UI refactor

quantui/ir_plot.py

@@ -18,8 +18,8 @@
 import numpy as np
 import plotly.graph_objects as go
 
-# x-axis range follows the standard IR convention: high → low wavenumber
-_XRANGE = [4000, 400]
+# x-axis range is low → high wavenumber (user-facing convention in QuantUI)
+_XRANGE = [400, 4000]
 _XGRID = np.arange(400, 4001, 1.0)  # 1 cm⁻¹ resolution for broadened mode
 
 

quantui/pubchem.py

@@ -334,7 +334,7 @@ def check_pubchem_availability() -> bool:
         url = f"{PUBCHEM_BASE_URL}/compound/cid/962/property/MolecularFormula/JSON"
         response = requests.get(url, timeout=5)
         return bool(response.status_code == 200)
-    except:
+    except Exception:
         return False
 
 
@@ -383,7 +383,7 @@ def smiles_to_xyz(smiles: str, optimize_3d: bool = True) -> Tuple[str, Dict[str,
             # Optimize with UFF force field
             try:
                 AllChem.UFFOptimizeMolecule(mol)
-            except:
+            except Exception:
                 logger.warning("UFF optimization failed, using unoptimized coordinates")
 
         # Extract coordinates

tests/test_app.py

@@ -866,9 +866,10 @@ def test_ir_accordion_exists(self):
         assert hasattr(app, "_ir_accordion")
         assert isinstance(app._ir_accordion, widgets.Accordion)
 
-    def test_ir_accordion_hidden_initially(self):
+    def test_ir_accordion_visible_and_collapsed_initially(self):
         app = QuantUIApp()
-        assert app._ir_accordion.layout.display == "none"
+        assert app._ir_accordion.layout.display == ""
+        assert app._ir_accordion.selected_index is None
 
     def test_ir_mode_toggle_exists(self):
         app = QuantUIApp()
@@ -914,13 +915,13 @@ def test_show_ir_spectrum_returns_true_with_data(self):
         ok = app._show_ir_spectrum(self._make_freq_result())
         assert ok is True
 
-    def test_accordion_revealed_via_activate(self):
-        # _show_ir_spectrum populates widget; _activate_ana_panel reveals it.
+    def test_accordion_expanded_via_activate(self):
+        # _show_ir_spectrum populates widget; _activate_ana_panel expands it.
         app = QuantUIApp()
         app._show_ir_spectrum(self._make_freq_result())
-        assert app._ir_accordion.layout.display == "none"  # still hidden
+        assert app._ir_accordion.selected_index is None  # still collapsed
         app._activate_ana_panel("IR Spectrum")
-        assert app._ir_accordion.layout.display == ""
+        assert app._ir_accordion.selected_index == 0
 
     def test_fwhm_slider_shown_when_broadened(self):
         app = QuantUIApp()
@@ -948,9 +949,10 @@ def test_orb_accordion_exists(self):
         app = QuantUIApp()
         assert hasattr(app, "_orb_accordion")
 
-    def test_orb_accordion_hidden_initially(self):
+    def test_orb_accordion_visible_collapsed_initially(self):
         app = QuantUIApp()
-        assert app._orb_accordion.layout.display == "none"
+        assert app._orb_accordion.layout.display == ""
+        assert app._orb_accordion.selected_index is None
 
     def test_orb_diagram_html_exists(self):
         app = QuantUIApp()
@@ -968,11 +970,11 @@ def test_orb_iso_controls_hidden_initially(self):
         app = QuantUIApp()
         assert app._orb_iso_controls.layout.display == "none"
 
-    def test_orb_accordion_hidden_after_run_clicked(self):
+    def test_orb_accordion_collapsed_after_run_clicked(self):
         app = QuantUIApp()
-        app._orb_accordion.layout.display = ""
+        app._orb_accordion.selected_index = 0
         app._on_run_clicked(None)
-        assert app._orb_accordion.layout.display == "none"
+        assert app._orb_accordion.selected_index is None
 
 
 class TestShowOrbitalDiagram:
@@ -997,29 +999,35 @@ def test_show_orbital_diagram_returns_true_with_mo_data(self):
         ok = app._show_orbital_diagram(self._make_result_with_mo())
         assert ok is True
 
