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

package/README.md

@@ -59,17 +59,13 @@ export default {
 ```vue
 <script setup lang="ts">
 import { BaseButton, BaseInput, FormField } from '@morscherlab/mint-sdk'
-import { useToast, useAuth } from '@morscherlab/mint-sdk'
+import { useToast } from '@morscherlab/mint-sdk'
 import type { ButtonVariant } from '@morscherlab/mint-sdk'
 
 const { success } = useToast()
-const { login } = useAuth()
 
-async function handleSubmit() {
-  const result = await login(username, password)
-  if (result) {
-    success('Login successful!')
-  }
+function handleSubmit() {
+  success('Saved!')
 }
 </script>
 
@@ -79,7 +75,7 @@ async function handleSubmit() {
   </FormField>
 
   <BaseButton variant="primary" @click="handleSubmit">
-    Login
+    Save
   </BaseButton>
 </template>
 ```
@@ -198,73 +194,16 @@ async function saveCurrentExperiment() {
 }
 ```
 
-### 5. Use Biology Data Templates
+### 5. Biology Data Templates (deprecated)
 
-Plugin frontends can import standard biology template builders and adapters instead of inventing ad-hoc JSON shapes:
+> Deprecated in MINT 1.3 and removed in 1.4, with no SDK replacement: the
+> biology data templates (`@morscherlab/mint-sdk/templates`, `mint_sdk.templates`,
+> `mint add data-template*`), the `BioTemplate*` views, the `useBioTemplate*`
+> composables, `useTemplateCollection()`, `useExperimentSave()`, and the
+> template-only components `ReagentList`, `ReagentEditor`, `ExperimentTimeline`,
+> `SampleLegend` and `FitPanel`.
 
-```typescript
-import {
-  createWellPlateScreenCollection,
-  createTemplateCollection,
-  createPlateMapTemplate,
-  createSampleSheetTemplate,
-  ensureTemplateFromCollection,
-  listBioTemplateCatalog,
-  listBioTemplatePresets,
-  toPlateMapEditorState,
-  toTemplateDataFrame,
-} from '@morscherlab/mint-sdk/templates'
-
-const catalog = listBioTemplateCatalog()
-const presets = listBioTemplatePresets()
-const template = createPlateMapTemplate({
-  samples: ['Control', 'Treatment'],
-})
-const plateEditorState = toPlateMapEditorState(template)
-
-const sampleFrame = toTemplateDataFrame(createSampleSheetTemplate({
-  samples: [{ sampleId: 'S001', name: 'Control 1' }],
-}))
-// <DataFrame v-bind="sampleFrame" />
-
-const collection = createTemplateCollection([template])
-const loadedPlate = ensureTemplateFromCollection(collection, 'plate-map')
-
-const screenCollection = createWellPlateScreenCollection({
-  samples: ['Control', 'Treatment'],
-  compounds: { 'Drug A': [10, 1, 0.1] },
-  unit: 'uM',
-})
-```
-
-For frontend wiring, `useBioTemplateWorkspace()` combines the generated
-controls, sidebar/forms, renderer props, and SDK component bindings:
-
-```typescript
-import { useBioTemplateWorkspace } from '@morscherlab/mint-sdk'
-import { createWellPlateScreenCollection } from '@morscherlab/mint-sdk/templates'
-
-const collection = createWellPlateScreenCollection({
-  samples: ['Control', 'Treatment'],
-  compounds: { 'Drug A': [10, 1, 0.1] },
-})
-const workspace = useBioTemplateWorkspace(collection)
-
-// <AppSidebar v-bind="workspace.sidebar" />
-// <FormBuilder v-bind="workspace.form" />
-// <BioTemplateRenderer v-if="workspace.renderer" v-bind="workspace.renderer" />
-```
-
-For editable built-in presets, `useBioTemplatePresetWorkspace()` also manages
-the generated control values, collection updates, and current-experiment save:
-
-```typescript
-import { BioTemplatePresetWorkspaceView, useBioTemplatePresetWorkspace } from '@morscherlab/mint-sdk'
-
-const workspace = useBioTemplatePresetWorkspace('wellplate-screen')
-
-// <BioTemplatePresetWorkspaceView :workspace="workspace" />
-```
+### 6. Build Control Workspaces
 
 For custom plugin tools, pass one workspace model to `ControlWorkspaceView` to
 generate `AppTopBar`, `AppSidebar`, `FormBuilder`, component prop bindings, and
@@ -325,26 +264,6 @@ const workspaceModel = defineDoseDesignControlModel({
 </template>
 ```
 
-Built-in templates include `plate-map`, `sample-sheet`, `sample-prep`,
-`dose-response`, `calibration-curve`, `time-course`, `protocol-steps`, `assay-matrix`,
-`reagent-list`, `flow-cytometry-panel`, `instrument-run`, and `qpcr-plate`. In
-plugin projects, `mint add data-template <name> --page` generates the
-matching backend route, typed frontend composable, and starter view.
-Generated composables use `ensureTemplateEnvelope()` to validate backend
-template payloads before assigning typed frontend state. Use
-`createTemplateCollection()`, `extractTemplateCollection()`, and
-`ensureTemplateFromCollection()` when a plugin view reads or writes the shared
-`design_data.templates` layout. `mint add data-template-pack <name> --page`
-generates a pack-level composable that uses these helpers for curated
-experiment scaffolds.
-Use `mint add data-template-pack <name> --page` for curated sets such as
-`cell-culture-screen`, `omics-assay`, `longitudinal-study`, and
-`molecular-assay`.
-For no-scaffold defaults that can be saved directly to `design_data`, use
-template presets such as `createWellPlateScreenCollection()`,
-`createQpcrExpressionCollection()`, `createLcmsBatchCollection()`, and
-`createWesternBlotAssayCollection()`.
-
 ## Components
 
