@morscherlab/mint-sdk 1.3.0-beta.3 → 1.3.0-beta.5

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

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

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

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

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;

package/src/styles/components/well-plate.css

@@ -59,10 +59,9 @@
 /* Header cells */
 .mint-well-plate__col-header,
 .mint-well-plate__row-header {
-  font-family: var(--font-mono);
-  font-weight: 400;
+  font-weight: 500;
   text-align: center;
-  color: var(--text-secondary);
+  color: var(--text-muted);
 }
 
 .mint-well-plate__row-header {
@@ -83,9 +82,8 @@
   font-weight: 500;
   cursor: pointer;
   transition: background-color 0.15s ease, border-color 0.15s ease, box-shadow 0.15s ease, opacity 0.15s ease;
-  /* Empty well: solid hairline, no dash — dozens of dashed rings read as noise (2b). */
-  background-color: var(--bg-card);
-  border: 1px solid color-mix(in srgb, var(--text-secondary) 35%, var(--border-color));
+  background-color: var(--bg-tertiary);
+  border: 1px dashed var(--border-color);
 }
 
 .mint-well-plate__well--rounded {
@@ -97,7 +95,7 @@
 }
 
 .mint-well-plate__well--filled {
-  background-color: var(--bg-tertiary);
+  border-style: solid;
 }
 
 .mint-well-plate__well--disabled {
@@ -106,29 +104,27 @@
 }
 
 /* Well states */
-/* Neutral ring + shape only, so a ring never vanishes into a sample color (2b). */
 .mint-well-plate__well--selected {
-  box-shadow: 0 0 0 2px var(--bg-card), 0 0 0 3.5px var(--text-primary);
+  box-shadow: 0 0 0 2px var(--mint-success), 0 0 0 3px var(--bg-card);
 }
 
 .mint-well-plate__well--drag-over {
   box-shadow: 0 0 0 2px var(--color-primary);
-  background-color: var(--color-primary-soft);
+  background-color: color-mix(in srgb, var(--color-primary) 20%, transparent);
 }
 
 .mint-well-plate__well--hovered {
-  box-shadow: 0 0 0 1px var(--text-secondary);
+  box-shadow: 0 0 0 2px color-mix(in srgb, var(--mint-success) 50%, transparent);
 }
 
-/* !important: wellStyle() sets an inline solid `border` on every draggable well. */
 .mint-well-plate__well--drag-source {
-  border-style: dashed !important;
+  box-shadow: 0 0 0 2px var(--mint-warning);
   opacity: 0.5;
 }
 
 .mint-well-plate__well--drag-target {
-  box-shadow: 0 0 0 2px var(--bg-card), 0 0 0 3.5px var(--color-primary);
-  background-color: var(--color-primary-soft);
+  box-shadow: 0 0 0 2px var(--mint-success), 0 0 0 3px var(--bg-card);
+  background-color: color-mix(in srgb, var(--mint-success) 20%, transparent);
 }
 
 /* Optional semantic classes for `wellClass` callbacks. */
@@ -168,18 +164,6 @@
   color: var(--text-primary);
 }
 
-/* Q / i marker glyph when the centre holds a label or well ID (iQC has no other cue) */
-.mint-well-plate__corner-glyph {
-  position: absolute;
-  top: 3px;
-  left: 6px;
-  font-size: 10px;
-  font-weight: 700;
-  line-height: 1;
-  pointer-events: none;
-  color: var(--text-primary);
-}
-
 /* Well ID text */
 .mint-well-plate__well-id {
   font-weight: 500;
@@ -268,34 +252,21 @@
 /* Badge (injection count / custom method indicator) */
 .mint-well-plate__badge {
   position: absolute;
-  top: -5px;
-  right: -5px;
-  box-sizing: border-box;
-  min-width: 14px;
-  height: 14px;
-  padding: 0 3px;
+  top: -4px;
+  right: -4px;
+  width: 16px;
+  height: 16px;
   border-radius: 9999px;
-  box-shadow: 0 0 0 2px var(--bg-card);
-  font-family: var(--font-mono);
-  font-size: 9px;
+  font-size: 10px;
   font-weight: 700;
   display: flex;
   align-items: center;
   justify-content: center;
-  color: var(--bg-card);
+  color: white;
   pointer-events: none;
   line-height: 1;
 }
 
-/* Custom method: a plain dot (7a) */
-.mint-well-plate__badge--dot {
-  top: -2px;
-  right: -2px;
-  min-width: 8px;
-  height: 8px;
-  padding: 0;
-}
-
 /* Sample type legend bar */
 .mint-well-plate__sample-legend {
   margin-top: 0.5rem;
@@ -312,23 +283,15 @@
 }
 