-    def test_accordion_revealed_via_activate(self):
-        # _show_orbital_diagram populates widget; _activate_ana_panel reveals it.
+    def test_accordion_expanded_via_activate(self):
+        # _show_orbital_diagram populates widget; _activate_ana_panel expands it.
         app = QuantUIApp()
         app._show_orbital_diagram(self._make_result_with_mo())
-        assert app._orb_accordion.layout.display == "none"  # still hidden
+        assert app._orb_accordion.selected_index is None  # still collapsed
         app._activate_ana_panel("Energies")
-        assert app._orb_accordion.layout.display == ""
+        assert app._orb_accordion.selected_index == 0
 
-    def test_accordion_stays_hidden_when_no_mo_data(self):
+    def test_accordion_stays_collapsed_when_no_mo_data(self):
         from unittest.mock import MagicMock
 
         app = QuantUIApp()
         r = MagicMock()
         r.mo_energy_hartree = None
         r.mo_occ = None
         app._show_orbital_diagram(r)
-        assert app._orb_accordion.layout.display == "none"
+        assert app._orb_accordion.selected_index is None
 
     def test_diagram_html_populated(self):
         app = QuantUIApp()
         app._show_orbital_diagram(self._make_result_with_mo())
-        # plotly renders an interactive <div>; matplotlib fallback renders <img>
-        val = app._orb_diagram_html.value
+        # Plotly renders an interactive <div>; matplotlib fallback renders <img>.
+        # The diagram is now rendered via Output display_data (not HTML.value).
+        payloads = [
+            out.get("data", {}).get("text/html", "")
+            for out in app._orb_diagram_html.outputs
+            if out.get("output_type") == "display_data"
+        ]
+        val = "\n".join(payloads)
         assert "<div" in val or "<img" in val
 
     def test_isosurface_controls_hidden_when_no_mo_coeff(self):
@@ -1109,11 +1117,7 @@ def test_ir_accordion_in_analysis_tab(self):
 
 
 class TestAnaSwitcher:
-    """Panel switcher strip: buttons, state, activation, and deactivation."""
-
-    def test_eight_buttons_exist(self):
-        app = QuantUIApp()
-        assert len(app._ana_btns) == 8
+    """Analysis panel state: activation, deactivation, and placeholder swapping."""
 
     def test_panel_names(self):
         app = QuantUIApp()
@@ -1128,53 +1132,42 @@ def test_panel_names(self):
             "NMR",
         ]
 
-    def test_buttons_initially_dimmed(self):
-        app = QuantUIApp()
-        for btn in app._ana_btns:
-            assert btn.layout.opacity == "0.35"
-
     def test_no_panels_available_initially(self):
         app = QuantUIApp()
         assert len(app._ana_available) == 0
 
-    def test_all_accordions_hidden_initially(self):
+    def test_all_accordions_visible_and_collapsed_initially(self):
         app = QuantUIApp()
         for acc in app._ana_accordions:
-            assert acc.layout.display == "none"
-
-    def test_switcher_box_in_analysis_tab(self):
-        app = QuantUIApp()
-        assert app._ana_switcher_box in app.analysis_tab_panel.children
+            assert acc.layout.display == ""
+            assert acc.selected_index is None
 
     def test_activate_panel_marks_available(self):
         app = QuantUIApp()
         app._activate_ana_panel("Energies")
         assert "Energies" in app._ana_available
 
-    def test_activate_panel_sets_opacity(self):
-        app = QuantUIApp()
-        app._activate_ana_panel("Energies")
-        orb_btn = app._ana_btns[0]
-        assert orb_btn.layout.opacity == "1.0"
-
     def test_activate_panel_auto_selects(self):
         app = QuantUIApp()
         app._activate_ana_panel("Energies")
-        assert app._orb_accordion.layout.display == ""
         assert app._orb_accordion.selected_index == 0
 
     def test_activate_panel_no_auto_select(self):
         app = QuantUIApp()
         app._activate_ana_panel("Energies", auto_select=False)
-        assert app._orb_accordion.layout.display == "none"
+        # Panel is available but not expanded; still visible in DOM.
+        assert "Energies" in app._ana_available
+        assert app._orb_accordion.selected_index is None
+        assert app._orb_accordion.layout.display == ""
 
