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

package/src/composables/useRackEditor.ts

@@ -1,6 +1,6 @@
-import { ref, computed, type Ref, type ComputedRef } from 'vue'
-import type { Rack, SlotPosition, WellPlateFormat, Well } from '../types'
-import { PLATE_CONFIGS, rowLabel as plateRowLabel } from '../components/WellPlate.geometry'
+import { ref, computed, watch, type Ref, type ComputedRef } from 'vue'
+import type { Rack, SlotPosition, WellEditData, WellPlateFormat, WellSampleDropData, Well } from '../types'
+import { PLATE_CONFIGS, rowIndex, rowLabel as plateRowLabel } from '../components/WellPlate.geometry'
 
 export interface UseRackEditorOptions {
   defaultFormat?: WellPlateFormat
@@ -24,14 +24,82 @@ export interface UseRackEditorReturn {
   clearWell(rackId: string, wellId: string): void
   clearAllWells(rackId: string): void
   fillSeries(rackId: string, prefix?: string): void
+  /** Swaps two wells (a move when the target is empty). */
+  moveWell(rackId: string, sourceWellId: string, targetWellId: string): void
+  /** Puts every well in group `groupId` (an empty well becomes a sample); `undefined` empties them. */
+  assignWells(rackId: string, wellIds: string[], groupId: string | undefined): void
+
+  /**
+   * Applies every PlateEditor intent to this state, so the component can hold
+   * data it never mutates itself:
+   * `<PlateEditor :model-value="racks" :active-rack-id="activeRackId" v-on="plateEditorListeners" />`
+   */
+  plateEditorListeners: PlateEditorListeners
+
+  /** Steps back through every change to `racks` (at most 50), restoring the plate that was showing. */
+  undo(): void
+  redo(): void
+  canUndo: ComputedRef<boolean>
+  canRedo: ComputedRef<boolean>
+  /** Forgets every undo and redo step, e.g. after loading unrelated plates. */
+  clearHistory(): void
 
   getAllWells(): Array<{ rackId: string; wellId: string; well: Partial<Well> }>
   totalSampleCount: ComputedRef<number>
   reset(): void
 }
 
+/** Handlers for PlateEditor's intent events, keyed by event name (bind with `v-on`). */
+export interface PlateEditorListeners {
+  'update:activeRackId': (rackId: string) => void
+  'rack-add': () => void
+  'rack-remove': (rackId: string) => void
+  'rack-reorder': (rackIds: string[]) => void
+  'update:format': (rackId: string, format: WellPlateFormat) => void
+  'update:slot': (rackId: string, slot: SlotPosition) => void
+  'well-edit': (rackId: string, wellId: string, data: WellEditData) => void
+  'well-clear': (rackId: string, wellId: string) => void
+  'well-move': (rackId: string, sourceWellId: string, targetWellId: string) => void
+  'sample-drop': (rackId: string, wellId: string, data: WellSampleDropData, event: DragEvent) => void
+  'assign': (rackId: string, wellIds: string[], groupId: string | undefined) => void
+  'clear': (rackId: string) => void
+  'fill-series': (rackId: string) => void
+  'undo': () => void
+  'redo': () => void
+}
+
+const HISTORY_LIMIT = 50
+
 const SLOT_CYCLE: SlotPosition[] = ['R', 'G', 'B', 'Y']
 
+function wellFromEditData(data: WellEditData): Partial<Well> {
+  return {
+    state: 'filled',
+    sampleType: data.sampleType || undefined,
+    metadata: {
+      label: data.label,
+      injectionVolume: data.injectionVolume,
+      injectionCount: data.injectionCount,
+      customMethod: data.customMethod || null,
+    },
+  }
+}
+
+function wellFromDrop(data: WellSampleDropData, rack: Rack): Partial<Well> | null {
+  const label = (data.label ?? data.sampleName ?? data.id ?? '').trim()
+  if (!label) return null
+  return {
+    state: 'filled',
+    sampleType: data.sampleType ?? 'sample',
+    metadata: {
+      label,
+      injectionVolume: data.injectionVolume ?? rack.injectionVolume,
+      injectionCount: data.injectionCount ?? 1,
+      customMethod: data.customMethod ?? null,
+    },
+  }
+}
+
 
 let globalIdCounter = 0
 
@@ -64,7 +132,7 @@ export function useRackEditor(
 
   const racks = ref<Rack[]>(
     initialRacks && initialRacks.length > 0
-      ? initialRacks.map(r => ({ ...r }))
+      ? initialRacks.map(r => ({ ...r, wells: { ...r.wells } }))
       : [createDefaultRack('Rack 1', 0)]
   ) as Ref<Rack[]>
 
