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

package/src/composables/createFilePickerAdapter.ts

@@ -1,10 +1,26 @@
-import type { PickerAdapter, PickerNode, PickerRequest } from '../types/filePicker'
-import type { FileBrowserLocation, FileDirectoryListing, ServerMount } from '../types/fileBrowserTypes'
+import type { PickerAdapter, PickerNode, PickerRequest, PickerSearchResult } from '../types/filePicker'
+import type {
+  FileBrowserLocation,
+  FileDirectoryListing,
+  FileDirectoryTree,
+  FileEntry,
+  FileSearchResult,
+  ServerMount,
+} from '../types/fileBrowserTypes'
 import { pickerFormat } from './filePicker/validation'
 
 export interface FilePickerTransport {
   listMounts(request?: PickerRequest): Promise<ServerMount[]>
   browse(location: FileBrowserLocation, request?: PickerRequest): Promise<FileDirectoryListing>
+  /** `GET …/filesystem/tree`: one request fills the cache for the subfolders too. */
+  tree?(location: FileBrowserLocation, request?: PickerRequest): Promise<FileDirectoryTree>
+  /** `GET …/filesystem/search`: replaces the folder-by-folder search walk. */
+  search?(
+    location: FileBrowserLocation,
+    query: string,
+    recursive: boolean,
+    request?: PickerRequest,
+  ): Promise<FileSearchResult>
 }
 export interface FilePickerAdapterOptions {
   /** Show this directory's contents directly and prevent navigation outside it. */
@@ -82,36 +98,90 @@ export function createFilePickerAdapter(
           unavailableReason: mount.available === false ? 'This mount is offline.' : undefined,
         }
       })
+    } else if (transport.tree) {
+      const tree = await transport.tree(location, request)
+      check(request, token)
+      for (const listing of tree.listings ?? []) {
+        const at = { mount_id: listing.mount_id, path: listing.path }
+        validateLocation(at)
+        if (at.mount_id !== location.mount_id) throw new Error('Invalid file picker directory entry.')
+        // A capped subfolder is read on its own when opened, and reports the cap then.
+        if (!listing.truncated) listings.set(encodePlatformPickerPath(at.mount_id, at.path), toNodes(at, listing))
+      }
+      const cached = listings.get(key)
+      if (!cached)
+        throw new Error('This directory exceeds the server listing limit. Choose a smaller data directory.')
+      return cached
     } else {
       const listing = await transport.browse(location, request)
       check(request, token)
       if (listing.truncated)
         throw new Error('This directory exceeds the server listing limit. Choose a smaller data directory.')
-      const atRoot = root && location.mount_id === root.mount_id && location.path === root.path
-      nodes = (listing.entries ?? []).map((entry): PickerNode => {
-        if (!isRelativePath(entry.path) || !entry.name ||
-          entry.path !== `${location.path ? `${location.path}/` : ''}${entry.name}` ||
-          entry.name.includes('/')) throw new Error('Invalid file picker directory entry.')
-        const common = {
-          path: encodePlatformPickerPath(location.mount_id, entry.path),
-          parentPath: atRoot ? null : key,
-          parentName: `${mountLabels.get(location.mount_id) ?? location.mount_id}${location.path ? ` / ${location.path}` : ''}`,
-          name: entry.name, bytes: entry.size_bytes,
-        }
-        return entry.kind === 'directory'
-          // Counts may include only matching formats, not nested directories.
-          ? { ...common, kind: 'folder' }
-          : { ...common, kind: 'file', format: pickerFormat(entry.name) }
-      })
+      nodes = toNodes(location, listing)
     }
     listings.set(key, nodes)
     return nodes
   }
+  function toNodes(location: FileBrowserLocation, listing: FileDirectoryListing): PickerNode[] {
+    return (listing.entries ?? []).map((entry) => {
+      if (entry.path !== `${location.path ? `${location.path}/` : ''}${entry.name}`)
