@morscherlab/mint-sdk 1.2.10 → 1.3.0-beta.10

package/src/styles/variables.css

@@ -9,6 +9,24 @@
    CSS Variables - Light Mode
    ========================================================================== */
 :root {
+  /* Shared control values (SDK control refresh, 2026-09-25) — private aliases,
+     not new colors. Declared here: `html.dark` is the same element as
+     `:root`, so the var() references resolve against the dark palette too
+     (only the ink aliases need a dark value of their own).
+     Two focus rules only (never as `outline` — --focus-ring* are box-shadows):
+     - Field focus (input, select, textarea, popover triggers):
+         border-color: var(--color-primary); box-shadow: var(--focus-ring-soft);
+     - Pressable focus (buttons, checkbox, radio, toggle, slider thumb, chips):
+         box-shadow: var(--focus-ring-offset); */
+  /* Strong control border — unchecked checkbox/radio, toggle off track, dashed outlines (~3.2:1 light, ~4.2:1 dark). */
+  --_control-border-strong: color-mix(in srgb, var(--text-secondary) 75%, var(--border-color));
+  /* Field border on hover. */
+  --_field-border-hover: color-mix(in srgb, var(--text-secondary) 60%, var(--border-color));
+  /* Ink: primary / error text on card and tinted surfaces. The -hover tokens
+     have no dark value, so html.dark lifts these toward --text-primary. */
+  --_ink-primary: var(--color-primary-hover);
+  --_ink-error: var(--mint-error-hover);
+
   /* Background colors */
   --bg-primary: #F8FAFC;
   --bg-secondary: #FFFFFF;
@@ -89,7 +107,8 @@
   /* Motion — the SDK's standard easing curve. */
   --mint-ease-out-quart: cubic-bezier(0.25, 1, 0.5, 1);
 
-  /* Typography — Fira Code for data, code and routes. */
+  /* Typography — Fira Sans for UI text, Fira Code for data, code and routes. */
+  --font-sans: 'Fira Sans', system-ui, -apple-system, sans-serif;
   --font-mono: 'Fira Code', ui-monospace, SFMono-Regular, Menlo, monospace;
 
   /* Border radius */
@@ -172,6 +191,10 @@ html.dark {
   --border-color: #334155;
   --border-light: #1E293B;
 
+  /* Ink aliases (see :root): ~7:1 on --bg-card, tints included. */
+  --_ink-primary: color-mix(in srgb, var(--color-primary) 50%, var(--text-primary));
+  --_ink-error: color-mix(in srgb, var(--mint-error) 50%, var(--text-primary));
+
   /* Text colors */
   --text-primary: #F8FAFC;
   --text-secondary: #94A3B8;
@@ -225,7 +248,7 @@ html.dark {
    Base Styles
    ========================================================================== */
 html {
-  font-family: 'Fira Sans', system-ui, sans-serif;
+  font-family: var(--font-sans);
 }
 
 body {
@@ -236,7 +259,14 @@ body {
 }
 
 code, pre {
-  font-family: 'Fira Code', monospace;
+  font-family: var(--font-mono);
+}
+
+/* Native controls do not inherit the page font; Tailwind preflight covers this
+   in the platform, but SDK consumers without it render buttons and selects in
+   the UA font. */
+button, input, select, textarea {
+  font-family: inherit;
 }
 
 /* ==========================================================================
@@ -449,8 +479,6 @@ code, pre {
   display: block;
   font-size: 0.6875rem;
   font-weight: 500;
-  text-transform: uppercase;
-  letter-spacing: 0.05em;
   color: var(--text-secondary);
   margin-bottom: 0.375rem;
 }
@@ -600,9 +628,9 @@ code, pre {
 }
 
 .alert-info {
-  background-color: rgba(59, 130, 246, 0.1);
+  background-color: var(--mint-info-bg);
   color: #3B82F6;
-  border: 1px solid rgba(59, 130, 246, 0.2);
+  border: 1px solid var(--mint-info-border);
 }
 
