API, will be removed
             if isinstance(color, list) and isinstance(color[0], str):

crystal_toolkit/core/scene.py

@@ -72,7 +72,6 @@ def _repr_mimebundle_(self, include=None, exclude=None):
         """Render Scenes using crystaltoolkit-extension for Jupyter Lab."""
         return {
             "application/vnd.mp.ctk+json": self.to_json(),
-            "application/json": self.as_dict(),
             "text/plain": repr(self),
         }
 

tests/asy_test/core/test_jupyter.py

@@ -0,0 +1,35 @@
+import plotly.express as px
+from monty.json import MSONable
+
+from crystal_toolkit.core.jupyter import patch_msonable
+from crystal_toolkit.core.scene import Scene
+
+
+def test_patch_msonable():
+    patch_msonable()
+
+    class GetSceneClass(MSONable):
+        def get_scene(self):
+            return Scene(name="test_scene")
+
+    class GetPlotClass(MSONable):
+        def get_plot(self):
+            """Dummy plotly object"""
+            return px.scatter(x=[1, 2, 3], y=[1, 2, 3])
+
+    class AsDictClass(MSONable):
+        def __init__(self, a: int) -> None:
+            self.a = a
+
+    # The output of _ipython_display_ is None
+    # However, the logic for the creating the different output
+    # dictionaries should be executed so the following tests
+    # are still valuable.
+    as_dict_class = AsDictClass(1)
+    assert as_dict_class._ipython_display_() is None
+
+    get_scene_class = GetSceneClass()
+    assert get_scene_class._ipython_display_() is None
+
+    get_plot_class = GetPlotClass()
+    assert get_plot_class._ipython_display_() is None

crystal_toolkit/core/tests/test_legend.py → tests/asy_test/core/test_legend.py

@@ -86,15 +86,15 @@ def test_get_color(self):
         assert color == "#b30326"
 
         color = legend.get_color(self.sp1, site=self.site1)
-        assert color == "#dddcdb"
+        assert color == "#000000"
 
         color = legend.get_color(self.sp2, site=self.site2)
         assert color == "#7b9ef8"
 
         assert legend.get_legend()["colors"] == {
             "#7b9ef8": "-3.00",
             "#b30326": "5.00",
-            "#dddcdb": "0.00",
+            "#000000": "0.00",
         }
 
         # test accessible
@@ -144,7 +144,7 @@ def test_get_color(self):
         legend = Legend(self.struct_manual)
 
         assert legend.get_legend()["colors"] == {
-            "#0000ff": "O2-",
+            "#0000ff": "O²⁻",
             "#00ff00": "In",
             "#ff0000": "H",
         }