+        throw new Error('Invalid file picker directory entry.')
+      return toNode(location.mount_id, entry)
+    })
+  }
+  /** One entry, parented on the folder its mount-relative path names. */
+  function toNode(mountId: string, entry: FileEntry): PickerNode {
+    if (!isRelativePath(entry.path) || !entry.name || entry.name.includes('/') ||
+      (entry.path !== entry.name && !entry.path.endsWith(`/${entry.name}`)))
+      throw new Error('Invalid file picker directory entry.')
+    const parent = entry.path.slice(0, Math.max(0, entry.path.length - entry.name.length - 1))
+    const atRoot = root && mountId === root.mount_id && parent === root.path
+    const common = {
+      path: encodePlatformPickerPath(mountId, entry.path),
+      parentPath: atRoot ? null : encodePlatformPickerPath(mountId, parent),
+      parentName: `${mountLabels.get(mountId) ?? mountId}${parent ? ` / ${parent}` : ''}`,
+      name: entry.name, bytes: entry.size_bytes, modifiedAt: entry.modified_at,
+    }
+    return entry.kind === 'directory'
+      // Counts may include only matching formats, not nested directories.
+      ? { ...common, kind: 'folder' }
+      : { ...common, kind: 'file', format: pickerFormat(entry.name) }
+  }
+  async function serverSearch(
+    query: string,
+    scope: { path: string; recursive: boolean },
+    request: PickerRequest | undefined,
+  ): Promise<PickerNode[] | PickerSearchResult> {
+    const token = begin(request)
+    const decoded = scope.path ? decodePlatformPickerPath(scope.path) : undefined
+    const location = decoded ? { mount_id: decoded.mountId, path: decoded.path } : root!
+    validateLocation(location)
+    const result = await transport.search!(location, query, scope.recursive, request)
+    check(request, token)
+    const prefix = location.path ? `${location.path}/` : ''
+    const nodes = (result.entries ?? []).map((entry) => {
+      // "This folder" searches may return direct children only.
+      if (!entry.path.startsWith(prefix) || (!scope.recursive && entry.path.slice(prefix.length).includes('/')))
+        throw new Error('Invalid file picker directory entry.')
+      return toNode(location.mount_id, entry)
+    })
+    return result.truncated ? { nodes, truncated: true } : nodes
+  }
   return {
+    mounts: !root,
+    mountOf(path) {
+      try {
+        return encodePlatformPickerPath(decodePlatformPickerPath(path).mountId)
+      } catch {
+        return undefined // initialPath is caller input; the listing reports a bad one.
+      }
+    },
     invalidate,
     listRoot: async (request) => read('', request, begin(request)),
     listChildren: async (path, request) => read(path, request, begin(request)),
     async search(query, scope, request) {
+      // The mount list itself has no server to search, so it keeps the walk.
+      if (transport.search && (scope.path || root)) return serverSearch(query, scope, request)
       const token = begin(request)
       const matches: PickerNode[] = []
       const queue = [scope.path]
@@ -123,8 +193,7 @@ export function createFilePickerAdapter(
         const path = queue.shift()!
         if (visited.has(path)) continue
         visited.add(path)
-        if (visited.size > 500)
-          throw new Error('Search reached its folder limit. Search a smaller location or turn off Subfolders.')
+        if (visited.size > 500) return { nodes: matches, truncated: true }
         const nodes = await read(path, currentRequest, token)
         check(request, token)
         if (currentRequest?.refresh) {
@@ -136,8 +205,7 @@ export function createFilePickerAdapter(
           if (scope.recursive && node.kind === 'folder' && !node.unavailableReason)
             queue.push(node.path)
         }
-        if (matches.length > 10000)
-          throw new Error('Too many search results. Use a more specific search.')
+        if (matches.length > 10000) return { nodes: matches.slice(0, 10000), truncated: true }
       }
       return matches
     },