@@ -170,6 +238,118 @@ export function useRackEditor(
     }
   }
 
+  function moveWell(rackId: string, sourceWellId: string, targetWellId: string): void {
+    const rack = racks.value.find(r => r.id === rackId)
+    if (!rack) return
+    const { [sourceWellId]: source, [targetWellId]: target } = rack.wells
+    delete rack.wells[sourceWellId]
+    delete rack.wells[targetWellId]
+    if (target) rack.wells[sourceWellId] = placed(target, sourceWellId)
+    if (source) rack.wells[targetWellId] = placed(source, targetWellId)
+  }
+
+  /** A moved well keeps its position fields in step with its new key. */
+  function placed(well: Partial<Well>, wellId: string): Partial<Well> {
+    if (well.id === undefined) return well
+    const [, row = '', col = ''] = /^([A-Z]+)(\d+)$/.exec(wellId) ?? []
+    return { ...well, id: wellId, row: rowIndex(row), col: Number(col) - 1 }
+  }
+
+  function assignWells(rackId: string, wellIds: string[], groupId: string | undefined): void {
+    const rack = racks.value.find(r => r.id === rackId)
+    for (const wellId of wellIds) {
+      const sampleType = rack?.wells[wellId]?.sampleType ?? 'sample'
+      if (groupId) setWellData(rackId, wellId, { state: 'filled', sampleType, group: groupId })
+      else clearWell(rackId, wellId)
+    }
+  }
+
+  // History: the serialized racks before each change, with the plate that was showing.
+  // Every change counts, not just the intents: each public mutator call is its own step,
+  // and a change made outside them (an import assigning `racks`) becomes one at the next
+  // tick, so undo never skips past it.
+  interface Snapshot { racks: string; activeRackId: string }
+  const undoStack = ref<Snapshot[]>([])
+  const redoStack = ref<Snapshot[]>([])
+  const canUndo = computed(() => undoStack.value.length > 0)
+  const canRedo = computed(() => redoStack.value.length > 0)
+  /** The racks as the history last saw them. */
+  let known = JSON.stringify(racks.value)
+
+  function pushUndo(snapshot: Snapshot): void {
+    undoStack.value = [...undoStack.value, snapshot].slice(-HISTORY_LIMIT)
+    redoStack.value = []
+  }
+
+  /** Records a change made since the history last looked, as its own step. */
+  function absorb(): void {
+    const now = JSON.stringify(racks.value)
+    if (now === known) return
+    pushUndo({ racks: known, activeRackId: activeRackId.value })
+    known = now
+  }
+  watch(racks, absorb, { deep: true })
+
+  function step(from: Ref<Snapshot[]>, to: Ref<Snapshot[]>): void {
+    absorb()
+    const snapshot = from.value.pop()
+    if (snapshot === undefined) return
+    to.value.push({ racks: known, activeRackId: activeRackId.value })
+    racks.value = JSON.parse(snapshot.racks) as Rack[]
+    known = snapshot.racks
+    activeRackId.value = racks.value.some(rack => rack.id === snapshot.activeRackId)
+      ? snapshot.activeRackId
+      : racks.value[0]?.id ?? ''
+  }
+
+  const undo = (): void => step(undoStack, redoStack)
+  const redo = (): void => step(redoStack, undoStack)
+
+  function clearHistory(): void {
+    undoStack.value = []
+    redoStack.value = []
+    known = JSON.stringify(racks.value)
+  }
+
+  /** Runs `apply` and records the prior state when it changed anything. */
+  function recorded<Args extends unknown[], Result>(apply: (...args: Args) => Result) {
+    return (...args: Args): Result => {
+      absorb()
+      const before = { racks: known, activeRackId: activeRackId.value }
+      const result = apply(...args)
+      const after = JSON.stringify(racks.value)
+      if (after !== known) {
+        pushUndo(before)
+        known = after
+      }
+      return result
+    }
+  }
+
+  const plateEditorListeners: PlateEditorListeners = {
+    'update:activeRackId': setActiveRack,
+    'rack-add': recorded(() => { addRack() }),
+    'rack-remove': recorded(removeRack),
+    'rack-reorder': recorded((rackIds: string[]) => {
+      racks.value = rackIds.flatMap(id => racks.value.filter(rack => rack.id === id))
+    }),
+    'update:format': recorded((rackId: string, format: WellPlateFormat) => updateRack(rackId, { format })),
+    'update:slot': recorded((rackId: string, slot: SlotPosition) => updateRack(rackId, { slot })),
+    'well-edit': recorded((rackId: string, wellId: string, data: WellEditData) => setWellData(rackId, wellId, wellFromEditData(data))),
+    'well-clear': recorded(clearWell),
+    'well-move': recorded(moveWell),
+    'sample-drop': recorded((rackId: string, wellId: string, data: WellSampleDropData) => {
+      const rack = racks.value.find(r => r.id === rackId)
+      const well = rack && wellFromDrop(data, rack)
+      if (well) setWellData(rackId, wellId, well)
+    }),
+    'assign': recorded(assignWells),
+    'clear': recorded(clearAllWells),
+    'fill-series': recorded((rackId: string) => fillSeries(rackId)),
+    'undo': undo,
+    'redo': redo,
+  }
+
   function getAllWells(): Array<{ rackId: string; wellId: string; well: Partial<Well> }> {
     const result: Array<{ rackId: string; wellId: string; well: Partial<Well> }> = []
     for (const rack of racks.value) {
@@ -192,21 +372,31 @@ export function useRackEditor(
     const rack = createDefaultRack('Rack 1', 0)
     racks.value = [rack]
     activeRackId.value = rack.id
+    clearHistory()
   }
 