 /* ==========================================================================

package/src/templates/adapters.ts

@@ -62,6 +62,8 @@ export {
   toWellPlateWells,
 } from './plateMapAdapters'
 
+export { racksFromPlateState } from './componentPlateHelpers'
+
 export {
   toProtocolColumns,
   toProtocolDataFrame,
@@ -103,6 +105,7 @@ export {
   toTimeCourseSteps,
 } from './timeCourseAdapters'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toTemplateDataFrame(
   template: DataFrameTemplate | BioTemplateEnvelope<unknown>
 ): TemplateDataFrameAdapterResult {
@@ -132,6 +135,7 @@ export function toTemplateDataFrame(
   }
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toWellMapArray(wells: Record<string, Well>): Well[] {
   return Object.values(wells)
 }

package/src/templates/assayMatrixAdapters.ts

@@ -10,6 +10,7 @@ import type {
   AssayMatrixTemplateData,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toAssayMatrixRows(
   template: AssayMatrixTemplate | AssayMatrixTemplateData
 ): AssayMatrixRowsAdapterResult {
@@ -36,6 +37,7 @@ export function toAssayMatrixRows(
   })
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toAssayMatrixColumns(
   template: AssayMatrixTemplate | AssayMatrixTemplateData
 ): AssayMatrixColumnsAdapterResult {
@@ -54,6 +56,7 @@ export function toAssayMatrixColumns(
   ]
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toAssayMatrixDataFrame(
   template: AssayMatrixTemplate | AssayMatrixTemplateData
 ): AssayMatrixDataFrameAdapterResult {
@@ -64,7 +67,11 @@ export function toAssayMatrixDataFrame(
   }
 }
 
-/** Convert an assay-matrix template into SampleSelector options derived from assay samples. */
+/**
+ * Convert an assay-matrix template into SampleSelector options derived from assay samples.
+ *
+ * @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function toAssayMatrixSampleOptions(
   template: AssayMatrixTemplate | AssayMatrixTemplateData
 ): AssayMatrixSampleOptionsAdapterResult {

package/src/templates/assayMatrixBuilder.ts

@@ -17,6 +17,7 @@ import type {
   CreateAssayMatrixTemplateOptions,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createAssayMatrixTemplate(
   options: CreateAssayMatrixTemplateOptions
 ): AssayMatrixTemplate {

package/src/templates/builderPresetControls.ts

@@ -24,6 +24,7 @@ import type {
 
 export type BioTemplateControlValues = Record<string, unknown>
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function bioTemplatePresetControlValuesToOptions(
   name: 'wellplate-screen',
   values: BioTemplateControlValues

package/src/templates/calibrationCurveAdapters.ts

@@ -8,6 +8,7 @@ import type {
   CalibrationCurveTemplateData,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toCalibrationCurveRows(
   template: CalibrationCurveTemplate | CalibrationCurveTemplateData
 ): CalibrationCurveRowsAdapterResult {
@@ -33,6 +34,7 @@ export function toCalibrationCurveRows(
     }))
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toCalibrationCurveColumns(): CalibrationCurveColumnsAdapterResult {
   return [
     { key: 'order', label: 'Order', sortable: true, align: 'right' },
@@ -48,6 +50,7 @@ export function toCalibrationCurveColumns(): CalibrationCurveColumnsAdapterResul
   ]
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toCalibrationCurveDataFrame(
   template: CalibrationCurveTemplate | CalibrationCurveTemplateData
 ): CalibrationCurveDataFrameAdapterResult {

package/src/templates/calibrationCurveBuilder.ts

@@ -12,6 +12,7 @@ import type {
   CreateCalibrationCurveTemplateOptions,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createCalibrationCurveTemplate(
   options: CreateCalibrationCurveTemplateOptions
 ): CalibrationCurveTemplate {