package/src/composables/filePicker/localFiles.ts

@@ -29,6 +29,7 @@ export function localFilesAdapter(
       path,
       parentPath: parent,
       bytes: file.size,
+      modifiedAt: new Date(file.lastModified).toISOString(),
       format: pickerFormat(file.name),
       file,
     })

package/src/composables/filePicker/usePickerNavigation.ts

@@ -3,13 +3,33 @@ import type {
   PickerAdapter,
   PickerNode,
   PickerRequest,
+  PickerSort,
   PickerTreeRow,
 } from '../../types/filePicker'
 
+const byName = new Intl.Collator(undefined, { numeric: true, sensitivity: 'base' }).compare
+/** Folders first; undated rows go last in either time order. */
+function ordered(items: PickerNode[], sort: PickerSort | undefined): PickerNode[] {
+  if (!sort) return items
+  // Parse each timestamp once rather than on every comparison.
+  const times = new Map(items.map((node) => [node, node.modifiedAt ? Date.parse(node.modifiedAt) : NaN]))
+  const time = (node: PickerNode) => times.get(node)!
+  return [...items].sort((a, b) => {
+    if (a.kind !== b.kind) return a.kind === 'folder' ? -1 : 1
+    if (sort === 'name') return byName(a.name, b.name)
+    if (sort === 'name-desc') return byName(b.name, a.name)
+    const [ta, tb] = [time(a), time(b)]
+    if (Number.isNaN(ta) || Number.isNaN(tb))
+      return Number.isNaN(ta) === Number.isNaN(tb) ? byName(a.name, b.name) : Number.isNaN(ta) ? 1 : -1
+    return (sort === 'newest' ? tb - ta : ta - tb) || byName(a.name, b.name)
+  })
+}
+
 export function usePickerNavigation(
   adapter: () => PickerAdapter,
   request: () => PickerRequest,
   systemFilter: (node: PickerNode) => boolean = () => true,
+  sort: () => PickerSort | undefined = () => undefined,
 ) {
   const path = shallowRef('')
   const trail = ref<{ path: string; label: string }[]>([])
@@ -21,6 +41,8 @@ export function usePickerNavigation(
   const expansionErrors = ref(new Map<string, string>())
   const loading = shallowRef(false)
   const error = shallowRef('')
+  /** True when the current search results stopped at an adapter limit. */
+  const truncated = shallowRef(false)
   let epoch = 0
   let navigation = 0
   let controller: AbortController | undefined
@@ -154,14 +176,17 @@ export function usePickerNavigation(
     const options = { ...request(), ...(refresh && { refresh }), signal: controller.signal }
     loading.value = true
     error.value = ''
+    truncated.value = false
     entries.value = []
     try {
-      const items = query.trim()
+      const found = query.trim()
         ? await adapter().search(query.trim(), { path: path.value, recursive }, options)
         : path.value
           ? await loadChildren(path.value, [], refresh)
           : await adapter().listRoot(options)
       if (token !== navigation) return
+      const items = Array.isArray(found) ? found : found.nodes
+      truncated.value = !Array.isArray(found) && found.truncated
       register(items, query.trim() ? undefined : path.value)
       entries.value = items
       if (!query.trim()) prefetch(items)
@@ -215,8 +240,9 @@ export function usePickerNavigation(
   }
   const rows = computed(() => {
     const result: PickerTreeRow[] = []
+    const order = sort()
     function visit(items: PickerNode[], depth: number, ancestors: Set<string>) {
-      for (const item of items) {
+      for (const item of ordered(items, order)) {
         if (ancestors.has(item.path) || depth > 30) continue
         const node = nodes.value.get(item.path) ?? item
         if (!isAllowed(node)) continue
@@ -246,6 +272,7 @@ export function usePickerNavigation(
     expansionErrors,
     loading,
     error,
+    truncated,
     rows,
     isAllowed,
     clear,

