Design: confirming the design is one answer, one refresh, with a busy state

AGENTS.md

@@ -305,8 +305,10 @@ src/morphobricks_preprocessing/
                     comparable questions and CSV writes, the IDs toggle and the Image type card,
                     and reopen from the published file
   notebook_check_save.py the Check and save screen (sentences, one "same way?" per replicate,
-                    Yes, remove, the save click, the folded reopen); notebook_check_view.py its
-                    HTML; description_review.py (pure) the sentences and the CSV row diff;
+                    Yes, remove, the save click, the folded reopen); notebook_replicates.py its
+                    replicate boxes (rebuilt only when what they show changed);
+                    notebook_check_view.py its HTML; description_review.py (pure) the
+                    sentences and the CSV row diff;
                     description_candidate.py the checks on the exact bytes; description_reopen.py
                     the published file against the folders; published_answers.py (pure) the
                     published file as draft answers, retired IDs, reopened replicates
@@ -1099,7 +1101,8 @@ jupyter lab notebooks/MorphoBricks_Preprocessing.ipynb
   [docs/archive/plan-milestones-v0.1-v0.4.md](docs/archive/plan-milestones-v0.1-v0.4.md); the older
   status log of this file is in
   [docs/archive/agents-status-history-v0.1-v0.3.md](docs/archive/agents-status-history-v0.1-v0.3.md).
-- **Unreleased:** none yet; later changes go in a new "Unreleased" section of the changelog.
+- **Unreleased:** the faster *Looks right: confirm the design* click (see the changelog's
+  "Unreleased" section).
 - **Scope:** 2-D per plane (a Z-stack is refused as `z_stack_not_supported`; since v0.5.2 the
   notebook saves Z-stacks as recorded projections); acquisitions may have different channel
   lists (v0.5.2, Stage 3 S3.3: manifest version 5, histogram table schema version 5; units of

CHANGELOG.md

@@ -6,6 +6,21 @@ The design is `docs/restart/preprocessing-design-v0.4.md` in MorphoFeature, on b
 are in [docs/plan.md](docs/plan.md) §12. (The v0.3 to v0.4 migration guide was removed in
 v0.5.1: no run before v0.5.1 is read.)
 
+## Unreleased
+
+### Fixed
+
+- **Looks right: confirm the design** seemed to do nothing, or was very slow (owner, v0.5.2
+  Colab test). The click saved the answers twice and refreshed every page three times, each
+  time rebuilding one image-type row per folder and every replicate box of *Check and save*,
+  so it grew with the number of folders (headless: 1.0 s for 36 images, 5.3 s for 384, 7.7 s
+  for 900; about 2,400 to 14,500 widgets sent to the page). It now saves one answer, refreshes
+  once, and rebuilds the image-type rows and the replicate boxes only when what they show
+  changed (0.14 s, 0.29 s and 0.46 s; about 250 to 450 widgets). The button is disabled and
+  says *Confirming the design…* with a working line before any work, and the click ends with
+  the result, or with the reason it was not confirmed; an unexpected failure is said there,
+  the full report in Technical details. Nothing recorded changed.
+
 ## v0.5.2 (12 November 2026)
 
 Acquisitions may now have different channels (Stage 3 S3.3, owner decision of 11 November

pyproject.toml

@@ -179,6 +179,7 @@ baseline = "tools/code_rules_baseline.json"
 "morphobricks_preprocessing.notebook_masks_screen" = "ui"
 "morphobricks_preprocessing.notebook_check_save" = "ui"
 "morphobricks_preprocessing.notebook_check_view" = "ui"
+"morphobricks_preprocessing.notebook_replicates" = "ui"
 "morphobricks_preprocessing.notebook_described" = "ui"
 "morphobricks_preprocessing.notebook_mask_question" = "ui"
 "morphobricks_preprocessing.notebook_mask_step" = "ui"

src/morphobricks_preprocessing/notebook_channels_type.py

@@ -189,10 +189,21 @@ def answered(self) -> int:
         return sum(1 for u in self.types.layouts if u.usable and self.types.saved(u.key))
 
     def refresh(self) -> None:
-        """Rebuild the rows from the saved answers (without pictures while they are folded)."""
-        self.types.open(self.types.layouts)  # a fresh set of cells, built from the answers
-        self.pictured = not self.folded()
-        self._build_rows()
+        """Rebuild the rows from the saved answers (without pictures while they are folded).
+
+        The rows are rebuilt only when something they show changed: the folders, a saved
+        type, the pictures or the saved experiment's statuses. Every answer elsewhere (a
+        name, a pairing, the design's confirmation) refreshes this page too, and rebuilding
+        one row per folder each time made those clicks slow on large experiments (owner,
+        12 November 2026: *Looks right: confirm the design* seemed to do nothing).
+        """
+        pictured = not self.folded()
+        shown = self._shown(pictured)
+        if not self._same_rows(shown):
+            self.types.open(self.types.layouts)  # a fresh set of cells, built from the answers
+            self.pictured = pictured
+            self._build_rows()
+            self._built = (self.types.radios, shown)
         self.problem.value = self.types.message
         usable = sum(1 for u in self.types.layouts if u.usable)
         done = self.answered
@@ -202,6 +213,35 @@ def refresh(self) -> None:
             else ui.status("warn", f"Not finished: {usable - done} image type(s) to choose.")
         )
 
