@morscherlab/mint-sdk 1.3.0-beta.3 → 1.3.0-beta.5

package/src/__tests__/styles/menusShellRefresh.test.ts

@@ -25,8 +25,14 @@ describe('menus and app shell styles', () => {
     expect(css('app-top-bar.css')).toMatch(/\.mint-topbar\s*\{[^}]*padding:\s*0\.625rem 0\.75rem;/)
   })
 
-  it('should shrink the plugin tile to 20px beside the static plugin identity (5a)', () => {
-    expect(css('app-top-bar.css')).toMatch(/\.mint-topbar__brand:has\(\+ \.mint-topbar__plugin-identity\) \.mint-plugin-icon--topbar\s*\{[^}]*width:\s*1\.25rem;/)
+  // Shrinking the tile beside the identity also shrank structured icons inside their solid chip, drawing a ring.
+  it('should keep the 32px plugin tile beside the static plugin identity (5a)', () => {
+    expect(css('app-top-bar.css')).not.toMatch(/:has\(\+ \.mint-topbar__plugin-identity\)/)
+  })
+
+  // A slotted 36px logo shrank to 32px wide but kept its height, drawing a 32x36 tile.
+  it('should fit slotted identity content inside the 32px tile (5a)', () => {
+    expect(css('app-top-bar.css')).toMatch(/\.mint-topbar__identity > \*\s*\{[^}]*max-width:\s*100%;[^}]*max-height:\s*100%;/)
   })
 
   // 15px x 1.15 + 12px x 1.2 = 31.7px, so the title group fits the 32px control row.

package/src/__tests__/templates/templatesDeprecation.test.ts

@@ -1,31 +1,71 @@
 import { dirname, resolve } from 'node:path'
 import { fileURLToPath } from 'node:url'
-import { describe, expect, it } from 'vitest'
+import { beforeAll, describe, expect, it } from 'vitest'
 import ts from 'typescript'
 
 const TEMPLATES_INDEX = resolve(dirname(fileURLToPath(import.meta.url)), '../../templates/index.ts')
+const COMPONENTS_INDEX = resolve(dirname(fileURLToPath(import.meta.url)), '../../components/index.ts')
+const COMPOSABLES_DIR = resolve(dirname(fileURLToPath(import.meta.url)), '../../composables')
 
-// TypeScript ignores @deprecated on `export { ... } from` blocks; an import
-// site only shows the deprecation when the original declaration carries it.
-function undeprecatedTemplateValueExports(): string[] {
-  const program = ts.createProgram([TEMPLATES_INDEX], {
+// Composables removed in MINT 1.4 with the templates and sample grouping.
+const REMOVED_COMPOSABLE_FILES = [
+  'useBioTemplateComponents.ts',
+  'useBioTemplateControls.ts',
+  'useBioTemplatePackWorkspace.ts',
+  'useBioTemplatePresetWorkspace.ts',
+  'useBioTemplateWorkspace.ts',
+  'useTemplateCollection.ts',
+  'useExperimentSave.ts',
+  'useGroupAssignment.ts',
+].map(file => resolve(COMPOSABLES_DIR, file))
+
+// One program for every file: building one per file took longer than the test timeout on CI.
+let program: ts.Program
+let checker: ts.TypeChecker
+
+beforeAll(() => {
+  program = ts.createProgram([TEMPLATES_INDEX, COMPONENTS_INDEX, ...REMOVED_COMPOSABLE_FILES], {
     target: ts.ScriptTarget.ES2022,
     module: ts.ModuleKind.ESNext,
     moduleResolution: ts.ModuleResolutionKind.Bundler,
     noEmit: true,
   })
-  const checker = program.getTypeChecker()
-  const moduleSymbol = checker.getSymbolAtLocation(program.getSourceFile(TEMPLATES_INDEX)!)!
-  return checker
-    .getExportsOfModule(moduleSymbol)
+  checker = program.getTypeChecker()
+}, 60_000)
+
+function exportsOf(file: string): ts.Symbol[] {
+  return checker.getExportsOfModule(checker.getSymbolAtLocation(program.getSourceFile(file)!)!)
+}
+
+function isDeprecated(symbol: ts.Symbol): boolean {
+  return symbol.getJsDocTags(checker).some(tag => tag.name === 'deprecated')
+}
+
+// TypeScript ignores @deprecated on `export { ... } from` blocks; an import
+// site only shows the deprecation when the original declaration carries it.
+function undeprecatedValueExports(file: string): string[] {
+  return exportsOf(file)
     .map(symbol => (symbol.flags & ts.SymbolFlags.Alias ? checker.getAliasedSymbol(symbol) : symbol))
     .filter(symbol => symbol.flags & ts.SymbolFlags.Value)
-    .filter(symbol => !symbol.getJsDocTags(checker).some(tag => tag.name === 'deprecated'))
+    .filter(symbol => !isDeprecated(symbol))
     .map(symbol => symbol.getName())
 }
 