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'
@@ -32,19 +30,6 @@ export {
   type FieldState,
   type UseFormReturn,
 } from './useForm'
-export {
-  useAsync,
-  useAsyncBatch,
-  type AsyncError,
-  type AsyncState,
-  type UseAsyncReturn,
-  type UseAsyncOptions,
-} from './useAsync'
-export {
-  useWellPlateEditor,
-  type UseWellPlateEditorOptions,
-  type UseWellPlateEditorReturn,
-} from './useWellPlateEditor'
 export {
   useConcentrationUnits,
   type ConcentrationValue,
@@ -79,6 +64,7 @@ export {
   useRackEditor,
   type UseRackEditorOptions,
   type UseRackEditorReturn,
+  type PlateEditorListeners,
 } from './useRackEditor'
 export {
   useChemicalFormula,
@@ -92,6 +78,7 @@ export {
   useSequenceUtils,
   type SequenceType,
   type SequenceStats,
+  type SequenceProblems,
 } from './useSequenceUtils'
 export {
   useTimeUtils,
@@ -163,7 +150,6 @@ export {
   type UseGeneratedAnalysisReturn,
 } from './useGeneratedAnalysis'
 export { useAutoGroup, DEFAULT_COLORS, extractSamplesFromDesignData } from './useAutoGroup'
-export { usePluginConfig, type UsePluginConfigReturn } from './usePluginConfig'
 export {
   useReagentSeries,
   generateDilutionSeries,
@@ -257,29 +243,6 @@ export {
   type RequestSyncSuccessKind,
   type UseRequestSyncStateReturn,
 } from './useRequestSyncState'
-export {
-  useCommandHistory,
-  type CommandHistoryCommand,
-  type CommandHistoryExecuteOptions,
-  type CommandHistoryResult,
-  type UseCommandHistoryOptions,
-  type UseCommandHistoryReturn,
-} from './useCommandHistory'
-export {
-  useOptimisticMutation,
-  type OptimisticMutationContext,
-  type UseOptimisticMutationOptions,
-  type UseOptimisticMutationReturn,
-} from './useOptimisticMutation'
-export {
-  createPluginResourceClient,
-  useResourceCrud,
-  type PluginResourceClientOptions,
-  type ResourceCrudAdapter,
-  type ResourceKey,
-  type UseResourceCrudOptions,
-  type UseResourceCrudReturn,
-} from './useResourceCrud'
 export {
   detectDelimiter,
   parseDelimitedText,
@@ -350,38 +313,6 @@ export {
   type UseTextSearchOptions,
   type UseTextSearchReturn,
 } from './useTextSearch'
-export {
-  coordinateToWellId,
-  useWellPainting,
-  wellIdToCoordinate,
-  wellIdsInRectangle,
-  type UseWellPaintingOptions,
-  type UseWellPaintingReturn,
-  type WellCoordinate,
-  type WellPaintResult,
-  type WellPlateSource,
-} from './useWellPainting'
-export {
-  createColumnConditions,
-  createRowConditions,
-  createWellPlateWells,
-  useWellPlateAdapter,
-  type AxisConditionEntry,
-  type UseWellPlateAdapterReturn,
-  type WellPlateAdapterOptions,
-  type WellPlateAdapterSource,
-  type WellPlateEntry,
-} from './useWellPlateAdapter'
-export {
-  runWellPlateValidation,
-  useWellPlateValidation,
-  type UseWellPlateValidationOptions,
-  type UseWellPlateValidationReturn,
-  type WellPlateValidationRule,
-  type WellPlateValidationSeverity,
-  type WellPlateValidationSource,
-  type WellPlateValidationWarning,
-} from './useWellPlateValidation'
 export {
   controlsToFormSchema,
   controlsToSectionFormSchema,

package/src/composables/pluginWorkspaceModel.ts

@@ -2,7 +2,6 @@ import type {
   AccountMenuItem,
   PageSelectorItemInput,
   PillNavItemInput,
-  PluginSwitcherInfo,
   SidebarToolSection,
   TopBarSettingsConfig,
   TopBarVariant,
@@ -74,8 +73,6 @@ export interface PluginWorkspaceShellModel {
   pageSelector?: PageSelectorItemInput[]
   /** Resolved active page selector id. */
   currentPageSelectorId: string
-  /** Optional plugin switcher shown in the left navigation position. */
-  pluginSwitcher?: PluginSwitcherInfo
   /** Resolved centered pill navigation, generated from the control schema when omitted. */
   pillNav?: PillNavItemInput[]
   /** Resolved active centered pill id. */

package/src/composables/useAutoGroup.ts

@@ -59,6 +59,11 @@ function warnDeprecated(api: string) {
 // Re-export `parseCSV` for callers that imported it from this file.
 export { parseCSV } from './autoGroup/csv-shim'
 
+/**
+ * Sample-grouping engine behind `AutoGroupModal`.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4; no SDK replacement.
+ */
 export function useAutoGroup() {
   const inputMode = ref<InputMode>('paste')
   const rawText = ref('')
@@ -597,6 +602,11 @@ export function useAutoGroup() {
   }
 }
 
+/**
+ * Reads experiment `design_data` samples into the `useAutoGroup` CSV shape.
+ *
+ * @deprecated Scheduled for removal in MINT 1.4 together with `useAutoGroup`.
+ */
 export function extractSamplesFromDesignData(
   rawData: Record<string, unknown>,
   options: LoadExperimentDataOptions = {},

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 PlateMapEditor. */
+/**
+ * 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/useChemicalFormula.ts

