@morscherlab/mint-sdk 1.3.0-beta.1 → 1.3.0-beta.10

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/useFilePicker.ts

@@ -5,6 +5,7 @@ import type {
   PickerNode,
   PickerSelection,
   PickerSelectionMode,
+  PickerSort,
   PickerSource,
 } from '../types/filePicker'
 import type { SegmentedOption } from '../types'
@@ -20,6 +21,7 @@ interface PickerStateProps {
   capabilities: PickerCapabilities
   initialPath: string
   initialSelection: PickerSelection | null
+  defaultSort: PickerSort
   systemFilter?: (node: PickerNode, source: PickerSource) => boolean
 }
 type PickerEmit = {
@@ -50,6 +52,7 @@ export function useFilePicker(
   )
   const query = shallowRef('')
   const recursive = shallowRef(false)
+  const sort = shallowRef<PickerSort>(props.defaultSort)
   const skipBlanks = shallowRef(false)
   const reviewing = shallowRef(false)
   const localFiles = shallowRef<File[]>([])
@@ -61,6 +64,7 @@ export function useFilePicker(
     () => (source.value === 'localFile' ? localAdapter.value : props.adapter),
     () => ({ source: source.value }),
     (node) => props.systemFilter?.(node, source.value) !== false,
+    () => sort.value,
   )
   const capability = computed(() => props.capabilities[source.value])
   const selection = usePickerSelection(
@@ -182,6 +186,7 @@ export function useFilePicker(
     (open) => {
       clearTimeout(timer)
       if (open) {
+        sort.value = props.defaultSort
         if (!initialized) {
           path.value = props.initialPath
           if (path.value) trail.value = [{ path: path.value, label: 'Current folder' }]
@@ -348,9 +353,10 @@ export function useFilePicker(
   }
   async function selectLocalFiles() {
     const token = openGeneration
-    const items = props.selectionMode === 'single-file' || props.selectionMode === 'multi-file'
+    const found = props.selectionMode === 'single-file' || props.selectionMode === 'multi-file'
       ? await localAdapter.value.search('', { path: '', recursive: true })
       : nav.entries.value
+    const items = Array.isArray(found) ? found : found.nodes
     if (token !== openGeneration || !props.open || source.value !== 'localFile') return
     nav.register(items)
     const candidates = items.filter((node) => selection.selectable(node))
@@ -411,6 +417,7 @@ export function useFilePicker(
     source,
     query,
     recursive,
+    sort,
     skipBlanks,
     reviewing,
     nav,

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/usePlatformFilePickerAdapter.ts

@@ -1,11 +1,24 @@
 import type { PickerAdapter } from '../types/filePicker'
-import type { FileDirectoryListing, ServerMount } from '../types/fileBrowserTypes'
+import type {
+  FileBrowserLocation,
+  FileDirectoryListing,
+  FileDirectoryTree,
+  FileSearchResult,
+  ServerMount,
+} from '../types/fileBrowserTypes'
+import type { PickerRequest } from '../types/filePicker'
 import { useApi } from './useApi'
 import { getInjectedPlatformContext } from './platformContextHelpers'
 import { createFilePickerAdapter, type FilePickerAdapterOptions } from './createFilePickerAdapter'
 
 export { encodePlatformPickerPath, decodePlatformPickerPath } from './createFilePickerAdapter'
 
+function query(location: FileBrowserLocation, request?: PickerRequest): URLSearchParams {
+  const params = new URLSearchParams({ mount_id: location.mount_id, path: location.path })
+  if (request?.refresh) params.set('refresh', 'true')
+  return params
+}
+
 /** Adapt the authenticated MINT mount API without exposing absolute host paths. */
 export function usePlatformFilePickerAdapter(
   options: FilePickerAdapterOptions & { apiBaseUrl?: string } = {},
@@ -27,11 +40,20 @@ export function usePlatformFilePickerAdapter(
       }
     },
     browse(location, request) {
-      const query = new URLSearchParams({ mount_id: location.mount_id, path: location.path })
-      if (request?.refresh) query.set('refresh', 'true')
-      return api.get<FileDirectoryListing>(`/filesystem/browse?${query}`, {
+      return api.get<FileDirectoryListing>(`/filesystem/browse?${query(location, request)}`, {
+        signal: request?.signal,
+      })
+    },
+    tree(location, request) {
+      return api.get<FileDirectoryTree>(`/filesystem/tree?${query(location, request)}`, {
         signal: request?.signal,
       })
     },
+    search(location, text, recursive, request) {
+      const params = query(location, request)
+      params.set('q', text)
+      params.set('recursive', String(recursive))
+      return api.get<FileSearchResult>(`/filesystem/search?${params}`, { signal: request?.signal })
+    },
   }, options)
 }

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/action-menu.css

@@ -18,3 +18,13 @@
   min-width: 10rem;
   max-width: min(18rem, calc(100vw - 1rem));
 }
+
+.mint-action-menu__check {
+  flex-shrink: 0;
+  color: var(--color-primary);
+}
+
+/* Unchecked radio rows keep the check's width so labels stay aligned. */
+.mint-action-menu__check--off {
+  visibility: hidden;
+}

package/src/styles/components/app-page-selector.css

@@ -1,5 +1,5 @@
 /* AppTopBar page selector — left-side route/page dropdown.
-   Trigger speaks the field language (5a): 32px, hover changes the background
+   Trigger speaks the field language (5a): 36px (the identity tile height), hover changes the background
    only, open = field focus, inline 12px chevron. Menu = .mint-popover +
    .mint-menu-item (2d); __menu / __item stay as aliases. */
 