   return {
     racks,
     activeRack,
     activeRackId,
-    addRack,
-    removeRack,
-    reorderRacks,
-    updateRack,
+    // Wrapped here, not at the definitions, so assignWells' inner calls stay one step.
+    addRack: recorded(addRack),
+    removeRack: recorded(removeRack),
+    reorderRacks: recorded(reorderRacks),
+    updateRack: recorded(updateRack),
     setActiveRack,
-    setWellData,
-    clearWell,
-    clearAllWells,
-    fillSeries,
+    setWellData: recorded(setWellData),
+    clearWell: recorded(clearWell),
+    clearAllWells: recorded(clearAllWells),
+    fillSeries: recorded(fillSeries),
+    moveWell: recorded(moveWell),
+    assignWells: recorded(assignWells),
+    plateEditorListeners,
+    undo,
+    redo,
+    canUndo,
+    canRedo,
+    clearHistory,
     getAllWells,
     totalSampleCount,
     reset,

package/src/composables/useSequenceUtils.ts

@@ -6,6 +6,14 @@ export interface SequenceStats {
   molecularWeight?: number
 }
 
+/** What `validateSequence` would strip or flag, so a field can report it instead. */
+export interface SequenceProblems {
+  /** Ambiguous `N` bases (DNA/RNA only; `N` is asparagine in protein). */
+  ambiguousBases: number
+  /** Unique characters outside the alphabet, upper-cased, in order of appearance. Whitespace is ignored. */
+  invalidCharacters: string[]
+}
+
 const DNA_CHARS = /[^ATCGNatcgn]/g
 const RNA_CHARS = /[^AUCGNaucgn]/g
 const PROTEIN_CHARS = /[^ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]/g
@@ -35,8 +43,8 @@ export function useSequenceUtils() {
       return 'rna'
     }
 
-    // If only contains ATCGN characters, it's DNA
-    if (/^[ATCGN]+$/i.test(seq)) {
+    // If its letters are only ATCGN, it's DNA (line breaks, spaces and digits don't count)
+    if (/^[ATCGN]+$/i.test(seq.replace(/[^a-z]/gi, ''))) {
       return 'dna'
     }
 