@@ -10,21 +10,40 @@ export interface FormulaParseResult {
   error?: string
 }
 
-export type FormulaPartType = 'element' | 'subscript' | 'superscript' | 'paren' | 'dot' | 'charge'
+/** `coefficient` is a full-size multiplier at the start of a hydrate segment (the 5 in CuSO4·5H2O). */
+export type FormulaPartType = 'element' | 'subscript' | 'superscript' | 'paren' | 'dot' | 'charge' | 'coefficient'
 
 export interface FormulaPart {
   type: FormulaPartType
   text: string
 }
 
-// ~30 common elements with atomic weights
+// Every element with its standard atomic weight (mass number of the most stable isotope when none is defined)
 export const ATOMIC_WEIGHTS: Record<string, number> = {
   H: 1.008, He: 4.003, Li: 6.941, Be: 9.012, B: 10.81,
   C: 12.011, N: 14.007, O: 15.999, F: 18.998, Ne: 20.180,
   Na: 22.990, Mg: 24.305, Al: 26.982, Si: 28.086, P: 30.974,
   S: 32.065, Cl: 35.453, Ar: 39.948, K: 39.098, Ca: 40.078,
+  Sc: 44.956, Ti: 47.867, V: 50.942, Cr: 51.996,
   Mn: 54.938, Fe: 55.845, Co: 58.933, Ni: 58.693, Cu: 63.546,
-  Zn: 65.38, Br: 79.904, Ag: 107.868, I: 126.904, Au: 196.967,
+  Zn: 65.38, Ga: 69.723, Ge: 72.630, As: 74.922, Se: 78.971,
+  Br: 79.904, Kr: 83.798, Rb: 85.468, Sr: 87.62, Y: 88.906,
+  Zr: 91.224, Nb: 92.906, Mo: 95.95, Tc: 98, Ru: 101.07,
+  Rh: 102.906, Pd: 106.42, Ag: 107.868, Cd: 112.414, In: 114.818,
+  Sn: 118.710, Sb: 121.760, Te: 127.60, I: 126.904, Xe: 131.293,
+  Cs: 132.905, Ba: 137.327, La: 138.905, Ce: 140.116, Pr: 140.908,
+  Nd: 144.242, Pm: 145, Sm: 150.36, Eu: 151.964, Gd: 157.25,
+  Tb: 158.925, Dy: 162.500, Ho: 164.930, Er: 167.259, Tm: 168.934,
+  Yb: 173.045, Lu: 174.967, Hf: 178.49, Ta: 180.948, W: 183.84,
+  Re: 186.207, Os: 190.23, Ir: 192.217, Pt: 195.084, Au: 196.967,
+  Hg: 200.592, Tl: 204.38, Pb: 207.2, Bi: 208.980, Po: 209,
+  At: 210, Rn: 222, Fr: 223, Ra: 226, Ac: 227,
+  Th: 232.038, Pa: 231.036, U: 238.029, Np: 237, Pu: 244,
+  Am: 243, Cm: 247, Bk: 247, Cf: 251, Es: 252,
+  Fm: 257, Md: 258, No: 259, Lr: 266, Rf: 267,
+  Db: 268, Sg: 269, Bh: 270, Hs: 277, Mt: 278,
+  Ds: 281, Rg: 282, Cn: 285, Nh: 286, Fl: 289,
+  Mc: 290, Lv: 293, Ts: 294, Og: 294,
 }
 
 function parseFormulaSegment(formula: string): FormulaParseResult {
@@ -97,8 +116,15 @@ export function useChemicalFormula() {
       return { elements: {}, valid: false, error: 'Empty formula' }
     }
 
-    // Split on hydrate separator (· or .)
-    const parts = trimmed.split(/[·.]/)
+    // A trailing charge (SO4^2-, Fe2+, NH4+) does not change the composition. Like renderFormulaParts,
+    // digits before a bare sign are the charge only on a lone element (Fe2+); otherwise they are a
+    // subscript and the sign a unit charge (NH4+). Write Hg2^2+ for any other multiple charge.
+    const body = trimmed.replace(/^([A-Z][a-z]?)\d*[+-]$/, '$1').replace(/(\^\d*)?[+-]$/, '')
+    if (!body) {
+      return { elements: {}, valid: false, error: 'Empty formula' }
+    }
+    // Split on hydrate separator (·, . or *)
+    const parts = body.split(/[·.*]/)
     const combined: Record<string, number> = {}
 
     for (const part of parts) {
@@ -206,13 +232,10 @@ export function useChemicalFormula() {
           }
           parts.push({ type: 'subscript', text: numStr })
 