-    def test_activate_hides_other_accordions(self):
+    def test_activate_collapses_other_accordions(self):
         app = QuantUIApp()
         app._activate_ana_panel("Energies")
-        # All other accordions should be hidden
+        # Other accordions remain visible but collapsed (not hidden).
         for name, acc in zip(app._ana_panel_names, app._ana_accordions):
             if name != "Energies":
-                assert acc.layout.display == "none"
+                assert acc.layout.display == ""
+                assert acc.selected_index is None
 
     def test_deactivate_all_clears_available(self):
         app = QuantUIApp()
@@ -1183,32 +1176,34 @@ def test_deactivate_all_clears_available(self):
         app._deactivate_all_ana_panels()
         assert len(app._ana_available) == 0
 
-    def test_deactivate_all_hides_accordions(self):
+    def test_deactivate_all_collapses_accordions(self):
         app = QuantUIApp()
         app._activate_ana_panel("Energies")
         app._deactivate_all_ana_panels()
+        # All panels remain visible in the DOM but are collapsed.
         for acc in app._ana_accordions:
-            assert acc.layout.display == "none"
+            assert acc.layout.display == ""
+            assert acc.selected_index is None
 
-    def test_deactivate_all_dims_buttons(self):
+    def test_unavail_message_shown_initially(self):
         app = QuantUIApp()
-        app._activate_ana_panel("Energies")
-        app._deactivate_all_ana_panels()
-        for btn in app._ana_btns:
-            assert btn.layout.opacity == "0.35"
+        # Every panel starts with the unavailable placeholder visible.
+        for name in app._ana_panel_names:
+            assert app._ana_unavail_msgs[name].layout.display == ""
+            assert app._ana_content_boxes[name].layout.display == "none"
 
-    def test_click_unavailable_shows_warning(self):
+    def test_activate_swaps_placeholder_for_content(self):
         app = QuantUIApp()
-        app._on_ana_panel_click("Energies")
-        assert app._ana_unavail_html.layout.display == ""
-        assert "Energies" in app._ana_unavail_html.value
+        app._activate_ana_panel("Energies", auto_select=False)
+        assert app._ana_unavail_msgs["Energies"].layout.display == "none"
+        assert app._ana_content_boxes["Energies"].layout.display == ""
 
-    def test_click_available_selects_panel(self):
+    def test_deactivate_restores_placeholder(self):
         app = QuantUIApp()
-        app._activate_ana_panel("IR Spectrum", auto_select=False)
-        app._on_ana_panel_click("IR Spectrum")
-        assert app._ir_accordion.layout.display == ""
-        assert app._ana_active == "IR Spectrum"
+        app._activate_ana_panel("Energies", auto_select=False)
+        app._deactivate_all_ana_panels()
+        assert app._ana_unavail_msgs["Energies"].layout.display == ""
+        assert app._ana_content_boxes["Energies"].layout.display == "none"
 
 
 # ---------------------------------------------------------------------------

tests/test_code_quality.py

@@ -0,0 +1,29 @@
+"""Static analysis guards for patterns that fail silently at runtime."""
+
+import re
+from pathlib import Path
+
+SRC = Path(__file__).parent.parent / "quantui"
+
+
+def _grep(pattern: str) -> list[str]:
+    hits = []
+    for path in SRC.rglob("*.py"):
+        for i, line in enumerate(path.read_text(encoding="utf-8").splitlines(), 1):
+            if re.search(pattern, line):
+                hits.append(f"{path.relative_to(SRC.parent)}:{i}: {line.strip()}")
+    return hits
+
+
+def test_no_cdn_plotlyjs():
+    hits = _grep(r'include_plotlyjs\s*=\s*["\']cdn["\']')
+    assert not hits, "CDN plotlyjs detected (fails silently offline):\n" + "\n".join(
+        hits
+    )
+
+
+def test_no_bare_except_pass():
+    hits = _grep(r"^\s*except\s*(\(\s*\))?\s*:\s*(pass\s*)?$")
+    assert not hits, "Bare except/pass detected (swallows all errors):\n" + "\n".join(
+        hits
+    )