package/src/templates/catalog.ts

@@ -18,6 +18,7 @@ export interface BioTemplateCatalogEntry {
   add_command: string
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export const bioTemplateCatalog = [
   {
     name: 'plate-map',
@@ -31,7 +32,7 @@ export const bioTemplateCatalog = [
     python_example: 'PlateMapTemplate.create_96_well(name="Plate 1", samples=["Control", "Treatment"])',
     frontend_import: "import { toPlateMapEditorState, toWellPlateWells } from '@morscherlab/mint-sdk/templates'",
     frontend_adapters: ['toPlateMapEditorState', 'toWellPlateWells'],
-    components: ['PlateMapEditor', 'WellPlate', 'SampleLegend'],
+    components: ['PlateEditor', 'WellPlate', 'SampleLegend'],
     add_command: 'mint add data-template plate-map --page',
   },
   {
@@ -46,7 +47,7 @@ export const bioTemplateCatalog = [
     python_example: 'SampleSheetTemplate.from_rows([{"sample_id": "S001", "name": "Control 1", "group": "Control"}])',
     frontend_import: "import { toTemplateDataFrame, toSampleOptions } from '@morscherlab/mint-sdk/templates'",
     frontend_adapters: ['toTemplateDataFrame', 'toSampleDataFrame', 'toSampleRows', 'toSampleColumns', 'toSampleOptions'],
-    components: ['DataFrame', 'SampleSelector', 'AutoGroupModal', 'GroupAssigner'],
+    components: ['DataFrame', 'SampleSelector', 'GroupAssigner'],
     add_command: 'mint add data-template sample-sheet --page',
   },
   {
@@ -209,10 +210,12 @@ export const bioTemplateCatalog = [
   },
 ] as const satisfies readonly BioTemplateCatalogEntry[]
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function listBioTemplateCatalog(): readonly BioTemplateCatalogEntry[] {
   return bioTemplateCatalog
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function getBioTemplateInfo(name: string): BioTemplateCatalogEntry | undefined {
   return bioTemplateCatalog.find(entry => {
     const identifiers = [
@@ -225,6 +228,7 @@ export function getBioTemplateInfo(name: string): BioTemplateCatalogEntry | unde
   })
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function searchBioTemplateCatalog(query: string): readonly BioTemplateCatalogEntry[] {
   const normalized = query.trim().toLowerCase()
   if (!normalized) return bioTemplateCatalog

package/src/templates/componentBindingCatalog.ts

@@ -12,7 +12,7 @@ interface ComponentBinding {
 
 export const templateComponentBindings = {
   'plate-map': [
-    binding('plate-map', 'PlateMapEditor', ['toPlateMapEditorState'], ['modelValue', 'format', 'samples'], 'Edit plate layouts from plate-map template data.'),
+    binding('plate-map', 'PlateEditor', ['toPlateMapEditorState', 'racksFromPlateState'], ['modelValue', 'activeRackId', 'groups', 'formats', 'wellFields'], 'Edit plate layouts and assign sample groups from plate-map template data.'),
     binding('plate-map', 'WellPlate', ['toWellPlateWells'], ['format', 'wells', 'sampleColors', 'legendItems'], 'Render the active plate as a well grid.'),
   ],
   'sample-sheet': [

package/src/templates/componentBindings.ts

@@ -91,10 +91,12 @@ export interface BioTemplateComponentUsage {
   sfc: string
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function listBioTemplateComponentBindings(): Record<TemplateId, BioTemplateComponentBinding[]> {
   return cloneBindingMap(templateComponentBindings)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function getBioTemplateComponentBindings(
   target: BioTemplateComponentTarget
 ): BioTemplateComponentBinding[] {
@@ -102,6 +104,7 @@ export function getBioTemplateComponentBindings(
   return templateIds.flatMap(templateId => cloneBindings(templateComponentBindings[templateId]))
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toBioTemplateComponentProps(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope
 ): BioTemplateComponentPropsBinding[] {
@@ -113,14 +116,22 @@ export function toBioTemplateComponentProps(
   return Object.values(collection).flatMap(template => propsForTemplate(template))
 }
 