@@ -13,8 +13,8 @@
   align-items: center;
   gap: 0.5rem;
   width: 100%;
-  height: 2rem;
-  padding: 0 0.5rem 0 0.3125rem;
+  height: 2.25rem;
+  padding: 0 0.5rem 0 0.4375rem;
   border: 1px solid var(--border-color);
   background: var(--bg-card);
   color: var(--text-primary);

package/src/styles/components/app-pill-nav.css

@@ -21,7 +21,7 @@
   display: inline-flex;
   align-items: center;
   gap: 0.375rem;
-  height: 1.625rem;
+  height: 1.75rem;
   border: 0;
   padding: 0 0.875rem;
   border-radius: 9999px;

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

@@ -9,7 +9,7 @@
 .mint-topbar {
   display: block;
   width: 100%;
-  padding: 0.625rem 0.75rem;
+  padding: 0.75rem 1rem;
   background-color: var(--bg-secondary);
   box-sizing: border-box;
 }
@@ -19,7 +19,7 @@
   display: flex;
   align-items: center;
   gap: 0.5rem;
-  min-height: 2rem;
+  min-height: 2.375rem;
   position: relative;
 }
 
@@ -31,35 +31,28 @@
 }
 
 .mint-topbar__identity {
-  width: 2rem;
-  height: 2rem;
+  width: 2.25rem;
+  height: 2.25rem;
   display: inline-flex;
   align-items: center;
   justify-content: center;
   flex-shrink: 0;
 }
 
-/* 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;
+/* Slotted logos sized above 36px shrink to fit instead of stretching the tile. */
+.mint-topbar__identity > * {
+  max-width: 100%;
+  max-height: 100%;
 }
 
-/* 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;
+/* Left and right fields share the 36px identity tile height. */
+.mint-topbar .mint-experiment-popover__trigger,
+.mint-topbar .mint-experiment-popover__save-trigger {
+  height: 2.25rem;
 }
 
-.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;
+.mint-topbar .mint-experiment-popover__save-trigger {
+  width: 2.25rem;
 }
 
 /* Centered section — absolute so asymmetric left/right weight never shifts the
@@ -98,8 +91,8 @@
 }
 
 .mint-topbar__logo-icon {
-  width: 2rem;
-  height: 2rem;
+  width: 2.25rem;
+  height: 2.25rem;
   background-color: var(--color-primary);
   border-radius: var(--radius-md);
   display: flex;
@@ -118,7 +111,7 @@
   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 +129,6 @@
   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);
@@ -175,7 +155,7 @@
   opacity: 0.8;
 }
 
-/* Title + subtitle stay inside the 32px control row (5a: 52px bar). */
+/* Title + subtitle stay inside the 36px control row. */
 .mint-topbar-title-group {
   display: flex;
   flex-direction: column;

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;
 }
 

package/src/styles/components/experiment-selector-modal.css

@@ -5,6 +5,7 @@
   align-items: center;
   gap: 0.5rem;
   flex-wrap: wrap;
+  padding: 0 1.25rem;
 }
 
 .mint-experiment-selector__filter-select {
@@ -65,14 +66,6 @@ html.dark .mint-experiment-selector__filters-toggle--active {
   flex-shrink: 0;
 }
 
-/* Advanced filters row */
-.mint-experiment-selector__filters-advanced {
-  padding: 0.625rem;
-  border: 1px solid var(--border-light);
-  border-radius: var(--radius-md);
-  background-color: color-mix(in srgb, var(--bg-secondary) 72%, transparent);
-}
-
 /* Group toggle checkbox label */
 .mint-experiment-selector__group-toggle {
   display: inline-flex;
@@ -103,7 +96,8 @@ html.dark .mint-experiment-selector__filters-toggle--active {
 .mint-experiment-selector__footer {
   display: flex;
   justify-content: flex-start;
-  padding-top: 0.25rem;
+  padding: 0.5rem 1.25rem 0.75rem;
+  border-top: 1px solid var(--border-light);
 }
 
 .mint-experiment-selector__clear-btn {

package/src/styles/components/file-picker.css

@@ -106,6 +106,7 @@
   white-space: nowrap;
 }
 .mint-picker__scope,
+.mint-picker__sort,
 .mint-picker__link {
   padding: 2px 6px;
   border: 0;
@@ -116,10 +117,20 @@
   cursor: pointer;
   transition: background-color 150ms ease;
 }
-.mint-picker__scope {
+.mint-picker__scope,
+.mint-picker__sort {
   flex-shrink: 0;
   color: var(--text-secondary-strong);
 }
+.mint-picker__sort {
+  display: inline-flex;
+  align-items: center;
+  gap: 2px;
+}
+.mint-picker__sort svg {
+  width: 12px;
+  height: 12px;
+}
 .mint-picker__link {
   color: var(--_ink-primary);
 }
@@ -138,10 +149,13 @@
   cursor: not-allowed;
 }
 .mint-picker__scope:hover,
+.mint-picker__sort:hover,
+.mint-picker__sort[aria-expanded='true'],
 .mint-picker__link:hover {
   background: var(--bg-hover);
 }
 .mint-picker__scope:focus-visible,
+.mint-picker__sort:focus-visible,
 .mint-picker__link:focus-visible {
   outline: none;
   box-shadow: var(--focus-ring-offset);
@@ -185,6 +199,14 @@
 .mint-picker__list-head > span:nth-child(n + 3) {
   text-align: right;
 }
+.mint-picker__truncated {
+  margin: 0;
+  padding: 6px 12px;
+  border-bottom: 1px solid var(--border-light);
+  background: var(--bg-secondary);
+  font-size: 12px;
+  color: var(--text-secondary);
+}
 .mint-picker__row {
   box-sizing: border-box;
   height: 34px;