Updates continued

quantui/analytics.py

@@ -19,7 +19,7 @@
    compute device (CPU grey, GPU green), so a user can spot regressions
    or speedups visually as they run more calcs.
 
-Older perf-log records that pre-date the M-GPU follow-up don't have
+Older perf-log records that pre-date GPU support don't have
 ``gpu_used`` set — those are treated as "device unknown" and counted in
 their own bucket rather than guessed CPU.
 
@@ -46,7 +46,7 @@
 def _classify_device(record: dict) -> str:
     """Return ``"GPU"``, ``"CPU"``, or ``"Unknown"`` for one perf record.
 
-    Records written before the M-GPU follow-up (2026-05-25) don't have
+    Records written before GPU support (2026-05-25) don't have
     ``gpu_used`` at all — we don't backfill those as CPU because they
     pre-date GPU support entirely, so calling them "CPU" would muddy any
     speedup comparison. ``"Unknown"`` is the honest bucket.
@@ -353,7 +353,7 @@ def _timeline_html(records: list[dict], *, include_plotlyjs: bool) -> Optional[s
 
 
 # ---------------------------------------------------------------------------
-# Prediction-accuracy section (M-EST / EST.6, 2026-05-25)
+# Prediction-accuracy section (2026-05-25)
 # ---------------------------------------------------------------------------
 
 
@@ -555,7 +555,7 @@ def build_dashboard(out_path: Optional[Path] = None) -> Optional[Path]:
     method_counts = _counts_by(records, "method")
     calc_type_counts = _counts_by(records, "calc_type")
 
-    # M-EST / EST.6: prediction-accuracy data lives in its own log file.
+    # Prediction-accuracy data lives in its own log file.
     # Best-effort read — older installs without the file produce an
     # empty list and the section degrades to an empty-state message.
     try:

quantui/app_analysis.py

@@ -328,7 +328,7 @@ def pop_preopt_trajectory(app: Any, ctx: Any) -> bool:
     """Populate Trajectory panel for the frequency-time DFT geometry
     optimization trajectory.
 
-    POLISH.9 (2026-05-25): the wrapped operation is a full DFT geom-opt
+    The wrapped operation is a full DFT geom-opt
     at the user's method/basis, not the classical LJ pre-opt that lives
     in ``quantui/preopt.py``. The function name + ``preopt_trajectory.json``
     filename stay (renaming the saved file would break history replay of

quantui/app_builders.py

@@ -96,7 +96,7 @@ def _ok(flag: bool, extra: str = "") -> str:
         "Timing calibration: not yet run &mdash; use the Calibrate panel in History</div>"
     )
 
-    # GPU offload indicator (M-GPU / GPU.2). Detecting GPUs imports gpu4pyscf +
+    # GPU offload indicator. Detecting GPUs imports gpu4pyscf +
     # cupy and queries CUDA, which costs ~7 s — far too slow to block startup.
     # So the status HTML is rendered via this closure with the GPU row as a
     # "checking…" placeholder; the app re-renders it (via app._render_status_html)
@@ -259,7 +259,7 @@ def build_history_section(
         tooltip="Open the full PySCF output log in the Output tab",
     )
 
-    # M-EST / EST.4: 4-tier calibration selector. ToggleButtons works for
+    # 4-tier calibration selector. ToggleButtons works for
     # 4 options; switch to a Dropdown if a 5th tier is ever added. Tier 3
     # / tier 4 require PySCF (the geom-opt + freq dispatch); tier 1 / 2
     # are SP-only and gated separately by the run button.
@@ -295,10 +295,9 @@ def build_history_section(
         tooltip="Abandon the rest of the calibration (current step is also killed).",
         layout=layout_fn(width="90px", display="none"),
     )
-    # session 55 user request: replaced the hard 1800 s per-step timeout
-    # with a Skip button so the user can abandon ONE step that's running
-    # too long without losing the whole run. Distinct from Stop (which
-    # abandons everything remaining).
+    # Replaced the hard 1800 s per-step timeout with a Skip button so the
+    # user can abandon ONE step that's running too long without losing the
+    # whole run. Distinct from Stop (which abandons everything remaining).
     app._cal_skip_btn = widgets.Button(
         description="Skip step",
         button_style="info",
@@ -391,7 +390,7 @@ def build_history_section(
         if cal_last
         else ""
     )
-    # M-EST / EST.4: import tier sizes lazily so we can refer to all four
+    # Import tier sizes lazily so we can refer to all four
     # in the panel blurb. ``benchmark_suite`` / ``benchmark_suite_long``
     # are kept as positional args for back-compat but new code prefers
     # the four named tiers.
@@ -431,10 +430,9 @@ def build_history_section(
     app._cal_accordion = widgets.Accordion(children=[cal_panel], selected_index=None)
     app._cal_accordion.set_title(0, "Calibrate time estimates")
 