-/** Return resolved component bindings with concrete props for direct slot rendering. */
+/**
+ * Return resolved component bindings with concrete props for direct slot rendering.
+ *
+ * @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function toBioTemplateComponentBindings(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
 ): BioTemplateResolvedComponentBinding[] {
   return toBioTemplateComponentProps(target).map(toResolvedComponentBinding)
 }
 
-/** Return resolved component bindings keyed by stable template component id. */
+/**
+ * Return resolved component bindings keyed by stable template component id.
+ *
+ * @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function toBioTemplateComponentBindingsById(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
 ): BioTemplateComponentBindingsById {
@@ -129,7 +140,11 @@ export function toBioTemplateComponentBindingsById(
   )
 }
 
-/** Return component props keyed by stable binding id for direct `v-bind="componentPropsById[id]"` use. */
+/**
+ * Return component props keyed by stable binding id for direct `v-bind="componentPropsById[id]"` use.
+ *
+ * @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function toBioTemplateComponentPropsById(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
 ): BioTemplateComponentPropsById {
@@ -138,7 +153,11 @@ export function toBioTemplateComponentPropsById(
   )
 }
 
-/** 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 from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function toBioTemplateComponentPropsByComponent(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
 ): BioTemplateComponentPropsByComponent {
@@ -151,7 +170,11 @@ export function toBioTemplateComponentPropsByComponent(
   return grouped
 }
 
-/** 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 from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
 export function getBioTemplateComponentProps(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
   component: string,
@@ -177,6 +200,7 @@ function toResolvedComponentBinding(
   }
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toBioTemplateComponentImports(
   target: BioTemplateComponentTarget
 ): BioTemplateComponentImport[] {
@@ -195,6 +219,7 @@ export function toBioTemplateComponentImports(
   }))
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toBioTemplateComponentSnippets(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
   options: BioTemplateComponentSnippetOptions = {}
@@ -214,6 +239,7 @@ export function toBioTemplateComponentSnippets(
   })
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toBioTemplateComponentUsage(
   target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,
   options: BioTemplateComponentUsageOptions = {}

package/src/templates/componentDoseResponseProps.ts

@@ -34,7 +34,6 @@ export function doseResponseProps(template: DoseResponseTemplate): BioTemplateCo
         color: condition.color,
       })),
       showLegend: true,
-      showSampleTypeIndicator: true,
     }))
   }
 

package/src/templates/componentPlateHelpers.ts

@@ -1,8 +1,10 @@
 import type {
   PlateMapEditorState,
+  Rack,
+  Well,
   WellLegendItem,
 } from '../types'
-import { SAMPLE_COLOR_SCALE } from '../utils/color'
+import { SAMPLE_COLOR_SCALE, SLOT_ORDER } from '../utils/color'
 
 export function activePlateFromState(state: PlateMapEditorState) {
   return state.plates.find(plate => plate.id === state.activePlateId) ?? state.plates[0]
@@ -29,3 +31,22 @@ export function colorForIndex(index: number): string {
   const colors = SAMPLE_COLOR_SCALE.slice(0, 8)
   return colors[index % colors.length]
 }
+
+/**
+ * Plates as PlateEditor racks: slots assigned in order, a well's sample id moved to its group (the stored
+ * plate map keeps it in `sampleType`). Plate maps carry no injection volume.
+ * @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins.
+ */
+export function racksFromPlateState(state: PlateMapEditorState): Rack[] {
+  const sampleIds = new Set(state.samples.map(sample => sample.id))
+  const asRackWell = (well: Well): Partial<Well> =>
+    well.sampleType && sampleIds.has(well.sampleType) ? { ...well, sampleType: 'sample', group: well.sampleType } : well
+  return state.plates.map((plate, index) => ({
+    id: plate.id,
+    name: plate.name,
+    format: plate.format,
+    slot: SLOT_ORDER[index % SLOT_ORDER.length],
+    injectionVolume: 0,
+    wells: Object.fromEntries(Object.entries(plate.wells).map(([id, well]) => [id, asRackWell(well)])),
+  }))
+}