 describe('templates deprecation', () => {
+  it('should expose deprecated component tags to TypeScript consumers', () => {
+    const names = ['BioTemplateRenderer', 'SmartGroupModal', 'SampleSelector', 'DoseDesignWorkspaceView']
+    const tagged = exportsOf(COMPONENTS_INDEX).filter(isDeprecated).map(symbol => symbol.getName())
+
+    expect(names.filter(name => !tagged.includes(name))).toEqual([])
+  })
+
   it('should tag every template value export when the templates move out in MINT 1.4', () => {
-    expect(undeprecatedTemplateValueExports()).toEqual([])
+    expect(undeprecatedValueExports(TEMPLATES_INDEX)).toEqual([])
+  })
+
+  it('should tag every value export of the template and grouping composables when they are removed in MINT 1.4', () => {
+    const untagged = REMOVED_COMPOSABLE_FILES.flatMap(undeprecatedValueExports)
+
+    expect(untagged).toEqual([])
   })
 })

package/src/components/ActionMenu.vue

@@ -1,7 +1,7 @@
 <script setup lang="ts">
 /** Compact overflow actions with an IconButton trigger and a viewport-safe teleported menu. */
 import { computePosition, flip, offset, shift } from '@floating-ui/dom'
-import { Ellipsis } from 'lucide-vue-next'
+import { Check, Ellipsis } from 'lucide-vue-next'
 import { nextTick, onMounted, ref, watch } from 'vue'
 import { useDropdownState } from '../composables/useDropdownState'
 import { useMenuKeyboard } from '../composables/useMenuKeyboard'
@@ -167,10 +167,18 @@ watch(isOpen, async (opened) => {
           v-else
           type="button"
           :class="['mint-menu-item mint-action-menu__item', { 'mint-menu-item--danger mint-action-menu__item--danger': item.danger }]"
-          role="menuitem"
+          :role="item.checked === undefined ? 'menuitem' : 'menuitemradio'"
+          :aria-checked="item.checked"
           :disabled="item.disabled"
           @click="handleSelect(item)"
         >
+          <Check
+            v-if="item.checked !== undefined"
+            class="mint-action-menu__check"
+            :class="{ 'mint-action-menu__check--off': !item.checked }"
+            :size="14"
+            aria-hidden="true"
+          />
           {{ item.label }}
         </button>
       </template>

package/src/components/AppTopBar.vue

@@ -144,8 +144,8 @@ const hasPlatformPageSelector = computed(() =>
   props.pageSelector === undefined && (plugin.value?.nav_items?.length ?? 0) > 1,
 )
 const hasPageSelector = computed(() => (props.pageSelector?.length ?? 0) > 1 || hasPlatformPageSelector.value)
-/** Integrated plugins show their name + version as a static identity; it stands in for the title. */
-const identityName = computed(() => (isIntegrated.value ? plugin.value?.name : undefined))
+/** Integrated plugins show their name as a static identity in place of the title; the page selector replaces it. */
+const identityName = computed(() => (isIntegrated.value && !hasPageSelector.value ? plugin.value?.name : undefined))
 const hasPillNav = computed(() => !!props.pillNav?.length)
 const hasAccountMenu = computed(() => !!props.accountMenu?.length)
 const hasTitleGroup = computed(
@@ -304,9 +304,7 @@ const effectiveCurrentPageSelectorId = computed(() =>
       <!-- Left: static plugin identity (not a control) -->
       <span v-if="identityName" class="mint-topbar__plugin-identity">
         <span class="mint-topbar__plugin-name">{{ identityName }}</span>
-        <span v-if="plugin?.version" class="mint-topbar__plugin-version">v{{ plugin.version }}</span>
       </span>
-      <span v-if="identityName && hasPageSelector" class="mint-topbar__divider" aria-hidden="true" />
 