-    # POLISH.3 (M-POLISH, 2026-05-25): the History tab is now purely
-    # the result-browser. Performance stats + Calibrate accordions
-    # moved to the System Settings tab — see below — so the user finds
-    # benchmarking + system state in one logical place.
+    # The History tab is now purely the result-browser. Performance stats
+    # + Calibrate accordions moved to the System Settings tab — see below —
+    # so the user finds benchmarking + system state in one logical place.
     app.history_panel = widgets.VBox(
         [
             widgets.HTML(
@@ -455,7 +453,7 @@ def build_history_section(
         ]
     )
 
-    # POLISH.3: now that the calibration + performance accordions exist
+    # Now that the calibration + performance accordions exist
     # (created above in this function), append them to the System
     # Settings tab. ``_status_tab_panel`` was built earlier in
     # ``build_status_panel`` without these — extend its children tuple.
@@ -503,7 +501,7 @@ def build_shared_widgets(
     app.mol_summary_compact = widgets.HTML(value="")
     # Fixed heights reserve space so swapping content (backend/palette toggle)
     # or streaming output never resizes the container — which would reflow the
-    # page and jump the scrollbar (BUG-SCROLL). The molecule viewer renders at
+    # page and jump the scrollbar. The molecule viewer renders at
     # render_molecule_html's default 500px; the run log scrolls internally.
     # overflow hidden (not auto): the 3D viewer is a fixed-size canvas, so it
     # needs no scrollbar — clipping a few px of margin avoids an internal
@@ -570,7 +568,7 @@ def build_shared_widgets(
         [app.viz_style_dd, app.viz_lighting_dd],
         layout=layout_fn(gap="8px", margin="2px 0 0 0", align_items="center"),
     )
-    # UXP.7: method / basis descriptor cards replace the old inline
+    # Method / basis descriptor cards replace the old inline
     # ``notes_output`` educational-notes block. Two compact HTML cards
     # (icon + one-line) sit to the right of the dropdowns; populated here with
     # the defaults and refreshed by ``update_notes`` on every dropdown change.
@@ -644,7 +642,7 @@ def build_shared_widgets(
         '<span style="font-size:11px;color:#94a3b8"> &mdash; fast MMFF/UFF '
         "cleanup of a rough structure</span>"
     )
-    # Interactive pre-opt (M-PREOPT PREOPT.2/.3): run the bonded-FF pre-opt on
+    # Interactive pre-opt: run the bonded-FF pre-opt on
     # demand, watch it relax in-place, then keep or revert.
     app.preopt_preview_btn = widgets.Button(
         description="Preview",
@@ -696,7 +694,7 @@ def build_shared_widgets(
 