 .mint-well-plate__sample-legend-dot {
-  display: inline-flex;
-  align-items: center;
-  justify-content: center;
-  box-sizing: border-box;
   width: 0.875rem;
   height: 0.875rem;
   border-radius: var(--radius-sm);
   flex-shrink: 0;
-  font-family: var(--font-mono);
-  font-size: 0.625rem;
-  font-weight: 600;
-  line-height: 1;
 }
 
 .mint-well-plate__sample-legend-text {
   font-size: 0.75rem;
-  color: var(--text-secondary);
+  color: var(--text-muted);
 }
 
 /* Empty / loading / error placeholder host (content comes from EmptyState) */

package/src/types/auth.ts

@@ -20,40 +20,3 @@ export interface UserInfo {
   roleObj?: RoleInfo | null
   isActive: boolean
 }
-
-// Login response from API
-export interface LoginResponse {
-  access_token: string
-  token_type: string
-  expires_in: number
-}
-
-// Token verification response
-export interface TokenVerifyResponse {
-  valid: boolean
-  username: string | null
-  expires_at: string | null
-}
-
-// Registration request
-export interface RegisterRequest {
-  username: string
-  password: string
-  email?: string
-  shortname?: string
-}
-
-// Profile update request
-export interface UpdateProfileRequest {
-  email?: string
-  shortname?: string
-  current_password?: string
-  new_password?: string
-}
-
-// Passkey credential info
-export interface CredentialInfo {
-  credential_id: string
-  device_name: string | null
-  created_at: string
-}

package/src/types/components.ts

@@ -13,6 +13,8 @@ interface ActionMenuItemBase {
   label: string
   disabled?: boolean
   danger?: boolean
+  /** Set on every item to make the menu a single choice (`menuitemradio`); true marks the current one. */
+  checked?: boolean
 }
 
 export type ActionMenuItem =
@@ -23,6 +25,8 @@ export type ActionMenuItem =
   | (ActionMenuItemBase & {
       href: string
       target?: '_self' | '_blank' | '_parent' | '_top'
+      /** Links navigate; only buttons can be single-choice items. */
+      checked?: never
     })
 
 // Input types

package/src/types/fileBrowserTypes.ts

@@ -83,3 +83,18 @@ export interface FileBrowserLocation {
   mount_id: string
   path: string
 }
+
+/** Several directory levels in one response, parents before children. */
+export interface FileDirectoryTree {
+  listings?: FileDirectoryListing[]
+  /** True when the server's entry budget stopped before the requested depth. */
+  truncated?: boolean
+}
+
+/** Entries whose name contains a query, below one directory. */
+export interface FileSearchResult {
+  entries?: FileEntry[]
+  searched_directories?: number
+  /** True when a directory, result or time budget ended the search early. */
+  truncated?: boolean
+}

package/src/types/filePicker.ts

@@ -3,6 +3,8 @@ export type PickerSource = 'server' | 'localFile'
 export type PickerSelectionMode = 'single-file' | 'multi-file' | 'folder' | 'folder+files'
 /** `list` shows one folder at a time (the default); `tree` adds disclosure triangles. */
 export type PickerView = 'list' | 'tree'
+/** Row order inside each folder; folders always come before files. */
+export type PickerSort = 'newest' | 'oldest' | 'name' | 'name-desc'
 
 interface PickerNodeBase {
   path: string
@@ -39,6 +41,11 @@ export interface PickerRequest {
    */
   refresh?: true
 }
+/** What a search found before a server or walk limit stopped it. */
+export interface PickerSearchResult {
+  nodes: PickerNode[]
+  truncated: boolean
+}
 export interface PickerAdapter {
   /**
    * `listRoot()` returns mount points. FilePicker then shows them as header
@@ -55,7 +62,7 @@ export interface PickerAdapter {
     query: string,
     scope: { path: string; recursive: boolean },
     request?: PickerRequest,
-  ): Promise<PickerNode[]>
+  ): Promise<PickerNode[] | PickerSearchResult>
 }
 export interface PickerCapability {
   /** Case-insensitive suffixes, including compound extensions such as mzML.gz. */

package/src/types/index.ts

@@ -218,9 +218,11 @@ export type {
   FileBrowserLocation,
   FileBrowserSortKey,
   FileDirectoryListing,
+  FileDirectoryTree,
   FileEntry,
   FileEntryKind,
   FilePathCrumb,
+  FileSearchResult,
   FileSelection,
   ServerMount,
 } from './fileBrowserTypes'
@@ -296,11 +298,6 @@ export type {
 export type {
   AuthConfig,
   UserInfo,
-  LoginResponse,
-  TokenVerifyResponse,
-  RegisterRequest,
-  UpdateProfileRequest,
-  CredentialInfo,
 } from './auth'
 
