@morscherlab/mint-sdk 1.3.0-beta.4 → 1.3.0-beta.6

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
+/** Interactive sample list with drag-and-drop group assignment, color labeling, and smart-group support. */
 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'
+/** 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'
 
@@ -100,7 +114,7 @@ export { default as ProtocolStepEditor } from './ProtocolStepEditor.vue'
 export { default as PlotlyChart } from './PlotlyChart.vue'
 export { default as ScientificNumber } from './ScientificNumber.vue'
 export { default as ChemicalFormula } from './ChemicalFormula.vue'
-/** Displays LC/MS or GC/MS acquisition sequence progress with ETA and remaining-time labels. @deprecated Scheduled for removal in MINT 1.4; instrument UI moves to the mld-ms plugins. */
+/** Displays LC/MS or GC/MS acquisition sequence progress with ETA and remaining-time labels. */
 export { default as SequenceProgressBar } from './SequenceProgressBar.vue'
 /** Status badge for instrument states: a tone dot (or dash / hollow shape for offline, never-reported and inactive) plus a label. */
 export { default as InstrumentStateBadge } from './InstrumentStateBadge.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/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'

package/src/composables/index.ts

@@ -4,8 +4,6 @@ export {
   type ApiClientOptions,
   type UseApiReturn,
 } from './useApi'
-export { useAuth } from './useAuth'
-export { usePasskey } from './usePasskey'
 export { useTheme } from './useTheme'
 export { useToast } from './useToast'
 export { usePlatformContext } from './usePlatformContext'
@@ -32,11 +30,6 @@ export {
   type FieldState,
   type UseFormReturn,
 } from './useForm'
-export {
-  useWellPlateEditor,
-  type UseWellPlateEditorOptions,
-  type UseWellPlateEditorReturn,
-} from './useWellPlateEditor'
 export {
   useConcentrationUnits,
   type ConcentrationValue,

package/src/composables/useAutoGroup.ts

@@ -62,7 +62,7 @@ export { parseCSV } from './autoGroup/csv-shim'
 /**
  * Sample-grouping engine behind `AutoGroupModal`.
  *
- * @deprecated Scheduled for removal in MINT 1.4; use `SmartGroupModal` instead.
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
  */
 export function useAutoGroup() {
   const inputMode = ref<InputMode>('paste')

package/src/composables/useBioTemplateComponents.ts

@@ -67,14 +67,22 @@ export interface UseBioTemplateComponentsReturn {
   ) => Record<string, unknown> | undefined
 }
 
-/** Return component props grouped by SDK component name for direct WellPlate/DoseCalculator binding. */
+/**
+ * Return component props grouped by SDK component name for direct WellPlate/DoseCalculator binding.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function toBioTemplateComponentPropsByComponent(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
 ): BioTemplateComponentPropsByComponent {
   return toTemplateComponentPropsByComponent(target)
 }
 
-/** Return the first props object for an SDK component, optionally restricted by template id or binding id. */
+/**
+ * Return the first props object for an SDK component, optionally restricted by template id or binding id.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function getBioTemplateComponentProps(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
   component: string,
@@ -83,7 +91,11 @@ export function getBioTemplateComponentProps(
   return getTemplateComponentProps(target, component, options)
 }
 
-/** Map built-in biology templates to SDK components such as WellPlate, DataFrame, DoseCalculator, and PlateEditor. */
+/**
+ * Map built-in biology templates to SDK components such as WellPlate, DataFrame, DoseCalculator, and PlateEditor.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useBioTemplateComponents(
   target: BioTemplateComponentTarget
 ): UseBioTemplateComponentsReturn {

package/src/composables/useBioTemplateControls.ts

@@ -21,7 +21,11 @@ export type {
   BioTemplateControlTarget,
 }
 
-/** Build FormBuilder schema, AppSidebar panels, and defaults for a built-in biology template or preset. */
+/**
+ * Build FormBuilder schema, AppSidebar panels, and defaults for a built-in biology template or preset.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useBioTemplateControls(
   target: BioTemplateControlTarget,
   options: ControlWorkspaceOptions = {},