     from quantui.config import SOLVENT_OPTIONS as _SOLVENT_OPTS
 
-    # POLISH.10: drop the default Checkbox description gutter + explicit width
+    # Drop the default Checkbox description gutter + explicit width
     # (style description_width "initial" + indent=False) that produced the
     # indent + horizontal scrollbar.
     app.solvent_cb = widgets.Checkbox(
@@ -921,7 +919,7 @@ def build_shared_widgets(
         layout=layout_fn(width="200px", height="36px"),
     )
     app.run_status = widgets.Label()
-    # M-PROGRESS A1: live elapsed-time chip next to the status text — a bg-thread
+    # Live elapsed-time chip next to the status text — a bg-thread
     # ticker updates it every ~1 s while a calc runs, so even a fully silent
     # native phase (first gradient / Hessian) visibly advances.
     app._run_elapsed_lbl = widgets.HTML(value="")
@@ -990,7 +988,7 @@ def build_shared_widgets(
         layout=layout_fn(width="130px"),
     )
     app.struct_export_status = widgets.Label()
-    # M-EXPORT / EXPORT.5: zip the entire result folder for emailing /
+    # Zip the entire result folder for emailing /
     # attaching to a writeup. Disabled until ``_last_result_dir`` is set.
     app._export_bundle_btn = widgets.Button(
         description="Export bundle (.zip)",
@@ -1031,7 +1029,7 @@ def build_theme_selector(app: Any, *, layout_fn: Any) -> None:
 def build_welcome_header(app: Any, *, layout_fn: Any = None) -> None:
     """Build the QuantUI welcome banner.
 
-    POLISH.1 third iteration (M-POLISH, 2026-05-25): the
+    Third iteration (2026-05-25): the
     ``<img src="data:image/svg+xml;base64,...">`` approach failed too
     — Voilà's HTML sanitizer (stricter than JupyterLab's) strips
     ``data:`` URIs from ``<img src>`` attributes. The third iteration
@@ -1317,7 +1315,7 @@ def build_calc_setup(app: Any, *, layout_fn: Any) -> None:
                     widgets.HTML("&ensp;&ensp;"),
                     widgets.VBox([app.charge_si, app.mult_si]),
                     widgets.HTML("&ensp;"),
-                    # UXP.7 descriptor cards — to the right of the inputs so
+                    # Descriptor cards — to the right of the inputs so
                     # they don't displace charge/multiplicity.
                     app._descriptor_cards_box,
                 ],
@@ -1404,7 +1402,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
             layout=layout_fn(width="130px"),
             tooltip="Export the current plot as HTML or PNG",
         )
-        # M-EXPORT / EXPORT.4: per-panel "Copy data" button that exports
+        # Per-panel "Copy data" button that exports
         # the underlying numerical data to CSV (saved to result_dir) and
         # also attempts to copy to the system clipboard via the browser
         # API. Status widget below is shared with the Save Plot path —
@@ -1447,7 +1445,6 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
     # Using `widgets.Output` here previously caused widget references inside
     # `with output: display(widget)` to be deferred/asynchronous, leaving the
     # accordion visibly empty even after _show_opt_trajectory logged success.
-    # See BUG-FRESH-TRAJ root-cause analysis in session 48.
     app.traj_output = widgets.VBox(layout=layout_fn(margin="0"))
     app.traj_accordion = widgets.Accordion(
         children=[app.traj_output],
@@ -1551,7 +1548,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
         style={"description_width": "120px"},
         layout=layout_fn(width="300px", display="none"),
         # continuous_update=False so dragging the slider only fires on
-        # release, not 30-60 times per second during the drag (BUG.9 fix).
+        # release, not 30-60 times per second during the drag.
         # Combined with the atomic outputs swap in _set_html_output this
         # eliminates the IR re-render storm that caused visible flicker.
         continuous_update=False,
@@ -1640,7 +1637,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
         orb_diagram_content,
         layout=layout_fn(width="100%"),
     )
-    # UXP.4: widen the preset buttons and add a "By index" mode that reveals a
+    # Widen the preset buttons and add a "By index" mode that reveals a
     # free-entry 0-based MO index input, so any orbital (not just the HOMO/LUMO
     # neighbourhood) can be rendered as an isosurface.
     app._orb_toggle = widgets.ToggleButtons(
@@ -1694,7 +1691,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
         ),
         layout=layout_fn(width="200px", margin="8px 0 4px 0"),
     )
-    # M-EXPORT / EXPORT.5: copy the last-generated cube to the top-level
+    # Copy the last-generated cube to the top-level
     # result dir under a friendly name (HOMO.cube / LUMO.cube / etc.).
     # Disabled until the first isosurface generation populates
     # ``app._last_cube_path``.
@@ -1711,7 +1708,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
     app._iso_export_status = widgets.HTML(
         value="", layout=layout_fn(margin="0 0 0 8px")
     )
-    # UXP.3: inline "calculating" spinner shown while a cube is being computed.
+    # Inline "calculating" spinner shown while a cube is being computed.
     # Hidden until on_iso_generate reveals it; hidden again on completion.
     app._iso_spinner = widgets.HTML(
         value='<span class="quantui-spinner"></span>',
@@ -2083,8 +2080,7 @@ def build_output_tab(app: Any, *, layout_fn: Any) -> None:
         button_style="danger",
         layout=layout_fn(width="140px", display="none"),
     )
-    # POLISH.8 (M-POLISH, 2026-05-25): the Log tab moved to be an
-    # Accordion inside the History tab — rationale in the roadmap. The
+    # The Log tab moved to be an Accordion inside the History tab. The
     # explanatory text no longer needs to say "Use View log in the
     # History tab" since the user IS in the History tab now.
     app.log_tab_panel = widgets.VBox(
@@ -2117,7 +2113,7 @@ def build_output_tab(app: Any, *, layout_fn: Any) -> None:
         layout=layout_fn(padding="8px 0"),
     )
 