+    def _shown(self, pictured: bool) -> tuple:
+        """Return what the rows show, to tell whether they must be rebuilt."""
+        layouts = self.types.layouts
+        units = self.reopen()
+        return (
+            layouts,
+            pictured,
+            self._thumbs() if pictured else None,
+            tuple((self.types.saved(u.key), self.types.note(u)) for u in layouts),
+            None if units is None else tuple(sorted(units.items())),
+        )
+
+    def _same_rows(self, shown: tuple) -> bool:
+        """Return True when the rows on the page were built for exactly ``shown``.
+
+        Objects (the layouts, the pictures) are compared by identity, the answers by value;
+        cells replaced since (:meth:`ImageTypeColumn.open`) are never kept.
+        """
+        built = getattr(self, "_built", None)
+        if built is None or built[0] is not self.types.radios:
+            return False
+        before = built[1]
+        return (
+            before[0] is shown[0]
+            and before[1] == shown[1]
+            and before[2] is shown[2]
+            and before[3:] == shown[3:]
+        )
+
     def unfolded(self) -> None:
         """Rebuild the rows with their pictures now that they are shown, unless they have them."""
         if not self.pictured and not self.folded() and ui.is_visible(self.widget):

src/morphobricks_preprocessing/notebook_check_save.py

@@ -18,7 +18,6 @@
 
 from __future__ import annotations
 
-import html
 from dataclasses import replace
 from datetime import date
 from pathlib import Path
@@ -31,7 +30,7 @@
 from .description import DescriptionError
 from .description_candidate import CandidateCheck, check_candidate
 from .description_removal import Removal, reconfirmations
-from .description_review import comparisons, replicates, short_names
+from .description_review import comparisons, short_names
 from .draft import DraftError
 from .draft_answers import (
     RepeatAnswer,
@@ -43,28 +42,20 @@
 from .fingerprint import changed_since_check
 from .mask_answers import masks_unanswered
 from .name_issues import NAME_CODES
-from .notebook_channel_thumbs import Thumb
 from .notebook_check_view import (
-    SAME_WAY,
-    SAME_WAY_HELP,
     blocked_html,
     changes_html,
     checks_html,
     comparisons_html,
-    member_html,
-    missing_html,
     names_html,
     removal_text,
-    replicate_title,
     run_stop_html,
     saved_html,
     todo_html,
 )
 from .notebook_description import _with_ids
 from .notebook_render import blocked_line
-from .notebook_row_fold import RowFold, row_status
-from .notebook_thumb_tile import ThumbTile, show_detail
-from .preview_crop import TilePictures
+from .notebook_replicates import _ReplicateBoxes
 from .published_answers import kept_date
 from .run import OutputLockedError
 from .run.description_file import PublicationRefused
@@ -79,15 +70,7 @@
 FOLDED = ("design_card", "names_card", "references_card", "channels_box", "masks_box")
 
 
-def _enlarge(detail: widgets.VBox, title: str, found: TilePictures | Thumb) -> None:
-    """Show a folder's enlarged picture in ``detail``, or why there is none."""
-    if isinstance(found, Thumb):
-        show_detail(detail, title, None, found.note)
-    else:
-        show_detail(detail, title, found, "")
-
-
-class _CheckSaveScreen:
+class _CheckSaveScreen(_ReplicateBoxes):
     """The *Check and save* screen, its save click and the folded reopening."""
 
     def _build_check_save(self) -> None:
@@ -319,92 +302,6 @@ def _candidate_check(self, answers: object) -> CandidateCheck | None:
         _, confirmations = self._publication_terms(state, candidate)
         return check_candidate(candidate, self.preflight, roles, published, confirmations)
 