       <!-- Left: page selector -->
       <AppTopBarPageSelectorInternal

package/src/components/EmptyState.vue

@@ -56,7 +56,9 @@ const defaultIconPaths = [
     <div class="mint-empty-state__body">
       <h3 v-if="title" class="mint-empty-state__title">{{ title }}</h3>
       <p v-if="description" class="mint-empty-state__description">{{ description }}</p>
-      <slot />
+      <div v-if="$slots.default" class="mint-empty-state__content">
+        <slot />
+      </div>
     </div>
     <div v-if="actionLabel" class="mint-empty-state__action">
       <BaseButton variant="secondary" @click="emit('action')">

package/src/components/FilePicker.vue

@@ -12,6 +12,7 @@ import { computed, ref, useTemplateRef } from 'vue'
 import BaseModal from './BaseModal.vue'
 import BaseButton from './BaseButton.vue'
 import BaseInput from './BaseInput.vue'
+import ActionMenu from './ActionMenu.vue'
 import SegmentedControl from './SegmentedControl.vue'
 import FileUploader from './FileUploader.vue'
 import FilePickerListInternal from './internal/FilePickerListInternal.vue'
@@ -24,6 +25,7 @@ import type {
   PickerNode,
   PickerSelection,
   PickerSelectionMode,
+  PickerSort,
   PickerSource,
   PickerView,
 } from '../types/filePicker'
@@ -39,6 +41,8 @@ interface Props {
   title?: string
   /** `list` shows one folder at a time; `tree` adds disclosure triangles. */
   view?: PickerView
+  /** Row order on each open; the user can change it from the path bar until closing. */
+  defaultSort?: PickerSort
   /** Host-owned visibility/selection filter; backend must still enforce access. */
   systemFilter?: (node: PickerNode, source: PickerSource) => boolean
 }
@@ -50,6 +54,7 @@ const props = withDefaults(defineProps<Props>(), {
   initialSelection: null,
   title: 'Choose data',
   view: 'list',
+  defaultSort: 'newest',
 })
 const emit = defineEmits<{
   'update:open': [open: boolean]
@@ -68,6 +73,7 @@ const {
   source,
   query,
   recursive,
+  sort,
   skipBlanks,
   reviewing,
   nav,
@@ -109,6 +115,19 @@ const sourceLabel = computed(() => {
   }
   return mounts.value.find((item) => item.path === props.adapter.mountOf?.(node.path))?.name ?? sourceNames.server
 })
+const SORT_LABELS: Record<PickerSort, string> = {
+  newest: 'Newest first',
+  oldest: 'Oldest first',
+  name: 'Name A–Z',
+  'name-desc': 'Name Z–A',
+}
+const sortItems = computed(() =>
+  (Object.keys(SORT_LABELS) as PickerSort[]).map((id) => ({
+    id,
+    label: SORT_LABELS[id],
+    checked: sort.value === id,
+  })),
+)
 const accepts = computed(() =>
   (capability.value?.formats ?? []).map((format) => `.${format.replace(/^\./, '')}`).join(' '),
 )
@@ -198,6 +217,28 @@ const summary = computed(() => {
           </template>
         </nav>
         <span v-if="accepts" class="mint-picker__accepts">Accepts {{ accepts }}</span>
+        <ActionMenu
+          label="Sort"
+          :items="sortItems"
+          @select="sort = $event.id as PickerSort"
+        >
+          <template #trigger="{ open: menuOpen, toggle, keydown }">
+            <button
+              type="button"
+              class="mint-picker__sort"
+              aria-haspopup="menu"
+              :aria-expanded="menuOpen"
+              :aria-label="`Sort: ${SORT_LABELS[sort]}`"
+              @click="toggle"
+              @keydown="keydown"
+            >
+              {{ SORT_LABELS[sort] }}
+              <svg viewBox="0 0 16 16" fill="none" stroke="currentColor" stroke-width="1.5" aria-hidden="true">
+                <path d="M4 6l4 4 4-4" />
+              </svg>
+            </button>
+          </template>
+        </ActionMenu>
         <button
           type="button"
           class="mint-picker__scope"
@@ -255,6 +296,7 @@ const summary = computed(() => {
             :loading="loading"
             :error="error"
             :query="query"
+            :truncated="nav.truncated.value"
             :mode="selectionMode"
             :selected="selection.selected"
             :selectable="selection.selectable"