@@ -58,6 +66,15 @@ export function useSequenceUtils() {
     }
   }
 
+  function findSequenceProblems(seq: string, type: 'dna' | 'rna' | 'protein'): SequenceProblems {
+    const alphabet = { dna: DNA_CHARS, rna: RNA_CHARS, protein: PROTEIN_CHARS }[type]
+    const invalid = seq.replace(/\s/g, '').match(alphabet) ?? []
+    return {
+      ambiguousBases: type === 'protein' ? 0 : (seq.match(/n/gi) ?? []).length,
+      invalidCharacters: [...new Set(invalid.map(ch => ch.toUpperCase()))],
+    }
+  }
+
   function reverseComplement(seq: string, type: 'dna' | 'rna'): string {
     const complementMap = type === 'dna' ? DNA_COMPLEMENT : RNA_COMPLEMENT
 
@@ -98,6 +115,7 @@ export function useSequenceUtils() {
   return {
     detectSequenceType,
     validateSequence,
+    findSequenceProblems,
     reverseComplement,
     calculateStats,
     formatFasta,

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/composables/workspaceRecipes.ts

@@ -88,6 +88,7 @@ export interface DoseDesignWorkspacePassthroughProps {
   subtitle?: string
   topBarVariant?: TopBarVariant
   sidebarWidth?: string
+  /** @deprecated No-op, removed in MINT 1.4. AppSidebar has one look now. */
   sidebarVariant?: 'default' | 'analysis'
   responsiveSidebar?: boolean
   sidebarPosition?: 'left' | 'right'

package/src/index.ts

@@ -25,7 +25,7 @@ export * from './stores'
 // Permissions
 export * from './permissions'
 
-// Instrument monitoring
+// Instrument monitoring. Deprecated: scheduled for removal in MINT 1.4 (moves to the mld-ms plugins).
 export * from './instrument'
 
 // Job state helpers
@@ -34,7 +34,7 @@ export * from './jobs'
 // Experimental generated analysis workspace
 export * from './generated/schema'
 
-// LCMS sequence helpers
+// LCMS sequence helpers. Deprecated: scheduled for removal in MINT 1.4, no SDK replacement.
 export * from './lcms'
 
 // Utils
@@ -60,6 +60,12 @@ export {
   type PluginSecretRef,
   type PluginSecretState,
 } from './utils/pluginSecrets'
+export {
+  sampleTypeMarker,
+  type SampleMarkerType,
+  type SampleTypeMarker,
+} from './utils/sampleTypeMarker'
+export { mintPlotlyTemplate } from './utils/plotlyTemplate'
 export {
   LCMS_DEFAULT_CONTROL_POSITIONS,
   createLcmsControlWellEditData,
@@ -79,7 +85,7 @@ export {
   type LcmsPlateType,
 } from './utils/rack'
 
-// Biology data templates
+// Biology data templates. Deprecated: scheduled for removal from the core SDK in MINT 1.4.
 export * from './templates'
 
 // Types

package/src/instrument.ts

@@ -1,15 +1,18 @@
 import type { SequenceProgress } from './types'
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function sequenceProgressPercent(progress: SequenceProgress | null | undefined): number {
   if (!progress || progress.total_samples <= 0) return 0
   return Math.round(clamp((progress.current_sample / progress.total_samples) * 100, 0, 100))
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function sequenceSamplesRemaining(progress: SequenceProgress | null | undefined): number {
   if (!progress) return 0
   return Math.max(0, progress.total_samples - progress.current_sample)
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function estimateSequenceRemainingSeconds(
   progress: SequenceProgress | null | undefined,
 ): number | null {
@@ -31,6 +34,7 @@ export function estimateSequenceRemainingSeconds(
   return null
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function estimateSequenceFinishDate(
   progress: SequenceProgress | null | undefined,
   now = new Date(),
@@ -45,6 +49,7 @@ export function estimateSequenceFinishDate(
   return new Date(now.getTime() + remaining * 1000)
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function formatSequenceRemaining(progress: SequenceProgress | null | undefined): string | null {
   const remaining = estimateSequenceRemainingSeconds(progress)
   if (remaining == null || remaining <= 0) return null
@@ -58,6 +63,7 @@ export function formatSequenceRemaining(progress: SequenceProgress | null | unde
   return mins > 0 ? `~${hours}h ${mins}m left` : `~${hours}h left`
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; instrument monitor helpers move to the mld-ms plugins. */
 export function formatSequenceEta(
   progress: SequenceProgress | null | undefined,
   locale?: Intl.LocalesArgument,

package/src/lcms.ts

@@ -1,8 +1,11 @@
 import type { LcmsPlateCell, LcmsPlateType } from './utils/rack'
 