-    # POLISH.8: wrap the log panel in an Accordion + append to the
+    # Wrap the log panel in an Accordion + append to the
     # History tab. ``history_panel`` was built in
     # ``build_history_section`` earlier in the app-init sequence
     # (see app.py: _build_history_section runs BEFORE _build_output_tab).
@@ -2222,8 +2218,8 @@ def build_help_section(app: Any, *, layout_fn: Any) -> None:
     app.help_content_html = widgets.HTML()
     app._render_help_topic()
 
-    # POLISH.2 (M-POLISH, 2026-05-25): the single-character "?" was
-    # visually noisy and hard to recognise as the global help toggle.
+    # The single-character "?" was visually noisy and hard to recognise
+    # as the global help toggle.
     # Field-level "?" buttons (method_help_btn / basis_help_btn earlier
     # in this file) keep the symbol — for inline-with-input help it's
     # universally understood.

quantui/app_exports.py

@@ -127,7 +127,7 @@ def export_molecule_and_label(app: Any) -> tuple[Any, str, str]:
 
 
 def on_iso_export_cube(app: Any, btn: Any) -> None:
-    """Copy the last-generated cube file to the result folder (EXPORT.5).
+    """Copy the last-generated cube file to the result folder.
 
     Reads ``app._last_cube_path`` (set by the isosurface render path in
     ``app_visualization.py``) and copies it to
@@ -160,7 +160,7 @@ def on_iso_export_cube(app: Any, btn: Any) -> None:
 
 
 def on_export_bundle(app: Any, btn: Any) -> None:
-    """Zip the entire result folder for sharing (EXPORT.5)."""
+    """Zip the entire result folder for sharing."""
     from quantui.results_storage import export_result_bundle
 
     result_dir = getattr(app, "_last_result_dir", None)

quantui/app_formatters.py

@@ -12,7 +12,7 @@ def _result_extra_rows(get: Any) -> str:
     ``get(key, default=None)`` reads a field from either a result object
     (``getattr``) or a saved ``result.json`` dict (``dict.get``). Used by BOTH
     :func:`format_result` (live) and :func:`format_past_result` (history) so the
-    two cards can never drift again — the M-CLEAN regression where the compute
+    two cards can never drift again — a past regression had the compute
     device / dipole / Mulliken rows existed only on the live card. Rows:
     post-HF correlation breakdown (MP2 / CCSD / (T)), solvent, compute device
     (always shown), dipole moment, Mulliken charges.
@@ -45,7 +45,7 @@ def _num(label: str, value: str) -> str:
     if _solvent is not None:
         rows += _num("Solvent (PCM)", str(_solvent))
 