package/src/components/WellPlate.colors.ts

@@ -1,16 +1,12 @@
 import type { HeatmapConfig } from '../types'
 
-/**
- * Group color for the built-in sample types when `sampleColors` has no entry.
- * Color encodes the group and shape encodes the type (3a): blank and QC render
- * neutral markers and ignore it; iQC takes it like a sample.
- */
+/** Color for the built-in sample types when `sampleColors` has no entry. */
 export const DEFAULT_SAMPLE_TYPE_COLORS: Record<string, string> = {
-  sample: 'var(--mint-sample-1)',
-  control: 'var(--mint-sample-2)',
-  blank: 'var(--mint-sample-1)',
-  qc: 'var(--mint-sample-1)',
-  iqc: 'var(--mint-sample-1)',
+  sample: '#10b981',
+  control: '#3b82f6',
+  blank: '#f97316',
+  qc: '#8b5cf6',
+  iqc: '#ec4899',
 }
 
 export const HEATMAP_COLORS: Record<string, string[]> = {

package/src/components/WellPlate.legend.ts

@@ -1,8 +1,8 @@
 import type { WellLegendItem } from '../types'
 
 export const DEFAULT_WELL_LEGEND_ITEMS: WellLegendItem[] = [
-  { type: 'sample', label: 'Sample', color: 'var(--mint-sample-1)' },
-  { type: 'blank', label: 'Blank', color: 'var(--mint-sample-1)' },
-  { type: 'qc', label: 'QC', color: 'var(--mint-sample-1)' },
-  { type: 'iqc', label: 'IQC', color: 'var(--mint-sample-1)' },
+  { type: 'sample', label: 'Sample', color: '#10b981' },
+  { type: 'blank', label: 'Blank', color: '#f97316' },
+  { type: 'qc', label: 'QC', color: '#8b5cf6' },
+  { type: 'iqc', label: 'IQC', color: '#ec4899' },
 ]

package/src/components/WellPlate.rendering.ts

@@ -1,5 +1,4 @@
 import type { HeatmapConfig, Well, WellPlateSelectionMode, WellShape } from '../types'
-import { sampleTypeMarker } from '../utils/sampleTypeMarker'
 import {
   DEFAULT_SAMPLE_TYPE_COLORS,
   getHeatmapColor,
@@ -55,13 +54,15 @@ export function wellStyle(well: Well, state: WellStyleState): Record<string, str
       ?? state.sampleColors[well.sampleType] ?? DEFAULT_SAMPLE_TYPE_COLORS[well.sampleType])
   if (!groupColor) return {} // empty / filled wells are styled by well-plate.css
 
-  const { background, border } = sampleTypeMarker(well.sampleType!, groupColor).style
-  return { backgroundColor: background, border }
+  return sampleTint(groupColor)
 }
 