+/** @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; no SDK replacement. */
 export type LcmsContainerType = 'VIAL' | 'PLATE'
 
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export interface LcmsSequenceItem {
   sample_type: string
   file_name: string
@@ -13,12 +16,14 @@ export interface LcmsSequenceItem {
   injection_volume: number
 }
 
+/** @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; no SDK replacement. */
 export const DEFAULT_LCMS_SEQUENCE_COLUMNS: LcmsSequenceTableColumn[] = [
   { key: 'index', label: '#' },
   { key: 'sample_type', label: 'Type' },
@@ -28,6 +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; no SDK replacement. */
 export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
   if (fileNames.length === 0) return ''
   const stripped = fileNames.map(fileName => fileName.replace(/_\d{3}$/, ''))
@@ -46,6 +52,7 @@ export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
   return common
 }
 
+/** @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)) {
@@ -55,10 +62,12 @@ export function extractLcmsSampleName(fileName: string, prefix = ''): string {
   return name || fileName
 }
 
+/** @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; no SDK replacement. */
 export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsPlateType | null {
   let maxCol = 0
   let maxRow = 0
@@ -72,6 +81,7 @@ export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsP
   return maxCol <= 9 && maxRow <= 6 ? '54vial' : '96well'
 }
 
+/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
 export function reconstructLcmsPlateCellsFromSequenceItems(
   items: readonly LcmsSequenceItem[],
 ): { cells: LcmsPlateCell[]; plateType: LcmsPlateType } | null {
@@ -102,6 +112,7 @@ export function reconstructLcmsPlateCellsFromSequenceItems(
   return { cells, plateType }
 }
 
+/** @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/permissions.ts

@@ -40,37 +40,9 @@ export interface AccessPolicy {
   plugin?: string
 }
 
-/**
- * An object that carries an access rule.
- *
- * The nested `access` policy is the supported shape. The four flat fields are
- * the pre-1.2 spelling of the same four `AccessPolicy` fields; they still work
- * but are deprecated, and `normalizeAccessPolicy()` lets the nested policy win
- * wherever both are given.
- */
+/** An object that carries an access rule in its nested `access` policy. */
 export interface AccessControlled {
-  /** The access policy. Preferred over the flat fields below. */
   access?: AccessPolicy
-  /**
-   * @deprecated Since MINT 1.2; use `access.visibleFor` instead. The flat
-   * duplicate is removed in 1.3.
-   */
-  visibleFor?: AccessAudienceInput
-  /**
-   * @deprecated Since MINT 1.2; use `access.requiresAdmin` instead. The flat
-   * duplicate is removed in 1.3.
-   */
-  requiresAdmin?: boolean
-  /**
-   * @deprecated Since MINT 1.2; use `access.permissions` instead. The flat
-   * duplicate is removed in 1.3.
-   */
-  permissions?: readonly string[]
-  /**
-   * @deprecated Since MINT 1.2; use `access.anyPermissions` instead. The flat
-   * duplicate is removed in 1.3.
-   */
-  anyPermissions?: readonly string[]
 }
 
 export function getRoleInfo(user: PermissionUser | null | undefined): RoleInfo | null {
@@ -129,40 +101,11 @@ export function canAccessPlugin(
   return Array.isArray(access) && access.includes(pluginName)
 }
 