-    # Compute device (M-GPU / GPU.2) — always shown; old saved results lack the
+    # Compute device — always shown; old saved results lack the
     # field and safely read "CPU".
     if bool(get("gpu_used", False)):
         _name = get("gpu_name")
@@ -466,7 +466,7 @@ def format_past_result(data: dict[str, Any], result_dir: Optional[Path] = None)
     ts = data.get("timestamp", "")
 
     # Shared 'extra' rows (correlation breakdown / solvent / device / dipole /
-    # Mulliken) — same builder as the live card so the two never drift (M-CLEAN).
+    # Mulliken) — same builder as the live card so the two never drift.
     _extra = _result_extra_rows(lambda k, d=None: data.get(k, d))
 
     # Embed thumbnail if saved

quantui/app_history.py

@@ -13,14 +13,14 @@
 
 
 class _LoadTimer:
-    """Per-stage timing collector for a history-load operation (HIST.2).
+    """Per-stage timing collector for a history-load operation.
 
     Used as: open one ``_LoadTimer`` at the top of each loader, wrap each
     interesting sub-stage in ``with timer.stage("name"):``, then call
     ``timer.emit(status=...)`` exactly once (from the loader's ``finally``
     block). One ``history_load_timing`` event is appended to
     ``event_log.jsonl`` per load with the total elapsed time and a per-stage
-    breakdown. The data drives the HIST.2 latency-optimization pass — until
+    breakdown. The data drives the latency-optimization pass — until
     we know which stage dominates, we don't know which to optimize.
 
     Failures inside ``calc_log.log_event`` are swallowed: telemetry must
@@ -223,7 +223,7 @@ def mol_from_result_dir(result_dir: Path, data: dict[str, Any]) -> Any:
 
 
 def _begin_history_load(app: Any, message: str, source_btns: tuple) -> None:
-    """Show immediate feedback when a history-load action starts (HIST.1).
+    """Show immediate feedback when a history-load action starts.
 
     Lights the toolbar activity indicator and disables the source buttons so
     a second click can't fire a parallel load. Both actions are best-effort —
@@ -242,7 +242,7 @@ def _begin_history_load(app: Any, message: str, source_btns: tuple) -> None:
 
 
 def _end_history_load(app: Any, source_btns: tuple) -> None:
-    """Restore UI state after a history-load action finishes (HIST.1).
+    """Restore UI state after a history-load action finishes.
 
     Mirrors :func:`_begin_history_load`. Called from the loader's ``finally``
     block so the activity indicator + buttons are always restored, even when
@@ -269,11 +269,11 @@ def history_load_results(
     """Display a history result card in the Results tab and navigate there.
 
     ``source_btns`` is an optional tuple of button widgets to disable while
-    the load is in flight (HIST.1 immediate-loading-feedback contract). Tests
+    the load is in flight (immediate-loading-feedback contract). Tests
     and callers that don't have a button reference can omit it.
 
     Stage timings are emitted as a single ``history_load_timing`` event on
-    completion (HIST.2 — drives latency-optimization decisions).
+    completion (drives latency-optimization decisions).
     """
     _begin_history_load(app, "Loading history result…", source_btns)
     timer = _LoadTimer("history_load_results", result_dir)
@@ -330,11 +330,11 @@ def history_load_analysis(
     """Load analysis panels for a history result and navigate to Analysis tab.
 
     ``source_btns`` is an optional tuple of button widgets to disable while
-    the load is in flight (HIST.1 immediate-loading-feedback contract). Tests
+    the load is in flight (immediate-loading-feedback contract). Tests
     and callers that don't have a button reference can omit it.
 
     Stage timings are emitted as a single ``history_load_timing`` event on
-    completion (HIST.2 — drives latency-optimization decisions). Stages cover
+    completion (drives latency-optimization decisions). Stages cover
     the four expected hotspots: pyscf.log read, context build, molecule
     reconstruction, 3D viewer render, and the analysis-context registry walk.
     """