-/** In-well glyph of the 3a sample-type marker: `Q` for QC, `i` for iQC. */
-export function sampleTypeGlyph(well: Well): string | null {
-  return well.sampleType ? sampleTypeMarker(well.sampleType, '').glyph : null
+/** 15% fill and 40% outline of a sample color; color-mix accepts hex and `var()` tokens alike. */
+export function sampleTint(color: string): { backgroundColor: string; border: string } {
+  return {
+    backgroundColor: `color-mix(in srgb, ${color} 15%, transparent)`,
+    border: `1px solid color-mix(in srgb, ${color} 40%, transparent)`,
+  }
 }
 
 let sampleTypeIndicatorWarned = false
@@ -89,10 +90,10 @@ export function wellBadge(
   if (!showBadges || !well.metadata) return null
   const count = well.metadata.injectionCount as number | undefined
   if (count && count > 1) {
-    return { text: String(count), color: 'var(--text-primary)' }
+    return { text: String(count), color: '#6366f1' }
   }
   if (well.metadata.customMethod) {
-    return { text: '', color: 'var(--color-purple)' } // custom method: a dot, no glyph
+    return { text: '+', color: '#ec4899' }
   }
   return null
 }

package/src/components/WellPlate.vue

@@ -25,7 +25,7 @@ import {
 } from './WellPlate.geometry'
 import { useWellPlateInteraction } from './WellPlate.interaction'
 import {
-  sampleTypeGlyph,
+  sampleTint,
   warnSampleTypeIndicatorDeprecated,
   wellBadge,
   wellClasses,
@@ -34,7 +34,6 @@ import {
 } from './WellPlate.rendering'
 import { DEFAULT_WELL_LEGEND_ITEMS } from './WellPlate.legend'
 import DataStateInternal from './internal/DataStateInternal.vue'
-import { sampleTypeMarker } from '../utils/sampleTypeMarker'
 
 interface Props {
   modelValue?: string[]
@@ -476,27 +475,13 @@ const tableStyle = computed(() => ({
                 >
                   {{ well.id }}
                 </span>
-                <!-- Sample-type marker glyph (Q / i) -->
-                <span
-                  v-else-if="sampleTypeGlyph(well)"
-                  class="mint-well-plate__indicator"
-                >
-                  {{ sampleTypeGlyph(well) }}
-                </span>
-                <!-- The glyph moves to a corner when a label or well ID takes the centre -->
-                <span
-                  v-if="sampleTypeGlyph(well) && (getWellLabel(well) || props.showWellIds)"
-                  class="mint-well-plate__corner-glyph"
-                >
-                  {{ sampleTypeGlyph(well) }}
-                </span>
 
                 <!-- Badge (injection count or custom method) -->
                 <span
                   v-if="getWellBadge(well)"
-                  :class="['mint-well-plate__badge', { 'mint-well-plate__badge--dot': !getWellBadge(well)?.text }]"
+                  class="mint-well-plate__badge"
                   :style="{ backgroundColor: getWellBadge(well)?.color }"
-                  :title="getWellBadge(well)?.text ? `${getWellBadge(well)?.text}x injections` : 'Custom method'"
+                  :title="getWellBadge(well)?.text === '+' ? 'Custom method' : `${getWellBadge(well)?.text ?? ''}x injections`"
                 >
                   {{ getWellBadge(well)?.text }}
                 </span>
@@ -531,11 +516,9 @@ const tableStyle = computed(() => ({
             class="mint-well-plate__sample-legend-item"
           >
             <span
-              v-for="marker in [sampleTypeMarker(item.type, item.color)]"
-              :key="item.type"
               class="mint-well-plate__sample-legend-dot"
-              :style="marker.style"
-            >{{ marker.glyph }}</span>
+              :style="sampleTint(item.color)"
+            />
             <span class="mint-well-plate__sample-legend-text">{{ item.label }}</span>
           </div>
         </div>