package/src/templates/componentPlateMapProps.ts

@@ -5,6 +5,7 @@ import {
 import {
   activePlateFromState,
   legendItemsFromPlateState,
+  racksFromPlateState,
   sampleColorsFromPlateState,
 } from './componentPlateHelpers'
 import { propsBinding } from './componentPropsFactory'
@@ -15,10 +16,12 @@ export function plateMapProps(template: PlateMapTemplate): BioTemplateComponentP
   const state = toPlateMapEditorState(template)
   const plate = activePlateFromState(state)
   return [
-    propsBinding('plate-map', 'PlateMapEditor', {
-      modelValue: state,
-      format: plate.format,
-      samples: state.samples,
+    propsBinding('plate-map', 'PlateEditor', {
+      modelValue: racksFromPlateState(state),
+      activeRackId: plate.id,
+      groups: state.samples,
+      formats: [plate.format],
+      wellFields: false,
     }),
     propsBinding('plate-map', 'WellPlate', {
       format: plate.format,
@@ -26,7 +29,6 @@ export function plateMapProps(template: PlateMapTemplate): BioTemplateComponentP
       sampleColors: sampleColorsFromPlateState(state),
       legendItems: legendItemsFromPlateState(state),
       showLegend: true,
-      showSampleTypeIndicator: true,
     }),
   ]
 }

package/src/templates/componentQpcrPlateProps.ts

@@ -21,7 +21,6 @@ export function qpcrPlateProps(template: QpcrPlateTemplate): BioTemplateComponen
         color: colorForIndex(index),
       })),
       showLegend: true,
-      showSampleTypeIndicator: true,
     }),
     frame,
   ]

package/src/templates/controlSchemas.ts

@@ -38,14 +38,17 @@ export type {
   BioTemplateControlTarget,
 } from './controlSchemaTypes'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function listBioTemplateControlSchemas(): Record<TemplateId, BioTemplateControlSchema> {
   return cloneSchemaMap(templateControlSchemas)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function listBioTemplatePresetControlSchemas(): Record<TemplatePresetId, BioTemplateControlSchema> {
   return cloneSchemaMap(presetControlSchemas)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function getBioTemplateControlSchema(
   target: BioTemplateControlTarget
 ): BioTemplateControlSchema | undefined {
@@ -61,6 +64,7 @@ export function getBioTemplateControlSchema(
   return mergeTemplateControlSchemas(resolved.templates, templateControlSchemas)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function requireBioTemplateControlSchema(
   target: BioTemplateControlTarget
 ): BioTemplateControlSchema {
@@ -71,6 +75,7 @@ export function requireBioTemplateControlSchema(
   return schema
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createBioTemplateControlToolkit(
   target: BioTemplateControlTarget,
   options: ControlSchemaOptions = {}
@@ -78,6 +83,7 @@ export function createBioTemplateControlToolkit(
   return useControlSchema(requireBioTemplateControlSchema(target), options)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function bioTemplateControlsToFormSchema(
   target: BioTemplateControlTarget,
   options: ControlSchemaOptions = {}
@@ -85,6 +91,7 @@ export function bioTemplateControlsToFormSchema(
   return controlsToFormSchema(requireBioTemplateControlSchema(target), options)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function bioTemplateControlsToSidebarPanels(
   target: BioTemplateControlTarget,
   options: ControlSchemaOptions = {}
@@ -92,6 +99,7 @@ export function bioTemplateControlsToSidebarPanels(
   return controlsToSidebarPanels(requireBioTemplateControlSchema(target), options)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function bioTemplateControlsToSectionFormSchemas(
   target: BioTemplateControlTarget,
   options: ControlSchemaOptions = {}
@@ -99,6 +107,7 @@ export function bioTemplateControlsToSectionFormSchemas(
   return controlsToSectionFormSchemas(requireBioTemplateControlSchema(target), options)
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function getBioTemplateControlDefaults(target: BioTemplateControlTarget) {
   return getControlDefaults(requireBioTemplateControlSchema(target))
 }