-    def _show_replicates(self, applied: object, answers: object, labels: list[str]) -> None:
-        """One box per replicate: folders, pictures, channels, and its own question."""
-        boxes, toggles = [], {}
-        units, counts = self._reopen_units(), self._channel_counts()
-        state = self._published()
-        saved_dates = (
-            {}
-            if state is None
-            else {key: r.confirmed_on for key, r in state.description.repeats.items()}
-        )
-        views = replicates(applied, answers)
-        for view in views:
-            toggle = ui.ConfirmToggle(
-                SAME_WAY,
-                SAME_WAY_HELP,
-                "Yes, the same way",
-                f"Confirmed on {view.confirmed_on}: one replicate." if view.confirmed_on else "",
-                "Undo",
-            )
-            toggle.set(view.confirmed_on is not None, notify=False)
-            toggle.observe(lambda value, label=view.label: self._same_way(label, value))
-            toggles[view.label] = toggle
-            members = [
-                widgets.HBox(
-                    [
-                        self._member_picture(
-                            (m.condition, m.source_repeat), self.replicates_detail
-                        ),
-                        widgets.HTML(member_html(m, labels, counts)),
-                    ]
-                )
-                for m in view.members
-            ]
-            body = [widgets.HTML(replicate_title(view)), *members, widgets.HTML(missing_html(view))]
-            box = widgets.VBox(
-                [*body, toggle.widget],
-                layout=widgets.Layout(
-                    border="1px solid #E2E8F0", padding="8px 12px", margin="0 0 10px 0"
-                ),
-            )
-            keys = [u.key for m in view.members for u in m.units]
-            # A box with a warning (an acquisition lacking a label) never folds, nor one whose
-            # date is not the published one (publication's R_CONFIRMED_ON_CHANGED names it).
-            settled = (
-                view.confirmed_on is not None
-                and not view.missing
-                and view.confirmed_on == saved_dates.get(view.label, view.confirmed_on)
-            )
-            boxes.append((box, row_status(units, keys, settled)))
-        self.same_way = toggles
-        shown = (
-            self._channel_thumbs,
-            [[(m.condition, m.source_repeat) for m in v.members] for v in views],
-        )
-        if shown != getattr(self, "_replicates_shown", None):  # other folders or pictures (#252)
-            self.replicates_detail.children = []  # an Enlarge of the boxes before is closed
-        self._replicates_shown = shown
-        if not hasattr(self, "_replicate_fold"):
-            self._replicate_fold = RowFold("replicate")
-        self.replicates_box.children = self._replicate_fold.arrange(boxes)
-
-    def _member_picture(self, key: tuple[str, str], detail: widgets.VBox) -> widgets.Widget:
-        """Return the picture of a folder's first image (channel 1, or in colour when RGB).
-
-        A large image gets its crop at native pixels beside it; **Enlarge** shows both in
-        ``detail``.
-        """
-        thumbs, layouts = self._channel_thumbs, self._channel_layouts
-        layout = next((u for u in layouts if u.key[:2] == key), None)
-        if thumbs is None or layout is None:
-            return widgets.HTML(
-                "<div class='mb-help' style='width:120px'>picture once the axis roles are "
-                "confirmed</div>"
-            )
-        colour = self.channel_types.shown(layout) == "rgb"
-        found = thumbs.tile(layout, colour)
-        if isinstance(found, Thumb):
-            return ThumbTile(None, problem=found.note, width="120px").widget
-        title = f"<b>{html.escape('/'.join(key))}</b> · {html.escape(layout.image or '')}"
-        return ThumbTile(
-            found,
-            colour=colour,
-            enlarge=lambda: _enlarge(detail, title, thumbs.enlarged(layout, colour)),
-            width="120px",
-        ).widget
-
     def _folder_cell(self, key: tuple[str, str], text: str) -> widgets.Widget:
         """Return a folder of the pairing card, with its picture."""
         return widgets.VBox([widgets.HTML(text), self._member_picture(key, self.pairing_detail)])
@@ -464,6 +361,7 @@ def _same_way(self, label: str, value: bool) -> None:
         repeats = {**answers.repeats, label: replace(entry, confirmed_on=day)}
         if not self._answer(replace(answers, repeats=repeats)):
             self.save_status.value = ui.status("error", "Not taken.", [str(self._refusal)])
+            self._replicates_built = None  # the clicked box shows an answer that was not taken
         self._refresh_check_save()
 
     def _remove(self, condition_id: str) -> None:

src/morphobricks_preprocessing/notebook_description.py

@@ -313,14 +313,22 @@ def _wanted_ids(self) -> dict[tuple[str, str], str]:
     def _confirm_ids(self) -> bool:
         """Adopt every ID as shown, or none: each refusal is listed with the reader's reason."""
         wanted = self._wanted_ids()
+        return self._adopt_ids(wanted, _with_ids(self.draft_answers, wanted))
+
+    def _adopt_ids(self, wanted: dict[tuple[str, str], str], answers: DraftAnswers) -> bool:
+        """Save ``answers`` (which adopt ``wanted``) in one answer, unless an ID is refused.
+
+        Each ID is first tried on its own, so every refusal is listed with the reader's
+        reason; then ``answers`` are saved once. Nothing is adopted when anything is refused.
+        """
         problems = []
         for (kind, key), text in wanted.items():
             try:
                 apply_answers(self._draft_base, _with_ids(self.draft_answers, {(kind, key): text}))
             except DraftError as exc:
                 problems.append((f"{KIND_NAMES[kind].capitalize()} {key}", exc))
         if not problems:
-            if self._answer(_with_ids(self.draft_answers, wanted)):
+            if self._answer(answers):
                 return True
             problems.append(("These IDs together", self._refusal))
         self._names_refusal = refusal_card(