package/src/components/index.ts

@@ -48,7 +48,8 @@ export { default as GeneratedResultRenderer } from './GeneratedResultRenderer.vu
 export { default as GeneratedPlotlyResult } from './GeneratedPlotlyResult.vue'
 export { default as ComponentBindingRenderer } from './ComponentBindingRenderer.vue'
 export { default as ControlWorkspaceView } from './ControlWorkspaceView.vue'
-export { default as DoseDesignWorkspaceView } from './DoseDesignWorkspaceView.vue'
+/** Complete ControlWorkspaceView page shell for WellPlate + DoseCalculator dose design. @deprecated Scheduled for removal in MINT 1.4; use `ControlWorkspaceView` instead, with `defineDoseDesignControlModel()`. */
+export { /** @deprecated Removed in MINT 1.4. */ default as DoseDesignWorkspaceView } from './DoseDesignWorkspaceView.vue'
 export { default as AppContainer } from './AppContainer.vue'
 export { default as PluginIcon } from './PluginIcon.vue'
 export { default as LayoutResizeHandle } from './LayoutResizeHandle.vue'
@@ -69,30 +70,43 @@ export { default as AdductText } from './AdductText.vue'
 export { default as SettingsModal } from './SettingsModal.vue'
 
 // Biological experiment components
-export { default as BioTemplateRenderer } from './BioTemplateRenderer.vue'
-export { default as BioTemplateExperimentWorkspaceView } from './BioTemplateExperimentWorkspaceView.vue'
-export { default as BioTemplatePackWorkspaceView } from './BioTemplatePackWorkspaceView.vue'
-export { default as BioTemplatePresetWorkspaceView } from './BioTemplatePresetWorkspaceView.vue'
+/** Render biology template envelopes with matching SDK components such as WellPlate, DoseCalculator, and DataFrame. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as BioTemplateRenderer } from './BioTemplateRenderer.vue'
+/** Current-experiment template workspace with load/save/reset controls and WellPlate/DataFrame/DoseCalculator previews. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as BioTemplateExperimentWorkspaceView } from './BioTemplateExperimentWorkspaceView.vue'
+/** Complete current-experiment workspace for a curated biology template pack with save/load controls and component-prop slots. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as BioTemplatePackWorkspaceView } from './BioTemplatePackWorkspaceView.vue'
+/** Complete editable biology template preset workspace for WellPlate/DoseCalculator, LC-MS, qPCR, generated controls, preview components, and current-experiment save wiring. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as BioTemplatePresetWorkspaceView } from './BioTemplatePresetWorkspaceView.vue'
 export { default as WellPlate } from './WellPlate.vue'
 export { default as PlateEditor } from './PlateEditor.vue'
-export { default as SampleLegend } from './SampleLegend.vue'
-export { default as ExperimentTimeline } from './ExperimentTimeline.vue'
+/** Clickable color-swatch legend for plate sample types, supporting selection, count display, add/remove, and custom color assignment. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as SampleLegend } from './SampleLegend.vue'
+/** Horizontal or vertical timeline of ordered protocol steps with status indicators, drag-to-reorder, and step-type iconography. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as ExperimentTimeline } from './ExperimentTimeline.vue'
 
 // Sample management components
-export { default as SampleSelector } from './SampleSelector.vue'
-/** Smart Group modal wired to the `useAutoGroup` engine. @deprecated Scheduled for removal in MINT 1.4; use `SmartGroupModal` instead. */
-export { default as AutoGroupModal } from './AutoGroupModal.vue'
-export { default as GroupAssigner } from './GroupAssigner.vue'
-export { default as SmartGroupModal } from './SmartGroupModal.vue'
-export { default as SmartGroupFieldRecipe } from './SmartGroupFieldRecipe.vue'
-export { default as SmartGroupManual } from './SmartGroupManual.vue'
+/** Interactive sample list with drag-and-drop group assignment, color labeling, and smart-group support. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as SampleSelector } from './SampleSelector.vue'
+/** Smart Group modal wired to the `useAutoGroup` engine. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as AutoGroupModal } from './AutoGroupModal.vue'
+/** Drag-and-drop two-zone assigner for splitting sample groups into control and treatment arms. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as GroupAssigner } from './GroupAssigner.vue'
+/** Smart Group modal with the auto Field Recipe and the manual cohort builder. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as SmartGroupModal } from './SmartGroupModal.vue'
+/** Smart Group auto mode: groups samples by a field recipe. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as SmartGroupFieldRecipe } from './SmartGroupFieldRecipe.vue'
+/** Smart Group manual mode: builds cohorts from selected samples. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as SmartGroupManual } from './SmartGroupManual.vue'
 