package/src/composables/useBioTemplatePackWorkspace.ts

@@ -90,6 +90,8 @@ export interface UseBioTemplatePackWorkspaceReturn {
  * const pack = useBioTemplatePackWorkspace('cell-culture-screen')
  * await pack.loadCurrent()
  * ```
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
  */
 export function useBioTemplatePackWorkspace(
   packId: TemplatePackId | string,

package/src/composables/useBioTemplatePresetWorkspace.ts

@@ -119,7 +119,11 @@ export interface BioTemplatePresetWorkspaceBindings {
   getComponentProps: UseBioTemplateWorkspaceReturn['getComponentProps']
 }
 
-/** Create a complete editable WellPlate/DoseCalculator workspace for dose design from a built-in biology template preset with current-experiment save wiring. */
+/**
+ * Create a complete editable WellPlate/DoseCalculator workspace for dose design from a built-in biology template preset with current-experiment save wiring.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useBioTemplatePresetWorkspace(
   presetId: TemplatePresetId,
   options: UseBioTemplatePresetWorkspaceOptions = {},

package/src/composables/useBioTemplateWorkspace.ts

@@ -60,7 +60,11 @@ export interface UseBioTemplateWorkspaceReturn extends BioTemplateWorkspaceCompo
   renderer: BioTemplateRendererBinding | null
 }
 
-/** One-stop wiring for BioTemplateRenderer, FormBuilder, AppSidebar, and template-aware SDK components. */
+/**
+ * One-stop wiring for BioTemplateRenderer, FormBuilder, AppSidebar, and template-aware SDK components.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useBioTemplateWorkspace(
   target: BioTemplateWorkspaceTarget,
   options: ControlWorkspaceOptions = {}

package/src/composables/useExperimentSave.ts

@@ -86,7 +86,11 @@ export interface UseExperimentSaveReturn {
   requireCurrentExperimentId: () => number
 }
 
-/** Persists experiment design, analysis, and built-in template preset data through the platform API. */
+/**
+ * Persists experiment design, analysis, and built-in template preset data through the platform API.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useExperimentSave(
   options: UseExperimentSaveOptions = {},
 ): UseExperimentSaveReturn {

package/src/composables/useGroupAssignment.ts

@@ -37,7 +37,11 @@ export interface UseGroupAssignmentReturn {
   clearAll: () => GroupAssignmentState
 }
 
-/** Shared two-zone group assignment model for control/treatment style workflows. */
+/**
+ * Shared two-zone group assignment model for control/treatment style workflows.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useGroupAssignment(options: UseGroupAssignmentOptions): UseGroupAssignmentReturn {
   const groups = computed(() => [...toValue(options.groups)])
   const group1 = computed(() => [...toValue(options.group1)])

package/src/composables/useTemplateCollection.ts

@@ -72,7 +72,11 @@ export interface UseTemplateCollectionReturn {
   requireCurrentExperimentId: () => number
 }
 
-/** Manages a biology template collection in the current experiment's design_data. */
+/**
+ * Manages a biology template collection in the current experiment's design_data.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useTemplateCollection(
   options: UseTemplateCollectionOptions = {},
 ): UseTemplateCollectionReturn {

package/src/index.ts

@@ -34,7 +34,7 @@ export * from './jobs'
 // Experimental generated analysis workspace
 export * from './generated/schema'
 
-// LCMS sequence helpers. Deprecated: scheduled for removal in MINT 1.4 (moves to the mld-ms plugins).
+// LCMS sequence helpers. Deprecated: scheduled for removal in MINT 1.4, no SDK replacement.
 export * from './lcms'
 
 // Utils

package/src/lcms.ts

@@ -1,11 +1,11 @@
 import type { LcmsPlateCell, LcmsPlateType } from './utils/rack'
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export type LcmsPolarity = 'POS' | 'NEG' | 'BOTH'
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export type LcmsContainerType = 'VIAL' | 'PLATE'
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export interface LcmsSequenceItem {
   sample_type: string
   file_name: string
@@ -16,14 +16,14 @@ export interface LcmsSequenceItem {
   injection_volume: number
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export interface LcmsSequenceTableColumn {
   key: keyof LcmsSequenceItem | 'index' | 'actions'
   label: string
   align?: 'left' | 'right'