tests/test_ir_plot.py

@@ -37,10 +37,10 @@ def test_trace_is_scatter(self):
         fig = plot_ir_spectrum(_SIMPLE_FREQS, _SIMPLE_INTS)
         assert isinstance(fig.data[0], go.Scatter)
 
-    def test_xaxis_inverted(self):
+    def test_xaxis_low_to_high(self):
         fig = plot_ir_spectrum(_SIMPLE_FREQS, _SIMPLE_INTS)
         x_range = list(fig.layout.xaxis.range)
-        assert x_range[0] > x_range[1], "x-axis must run high → low (4000 → 400)"
+        assert x_range[0] < x_range[1], "x-axis must run low → high (400 → 4000)"
 
     def test_xaxis_title_contains_wavenumber(self):
         fig = plot_ir_spectrum(_SIMPLE_FREQS, _SIMPLE_INTS)
@@ -106,10 +106,10 @@ def test_fwhm_affects_peak_width(self):
             y_wide.sum() > y_narrow.sum()
         ), "Wider FWHM should produce larger integrated area"
 
-    def test_xaxis_inverted_broadened(self):
+    def test_xaxis_low_to_high_broadened(self):
         fig = plot_ir_spectrum(_SIMPLE_FREQS, _SIMPLE_INTS, mode="broadened")
         x_range = list(fig.layout.xaxis.range)
-        assert x_range[0] > x_range[1]
+        assert x_range[0] < x_range[1]
 
 
 # ---------------------------------------------------------------------------

tests/test_pes_scan.py

@@ -191,17 +191,18 @@ def test_scan_steps_default(self):
         app = QuantUIApp()
         assert app._scan_steps.value == 10
 
-    def test_pes_scan_accordion_hidden_initially(self):
+    def test_pes_scan_accordion_visible_collapsed_initially(self):
         from quantui.app import QuantUIApp
 
         app = QuantUIApp()
-        assert app._pes_scan_accordion.layout.display == "none"
+        assert app._pes_scan_accordion.layout.display == ""
+        assert app._pes_scan_accordion.selected_index is None
 
     def test_pes_plot_html_empty_initially(self):
         from quantui.app import QuantUIApp
 
         app = QuantUIApp()
-        assert app._pes_plot_html.value == ""
+        assert len(app._pes_plot_html.outputs) == 0
 
     def test_on_calc_type_changed_to_pes_scan_populates_extras(self):
         from quantui.app import QuantUIApp
@@ -210,15 +211,18 @@ def test_on_calc_type_changed_to_pes_scan_populates_extras(self):
         app.calc_type_dd.value = "PES Scan"
         assert len(app.calc_extra_opts.children) > 0
 
-    def test_pes_scan_accordion_cleared_on_run_clicked(self):
+    def test_pes_scan_accordion_collapsed_on_run_clicked(self):
+        from IPython.display import HTML
+
         from quantui.app import QuantUIApp
 
         app = QuantUIApp()
-        app._pes_scan_accordion.layout.display = ""
-        app._pes_plot_html.value = "<div>old</div>"
+        app._pes_scan_accordion.selected_index = 0
+        app._pes_plot_html.append_display_data(HTML("<div>old</div>"))
+        assert len(app._pes_plot_html.outputs) == 1
         app._on_run_clicked(None)
-        assert app._pes_scan_accordion.layout.display == "none"
-        assert app._pes_plot_html.value == ""
+        assert app._pes_scan_accordion.selected_index is None
+        assert len(app._pes_plot_html.outputs) == 0
 
 
 # ── Format method ─────────────────────────────────────────────────────────────