 // Lab/Experiment components
 export { default as MoleculeInput } from './MoleculeInput.vue'
 export { default as ConcentrationInput } from './ConcentrationInput.vue'
 export { default as DoseCalculator } from './DoseCalculator.vue'
-export { default as ReagentEditor, type ReagentDefinition } from './ReagentEditor.vue'
-export { default as ReagentList } from './ReagentList.vue'
+/** Editor for a single reagent definition with axis orientation, dilution-series generator, and position-count validation for 96/384-well plates. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as ReagentEditor, type ReagentDefinition } from './ReagentEditor.vue'
+/** Sortable, searchable table of experiment reagents showing lot number, expiry, storage conditions, and stock level with low-stock warnings. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as ReagentList } from './ReagentList.vue'
 export { default as SampleHierarchyTree } from './SampleHierarchyTree.vue'
 export { default as ProtocolStepEditor } from './ProtocolStepEditor.vue'
 
@@ -138,6 +152,7 @@ export { default as ArtifactSelectorModal } from './ArtifactSelectorModal.vue'
 export { default as GeneratedPathInput } from './GeneratedPathInput.vue'
 export { default as ArtifactSaveDialog } from './ArtifactSaveDialog.vue'
 export { default as ExperimentPopover } from './ExperimentPopover.vue'
-export { default as FitPanel } from './FitPanel.vue'
+/** Control panel for running a curve-fit job with progress bar, results table, and error display. @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
+export { /** @deprecated Removed in MINT 1.4. */ default as FitPanel } from './FitPanel.vue'
 
 export { default as FilePicker } from './FilePicker.vue'

package/src/components/internal/FilePickerListInternal.vue

@@ -22,6 +22,8 @@ const props = defineProps<{
   loading: boolean
   error: string
   query: string
+  /** Search results stopped at a limit; the rows are the first matches only. */
+  truncated?: boolean
   mode: PickerSelectionMode
   selected: (node: PickerNode) => boolean
   selectable: (node: PickerNode) => boolean
@@ -171,6 +173,9 @@ function parts(name: string) {
     <div class="mint-picker__list-head" aria-hidden="true">
       <span /><span>Name</span><span>Size</span><span>Modified</span>
     </div>
+    <p v-if="truncated && !loading && !error && rows.length" class="mint-picker__truncated" role="status">
+      Showing the first {{ rows.length }} matches. Search a smaller folder or use a more specific search to see the rest.
+    </p>
     <div v-if="loading" class="mint-picker__skeleton">
       <Skeleton v-for="n in 6" :key="n" width="100%" height="1.25rem" />
     </div>
@@ -180,10 +185,14 @@ function parts(name: string) {
     </div>
     <div v-else-if="!rows.length" class="mint-picker__empty" role="status">
       <strong>{{
-        query ? 'No matching folders or files' : emptyTitle || 'No readable files'
+        truncated
+          ? 'Search stopped before finding a match'
+          : query ? 'No matching folders or files' : emptyTitle || 'No readable files'
       }}</strong>
       <span>{{
-        query ? 'Try a different search or include subfolders.' : 'Choose another location.'
+        truncated
+          ? 'Search a smaller folder or use a more specific search.'
+          : query ? 'Try a different search or include subfolders.' : 'Choose another location.'
       }}</span>
     </div>
     <template v-for="row in rows" v-else :key="row.node.path">

package/src/composables/autoGroup/index.ts

@@ -1,5 +1,5 @@
 // Internal engine for `useAutoGroup` / `AutoGroupModal`. Deprecated: scheduled
-// for removal in MINT 1.4 together with `useAutoGroup`; `SmartGroupModal` replaces it.
+// for removal in MINT 1.4 together with `useAutoGroup`; no SDK replacement.
 
 export { splitMulti, pickPrimaryDelimiter } from './tokenize'
 export type { Delimiter } from './tokenize'