-/**
- * Flatten an access rule — either shape, or a mix of both — into one policy.
- *
- * ## Precedence
- *
- * 1. A defined field on the nested `access` policy wins. It is the supported
- *    spelling, so an object that carries both shapes is read as "the nested
- *    policy, with the deprecated flat fields as leftovers".
- * 2. Otherwise the flat field on the rule itself is used.
- * 3. A field set to `undefined` on either side counts as unset and never
- *    masks the other side.
- *
- * Only `AccessPolicy` fields the flat shape never had (`audience`,
- * `requiresAuth`, `plugin`) can come from the nested policy alone; the four
- * duplicated fields are the ones this ordering exists for.
- */
-export function normalizeAccessPolicy(rule: AccessControlled | AccessPolicy | undefined): AccessPolicy {
-  if (!rule) return {}
-  const { access: nested, ...flat } = rule as AccessPolicy & { access?: AccessPolicy }
-  const policy = { ...flat } as Record<string, unknown>
-
-  for (const [field, value] of Object.entries(nested ?? {})) {
-    if (value !== undefined) policy[field] = value
-  }
-
-  return policy as AccessPolicy
-}
-
 export function canAccessByPolicy(
   user: PermissionUser | null | undefined,
-  rule: AccessControlled | AccessPolicy | undefined,
+  policy: AccessPolicy = {},
   isAuthenticated = user !== null && user !== undefined,
 ): boolean {
-  const policy = normalizeAccessPolicy(rule)
   if (policy.requiresAuth && !isAuthenticated) return false
   if (policy.requiresAdmin && !isAdminUser(user)) return false
   if (!audienceAllowsUser(policy.visibleFor ?? policy.audience, user)) return false

package/src/styles/components/action-menu.css

@@ -1,4 +1,6 @@
-/* ActionMenu — compact square trigger with a teleported, viewport-safe menu. */
+/* ActionMenu — compact square trigger with a teleported, viewport-safe menu.
+   Surface and rows come from .mint-popover / .mint-menu-item (popover.css, 2d);
+   __panel and __item stay as aliases and own only placement. */
 
 .mint-action-menu {
   display: inline-flex;
@@ -13,47 +15,16 @@
 .mint-action-menu__panel {
   position: fixed;
   z-index: 1000;
-  display: flex;
   min-width: 10rem;
   max-width: min(18rem, calc(100vw - 1rem));
-  flex-direction: column;
-  padding: 0.25rem;
-  border: 1px solid var(--border-color);
-  border-radius: var(--radius-md);
-  background: var(--bg-secondary);
-  box-shadow: var(--shadow-md);
 }
 
-.mint-action-menu__item {
-  display: flex;
-  width: 100%;
-  align-items: center;
-  padding: 0.4375rem 0.625rem;
-  border: 0;
-  border-radius: 0.375rem;
-  background: transparent;
-  color: var(--text-primary);
-  font-family: inherit;
-  font-size: 0.78125rem;
-  line-height: 1.25;
-  text-align: left;
-  text-decoration: none;
-  cursor: pointer;
-  transition: background-color var(--mint-transition);
-}
-
-.mint-action-menu__item:hover:not(:disabled),
-.mint-action-menu__item:focus-visible {
-  outline: none;
-  background: var(--bg-hover);
-}
-
-.mint-action-menu__item--danger {
-  color: var(--mint-error);
+.mint-action-menu__check {
+  flex-shrink: 0;
+  color: var(--color-primary);
 }
 
-.mint-action-menu__item:disabled {
-  color: var(--text-muted);
-  cursor: not-allowed;
-  opacity: var(--mint-disabled-opacity);
+/* Unchecked radio rows keep the check's width so labels stay aligned. */
+.mint-action-menu__check--off {
+  visibility: hidden;
 }

package/src/styles/components/adduct-text.css

@@ -16,7 +16,7 @@
 .mint-adduct-text--sans { font-family: var(--font-sans); font-feature-settings: 'liga' 1, 'calt' 1; font-weight: 650; }
 
 .mint-adduct-text--xs {
-  font-size: 0.625rem;
+  font-size: 0.6875rem;
   line-height: 1rem;
 }
 
@@ -31,12 +31,24 @@
   background: var(--bg-tertiary);
 }
 
+/* On a filled surface the text inherits that surface's ink (9c: the old
+   white literal went white-on-white on light cards). */
 .mint-adduct-text--on-primary {
-  color: rgb(255 255 255 / 0.82);
+  color: inherit;
 }
 
 .mint-adduct-text--badge.mint-adduct-text--on-primary {
-  background: rgb(255 255 255 / 0.2);
+  background: color-mix(in srgb, currentColor 20%, transparent);
+}
+
+/* Charge as a superscript by relative offset, so the line box keeps its height. */
+.mint-adduct-text__charge {
+  position: relative;
+  top: -0.5em;
+  font-size: 0.72em;
+  line-height: 0;
+  vertical-align: baseline;
+  color: inherit;
 }
 
 .mint-adduct-text--muted,