-          // Check for charge after subscript (e.g., Fe2+ or SO4^2-)
-          if (i < trimmed.length && (trimmed[i] === '+' || trimmed[i] === '-')) {
+          // On a lone element the digits before a trailing sign are the charge (Fe2+);
+          // elsewhere they stay a subscript and the sign renders as a unit charge (NH4+).
+          if (parts.length === 2 && i === trimmed.length - 1 && (trimmed[i] === '+' || trimmed[i] === '-')) {
             parts.push({ type: 'charge', text: numStr + trimmed[i] })
-            // Remove the subscript we just added since it's actually part of charge
-            // Actually, for cases like Fe2+, the 2+ is the charge, not a subscript
-            // But for H2O the 2 is a subscript. We need context.
-            // Simplification: if followed by +/-, treat trailing digits as part of charge
             parts.splice(parts.length - 2, 1) // Remove the subscript
             i++
             continue
@@ -231,9 +254,12 @@ export function useChemicalFormula() {
         // Could be a subscript or coefficient depending on context
         // If next char is uppercase, it's a coefficient (render as element-like text)
         // If at end or followed by +/-, it's a charge component
+        const prev = parts[parts.length - 1]
         if (i < trimmed.length && (trimmed[i] === '+' || trimmed[i] === '-')) {
           parts.push({ type: 'charge', text: numStr + trimmed[i] })
           i++
+        } else if (!prev || prev.type === 'dot') {
+          parts.push({ type: 'coefficient', text: numStr })
         } else {
           parts.push({ type: 'subscript', text: numStr })
         }
@@ -247,8 +273,8 @@ export function useChemicalFormula() {
         continue
       }
 
-      // Dot as hydrate separator
-      if (ch === '.') {
+      // Dot or asterisk as hydrate separator
+      if (ch === '.' || ch === '*') {
         parts.push({ type: 'dot', text: '·' })
         i++
         continue

package/src/composables/useDropdownState.ts

@@ -7,6 +7,11 @@ export interface UseDropdownStateOptions {
   /** Close the panel when the page scrolls or the viewport resizes. Default `false`. */
   closeOnScroll?: boolean
   insideRefs?: Array<Ref<HTMLElement | null>>
+  /**
+   * Element that counts as "inside" for outside-click closing, typically a
+   * `useTemplateRef()`. Without one, bind the returned `rootRef` instead.
+   */
+  rootRef?: Ref<HTMLElement | null>
   /**
    * Element focus returns to when the panel closes with `close(true)` (Escape).
    * Pass one when the trigger lives outside `rootRef`; otherwise bind the
@@ -38,7 +43,7 @@ export interface UseDropdownStateReturn {
  */
 export function useDropdownState(options: UseDropdownStateOptions = {}): UseDropdownStateReturn {
   const isOpen = ref(false)
-  const rootRef = ref<HTMLElement | null>(null)
+  const rootRef = options.rootRef ?? ref<HTMLElement | null>(null)
   const triggerRef = options.triggerRef ?? ref<HTMLElement | null>(null)
   const closeOnOutsideClick = options.closeOnOutsideClick ?? true
   const closeOnEscape = options.closeOnEscape ?? true

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/useFileBrowser.ts

@@ -53,7 +53,7 @@ export interface UseFileBrowserReturn {
   truncated: Ref<boolean>
   search: Ref<string>
   sort: Ref<FileBrowserSortKey>
-  /** Controlled selection, ready to bind to FileBrowserModal. */
+  /** Paths the user has picked, keyed by mount and path. */
   selected: Ref<FileSelection[]>
   isLoading: ComputedRef<boolean>
   error: Ref<string | null>
@@ -69,7 +69,8 @@ export interface UseFileBrowserReturn {
 }
 
 /**
- * Drives FileBrowserModal against the platform's `/api/filesystem` routes.
+ * Browses the platform's `/api/filesystem` routes for a custom file UI. For the
+ * ready-made dialog, use `FilePicker` with `usePlatformFilePickerAdapter()`.
  *
  * Requires the `filesystem.browse` permission and a deployment that declares
  * mounts; with none configured the routes are absent and `mounts` stays empty.