 // Platform types

package/src/utils/rack.ts

@@ -1,11 +1,11 @@
 import type { Rack, SlotPosition, Well, WellEditData, WellPlateFormat } from '../types'
 
-/** @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 LcmsPlateType = '96well' | '54vial'
-/** @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 LcmsControlSampleType = 'blank' | 'qc' | 'iqc'
 
-/** @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 LcmsPlateCell {
   row: string
   column: number
@@ -17,7 +17,7 @@ export interface LcmsPlateCell {
   slot?: SlotPosition | null
 }
 
-/** @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 LcmsPlateCellsToRackOptions {
   rackId?: string
   rackName?: string
@@ -27,14 +27,14 @@ export interface LcmsPlateCellsToRackOptions {
   injectionVolume?: 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 LcmsPlateCellsToRacksOptions extends Omit<LcmsPlateCellsToRackOptions, 'rackId' | 'rackName' | 'slot'> {
   defaultSlot?: SlotPosition
   rackId?: (slot: SlotPosition, index: number) => string
   rackName?: (slot: SlotPosition, index: number) => string
 }
 
-/** @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 LCMS_DEFAULT_CONTROL_POSITIONS: Record<LcmsPlateType, Record<LcmsControlSampleType, { row: string; column: number }>> = {
   '96well': {
     blank: { row: 'H', column: 12 },
@@ -50,24 +50,24 @@ export const LCMS_DEFAULT_CONTROL_POSITIONS: Record<LcmsPlateType, Record<LcmsCo
 
 const SLOT_ORDER: SlotPosition[] = ['R', 'G', 'B', 'Y']
 
-/** @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 lcmsPlateTypeToRackFormat(plateType: LcmsPlateType): WellPlateFormat {
   return plateType === '96well' ? 96 : 54
 }
 
-/** @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 rackFormatToLcmsPlateType(format: WellPlateFormat): LcmsPlateType {
   if (format === 96) return '96well'
   if (format === 54) return '54vial'
   throw new Error(`LCMS plate cells support only 54-vial racks and 96-well plates; received format ${format}.`)
 }
 
-/** @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 lcmsWellId(row: string, column: number): string {
   return `${row.toUpperCase()}${column}`
 }
 
-/** @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 parseLcmsWellId(wellId: string): { row: string; column: number } {
   const match = /^([A-Za-z]+)(\d+)$/.exec(wellId.trim())
   if (!match) {
@@ -80,7 +80,7 @@ export function parseLcmsWellId(wellId: string): { row: string; column: 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 function lcmsPlateCellsToRack(cells: LcmsPlateCell[], options: LcmsPlateCellsToRackOptions = {}): Rack {
   const format = options.format ?? (options.plateType ? lcmsPlateTypeToRackFormat(options.plateType) : inferRackFormat(cells))
   const slot = options.slot ?? cells.find(cell => cell.slot)?.slot ?? 'R'
@@ -116,7 +116,7 @@ export function lcmsPlateCellsToRack(cells: LcmsPlateCell[], options: LcmsPlateC
   }
 }
 
-/** @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 lcmsPlateCellsToRacks(cells: LcmsPlateCell[], options: LcmsPlateCellsToRacksOptions = {}): Rack[] {
   const bySlot = new Map<SlotPosition, LcmsPlateCell[]>()
   const defaultSlot = options.defaultSlot ?? 'R'
@@ -138,7 +138,7 @@ export function lcmsPlateCellsToRacks(cells: LcmsPlateCell[], options: LcmsPlate
     }))
 }
 
-/** @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 rackToLcmsPlateCells(rack: Rack): LcmsPlateCell[] {
   return Object.entries(rack.wells)
     .map(([wellId, well]) => wellToLcmsPlateCell(rack, wellId, well))
@@ -146,18 +146,18 @@ export function rackToLcmsPlateCells(rack: Rack): LcmsPlateCell[] {
     .sort(comparePlateCells)
 }
 
-/** @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 racksToLcmsPlateCells(racks: Rack[]): LcmsPlateCell[] {
   return racks.flatMap(rackToLcmsPlateCells)
 }
 
-/** @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 getLcmsDefaultControlWellId(plateType: LcmsPlateType, sampleType: LcmsControlSampleType): string {
   const position = LCMS_DEFAULT_CONTROL_POSITIONS[plateType][sampleType]
   return lcmsWellId(position.row, position.column)
 }
 
-/** @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 createLcmsControlWellEditData(
   sampleType: LcmsControlSampleType,
   options: {