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export const DEFAULT_LCMS_SEQUENCE_COLUMNS: LcmsSequenceTableColumn[] = [
   { key: 'index', label: '#' },
   { key: 'sample_type', label: 'Type' },
@@ -33,7 +33,7 @@ export const DEFAULT_LCMS_SEQUENCE_COLUMNS: LcmsSequenceTableColumn[] = [
   { key: 'injection_volume', label: 'Inj Vol', align: 'right' },
 ]
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
   if (fileNames.length === 0) return ''
   const stripped = fileNames.map(fileName => fileName.replace(/_\d{3}$/, ''))
@@ -52,7 +52,7 @@ export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
   return common
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function extractLcmsSampleName(fileName: string, prefix = ''): string {
   let name = fileName.replace(/_\d{3}$/, '')
   if (prefix && name.startsWith(prefix)) {
@@ -62,12 +62,12 @@ export function extractLcmsSampleName(fileName: string, prefix = ''): string {
   return name || fileName
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function lcmsWellIdFromPosition(position: string): string {
   return position.includes(':') ? position.split(':').pop() ?? position : position
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsPlateType | null {
   let maxCol = 0
   let maxRow = 0
@@ -81,7 +81,7 @@ export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsP
   return maxCol <= 9 && maxRow <= 6 ? '54vial' : '96well'
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function reconstructLcmsPlateCellsFromSequenceItems(
   items: readonly LcmsSequenceItem[],
 ): { cells: LcmsPlateCell[]; plateType: LcmsPlateType } | null {
@@ -112,7 +112,7 @@ export function reconstructLcmsPlateCellsFromSequenceItems(
   return { cells, plateType }
 }
 
-/** @deprecated Scheduled for removal in MINT 1.4; LC-MS helpers move to the mld-ms plugins. */
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function basenameFromWindowsPath(path: string | null | undefined): string {
   if (!path) return ''
   return path.split(/[\\/]/).pop() ?? path

package/src/styles/components/app-top-bar.css

@@ -39,29 +39,18 @@
   flex-shrink: 0;
 }
 
+/* Slotted logos sized above 32px shrink to fit instead of turning into a 32x36 tile. */
+.mint-topbar__identity > * {
+  max-width: 100%;
+  max-height: 100%;
+}
+
 /* The 36px plugin tile would push the bar past 52px; the bar uses the 32px control height. */
 .mint-topbar__identity .mint-plugin-icon--topbar {
   width: 2rem;
   height: 2rem;
 }
 
-/* Integrated: the tile joins the static identity as a 20px mark (icon + name + version). */
-.mint-topbar__brand:has(+ .mint-topbar__plugin-identity) .mint-topbar__identity {
-  width: auto;
-  padding-left: 0.125rem;
-}
-
-.mint-topbar__brand:has(+ .mint-topbar__plugin-identity) .mint-plugin-icon--topbar {
-  width: 1.25rem;
-  height: 1.25rem;
-  border-radius: var(--radius-sm);
-}
-
-.mint-topbar__brand:has(+ .mint-topbar__plugin-identity) .mint-plugin-icon--topbar :is(.mint-plugin-icon__svg, .mint-plugin-icon__img) {
-  width: 0.75rem;
-  height: 0.75rem;
-}
-
 /* Centered section — absolute so asymmetric left/right weight never shifts the
    pill-nav off the topbar midline. Pointer-events: none lets the pill-nav
    overlay the background while remaining interactive via its own children. */
@@ -118,7 +107,7 @@
   color: var(--text-primary);
 }
 
-/* Static plugin identity: name + mono version, not a control (5a) */
+/* Static plugin identity: name only, not a control (5a) */
 .mint-topbar__plugin-identity {
   display: inline-flex;
   align-items: baseline;
@@ -136,19 +125,6 @@
   text-overflow: ellipsis;
 }
 
-.mint-topbar__plugin-version {
-  font-family: var(--font-mono);
-  font-size: 0.6875rem;
-  color: var(--text-secondary);
-}
-
-.mint-topbar__divider {
-  width: 1px;
-  height: 1.25rem;
-  flex-shrink: 0;
-  background-color: var(--border-color);
-}
-
 /* Variant: card - inline card with margins and rounded corners */
 .mint-topbar--card {
   width: calc(100% - 2rem);

package/src/styles/components/empty-state.css

@@ -115,8 +115,9 @@
   color: var(--text-muted);
 }
 
-/* Action */
-.mint-empty-state--illustrated .mint-empty-state__action {
+/* Action — slotted content sits in a block so a child's own larger top margin collapses into this one. */
+.mint-empty-state--illustrated .mint-empty-state__action,
+.mint-empty-state--illustrated .mint-empty-state__content {
   margin-top: 0.625rem;
 }