package/src/templates/defaultBioTemplateBuilder.ts

@@ -16,6 +16,7 @@ import type {
   TemplateId,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createDefaultBioTemplate(templateId: TemplateId | string): BioTemplateEnvelope<unknown> {
   const template = getBioTemplateInfo(templateId)
   if (!template) {

package/src/templates/doseResponseAdapters.ts

@@ -12,6 +12,7 @@ import type {
   DoseResponseTemplateData,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toDoseConditions(
   template: DoseResponseTemplate | DoseResponseTemplateData
 ): DoseConditionsAdapterResult {
@@ -25,6 +26,7 @@ export function toDoseConditions(
   }))
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toDoseLayoutState(
   template: DoseResponseTemplate | DoseResponseTemplateData
 ): PlateMapEditorState | undefined {

package/src/templates/doseResponseBuilder.ts

@@ -15,6 +15,7 @@ import type {
   PlateMapTemplateData,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createDoseResponseTemplate(
   options: CreateDoseResponseTemplateOptions
 ): DoseResponseTemplate {

package/src/templates/elisaAssayCollectionBuilder.ts

@@ -11,6 +11,7 @@ import type {
   TemplateCollectionEnvelope,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createElisaAssayCollection(
   options: CreateElisaAssayCollectionOptions = {}
 ): TemplateCollectionEnvelope {

package/src/templates/flowCytometryAssayCollectionBuilder.ts

@@ -8,6 +8,7 @@ import type {
   TemplateCollectionEnvelope,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createFlowCytometryAssayCollection(
   options: CreateFlowCytometryAssayCollectionOptions = {}
 ): TemplateCollectionEnvelope {

package/src/templates/flowCytometryPanelBuilder.ts

@@ -14,6 +14,7 @@ import type {
   FlowPanelMarker,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function createFlowCytometryPanelTemplate(
   options: CreateFlowCytometryPanelTemplateOptions
 ): FlowCytometryPanelTemplate {

package/src/templates/flowPanelAdapters.ts

@@ -8,6 +8,7 @@ import type {
   FlowPanelRowsAdapterResult,
 } from './types'
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toFlowPanelRows(
   template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData
 ): FlowPanelRowsAdapterResult {
@@ -34,6 +35,7 @@ export function toFlowPanelRows(
   })
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toFlowPanelColumns(): FlowPanelColumnsAdapterResult {
   return [
     { key: 'marker', label: 'Marker', sortable: true },
@@ -47,6 +49,7 @@ export function toFlowPanelColumns(): FlowPanelColumnsAdapterResult {
   ]
 }
 
+/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
 export function toFlowPanelDataFrame(
   template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData
 ): FlowPanelDataFrameAdapterResult {

package/src/templates/index.ts

@@ -1,3 +1,6 @@
+// Biology data templates. Deprecated for removal from the core SDK in MINT 1.4:
+// the @deprecated tags sit on each declaration, because TypeScript ignores them
+// on `export { ... } from` blocks.
 export {
   assertTemplateEnvelope,
   bioTemplatePresetControlValuesToOptions,
@@ -121,6 +124,7 @@ export {
   toInstrumentRunRows,
   toInstrumentRunScheduleEvents,
   toInstrumentRunSteps,
+  racksFromPlateState,
   toPlateMapEditorState,
   toProtocolColumns,
   toProtocolDataFrame,