 ### Base Components
@@ -358,6 +277,11 @@ template presets such as `createWellPlateScreenCollection()`,
 - `FormField` - Form field wrapper with label, error, and hint
 - `FormBuilder` - Schema-driven forms from full `schema` objects or compact `controls`
 
+Contributor rule: SDK components compose SDK fields (`FormField` + `BaseInput`,
+`BaseSelect`, `BaseTextarea`, `UnitInput`, `SearchableSelect`, `BaseButton`) and
+never restyle them. A component stylesheet may size and place a field; it does
+not define its own input, select, textarea, unit or button looks.
+
 ### Feedback Components
 - `AlertBox` - Alert messages (success, error, warning, info)
 - `AppToastContainer` - Toast notification container for the global `useToast()` queue
@@ -371,30 +295,44 @@ template presets such as `createWellPlateScreenCollection()`,
 - `AppTopBar` - Application header with slots
 - `AppSidebar` - Context sidebar that accepts panels/forms or a compact `controls` schema
 
-### Biological Template Components
-- `BioTemplateRenderer` - Render template envelopes or collections with matching SDK components
-- `BioTemplateExperimentWorkspaceView` - Current-experiment load/save/reset workspace for one template or collection
-- `BioTemplatePresetWorkspaceView` - Full editable preset workspace from `useBioTemplatePresetWorkspace()`
-
 ### File & Data Components
 - `FileUploader` - Drag-and-drop file upload with file/folder mode support
 
 ### Sample Management Components
-- `SampleSelector` - Hierarchical sample grouping with auto-group, CSV metadata import, and optional experiment `design_data` sample loading
-- `AutoGroupModal` - Smart sample grouping wizard for names and design metadata
-- `GroupAssigner` - Drag-and-drop group assignment for comparisons (e.g., Control vs Treatment)
+
+Deprecated in MINT 1.3 and removed in 1.4, with no SDK replacement: sample
+grouping as a whole (`SampleSelector`, `SmartGroupModal`,
+`SmartGroupFieldRecipe`, `SmartGroupManual`, `AutoGroupModal`,
+`useAutoGroup`, `GroupAssigner`, `useGroupAssignment`).
 
 ### Removed Compatibility APIs
 
 The public SDK no longer exports `ToastNotification`, `GroupingModal`,
-`SettingsButton`, `FormSection`, `FormFieldRenderer`, `usePluginApi()`,
-`usePluginConfig()`, the identity-only `usePluginClient()`, or the legacy
-`useJobsStatusTray()` job adapter API.
-Use `AppToastContainer`, `AutoGroupModal`, `AppTopBar` settings or
+`SettingsButton`, `FormSection`, `FormFieldRenderer`, `usePluginApi()`, or
+`usePluginConfig()`. The identity-only `usePluginClient()` and the legacy
+`useJobsStatusTray()` job adapter API remain deprecated until MINT 1.4.
+Use `AppToastContainer`, `AppTopBar` settings or
 `SettingsModal`, `FormBuilder`, `usePluginSettings()`, generated
 `useGeneratedPluginClient()` helpers, and source-driven `usePluginJobCenter()`
-instead. `mint doctor` still detects old imports and reports the replacement
-path.
+instead.
+
+MINT 1.3 also removed `ColorSlider` (pass `colorStops`, `thresholds`,
+`showLabels`, `minLabel` and `maxLabel` to `BaseSlider`), `DropdownButton`
+(`BaseSelect` or `SearchableSelect` for values, `ActionMenu` for actions),
+`InstrumentAlertLog`, `InstrumentStatusCard`, `LcmsSequenceTable`, `useAsync()`,
+`useOptimisticMutation()` (use `useRequestSyncState()`), `useResourceCrud()`
+(use `useGeneratedPluginClient()`), `useCommandHistory()`,
+`useWellPlateAdapter()`, `useWellPlateValidation()` (no SDK replacement; keep
+them in the plugin), `useWellPainting()` and `useWellPlateEditor()` (use
+`useRackEditor()` with `PlateEditor`). `mint doctor` still detects old imports
+and reports the replacement path.
+
+MINT 1.3 removed `AppPluginSwitcher` and its `PluginSwitcherPlugin` /
+`PluginSwitcherInfo` types, with the `pluginSwitcher` prop and
+`plugin-switcher-*` events on `AppTopBar` and `PluginWorkspaceView`: integrated
+plugins now show their icon, name and version as a static identity in
+`AppTopBar`. `ProgressBar` lost its segmented variant (`variant`, `steps`,
+`currentStep`); use `StepWizard` for step progress and the rail for percentages.
 
 ## Composables
 
@@ -520,35 +458,6 @@ callers can present a single sign-in prompt without risking duplicate writes.
 Clients created with `withAuth: false` retain their existing auth state and
 receive the original HTTP error.
 
-### `useAuth()`
-Authentication methods.
-
-```typescript
-const { login, logout, initializeAuth, getCurrentUser } = useAuth()
-
-// Initialize on app mount
-await initializeAuth()
-
-// Login
-const success = await login(username, password)
-
-// Get current user
-const user = await getCurrentUser()
-```
-
-### `usePasskey()`
-WebAuthn/FIDO2 passkey support.
-
-```typescript
-const { isSupported, registerPasskey, loginWithPasskey } = usePasskey()
-
-if (isSupported()) {
-  await registerPasskey('My Device')
-  // or
-  await loginWithPasskey()
-}
-```
-
 ### `useTheme()`
 Theme switching.
 
@@ -651,7 +560,6 @@ import type {
   // Auth
   AuthConfig,
   UserInfo,
-  LoginResponse,
 
   // Platform
   PluginInfo,