@morscherlab/mint-sdk 1.2.0-beta.7 → 1.2.0-beta.9

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

@@ -0,0 +1,30 @@
+/* DataStateInternal — shared loading / error / empty presentation for data components */
+
+.mint-data-state {
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: center;
+  background-color: var(--bg-primary);
+}
+
+.mint-data-state--loading {
+  gap: 0.75rem;
+  padding: 2.5rem 2rem;
+  color: var(--text-muted);
+}
+
+.mint-data-state--loading.mint-data-state--sm {
+  padding: 1.25rem 1rem;
+}
+
+.mint-data-state--loading.mint-data-state--lg {
+  padding: 3.5rem 2rem;
+}
+
+.mint-data-state__loading-text {
+  font-size: 0.875rem;
+  color: var(--text-muted);
+  margin: 0 !important;
+  padding: 0 !important;
+}

package/src/styles/components/dataframe.css

@@ -187,6 +187,23 @@
   text-align: center;
 }
 
+/* Sortable headers are real buttons; strip the native chrome so the cell keeps
+   its table-header appearance while staying keyboard-operable. */
+.mint-dataframe__th-button {
+  display: block;
+  width: 100%;
+  margin: 0;
+  padding: 0;
+  border: 0;
+  background: none;
+  color: inherit;
+  font: inherit;
+  letter-spacing: inherit;
+  text-transform: inherit;
+  text-align: inherit;
+  cursor: inherit;
+}
+
 .mint-dataframe__th-content {
   display: inline-flex;
   align-items: center;
@@ -308,7 +325,7 @@
 }
 
 .mint-dataframe__row--clickable:focus-visible {
-  outline: 2px solid var(--focus-ring-color, var(--color-primary));
+  outline: 2px solid var(--color-primary);
   outline-offset: -2px;
 }
 
@@ -352,32 +369,15 @@ html.dark .mint-dataframe__row--selected > .mint-dataframe__td {
   border-bottom: none;
 }
 
-/* Empty state */
-.mint-dataframe__empty {
+/* Empty / error placeholder host (content comes from EmptyState) */
+.mint-dataframe__state {
   display: flex;
-  flex-direction: column;
   align-items: center;
   justify-content: center;
   min-height: 12rem;
-  padding: 2.5rem 2rem;
-  color: var(--text-muted);
   background-color: var(--bg-primary);
 }
 
-.mint-dataframe__empty-icon {
-  width: 2.5rem;
-  height: 2.5rem;
-  opacity: 0.5;
-  margin-bottom: 0.5rem;
-}
-
-.mint-dataframe__empty-text {
-  font-size: 0.875rem;
-  margin-top: 0 !important;
-  margin-bottom: 0 !important;
-  padding: 0 !important;
-}
-
 /* Loading overlay */
 .mint-dataframe__loading {
   position: absolute;
@@ -395,18 +395,6 @@ html.dark .mint-dataframe__loading {
   background-color: rgba(0, 0, 0, 0.4);
 }
 
-.mint-dataframe__loading-spinner {
-  width: 1.5rem;
-  height: 1.5rem;
-  color: var(--color-primary);
-  animation: mint-dataframe-spin 1s linear infinite;
-}
-
-@keyframes mint-dataframe-spin {
-  from { transform: rotate(0deg); }
-  to { transform: rotate(360deg); }
-}
-
 /* Footer / Pagination */
 .mint-dataframe__footer {
   display: flex;
@@ -502,11 +490,17 @@ html.dark .mint-dataframe__loading {
   transition: background-color 0.15s ease;
 }
 
-.mint-dataframe__resize-handle:hover::after {
+.mint-dataframe__resize-handle:hover::after,
+.mint-dataframe__resize-handle:focus-visible::after {
   width: 2px;
   background-color: var(--color-primary);
 }
 
+.mint-dataframe__resize-handle:focus-visible {
+  outline: none;
+  box-shadow: var(--focus-ring);
+}
+
 /* Row delete action column */
 .mint-dataframe__th--actions,
 .mint-dataframe__td--actions {
@@ -539,8 +533,8 @@ html.dark .mint-dataframe__loading {
 }
 
 .mint-dataframe__delete-btn:hover {
-  background-color: color-mix(in srgb, var(--color-error, #ef4444) 14%, transparent);
-  color: var(--color-error, #ef4444);
+  background-color: color-mix(in srgb, var(--mint-error) 14%, transparent);
+  color: var(--mint-error);
 }
 
 .mint-dataframe__delete-btn:focus-visible {

package/src/styles/components/experiment-data-viewer.css

@@ -27,10 +27,10 @@
   flex-direction: column;
   gap: 12px;
 }
-.mint-data-viewer__empty {
-  text-align: center;
-  padding: 32px;
-  color: var(--text-muted);
+.mint-data-viewer__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
 }
 
 /* Summary view */

package/src/styles/components/experiment-timeline.css

@@ -291,7 +291,7 @@
 .mint-timeline__expanded {
   margin-top: 0.75rem;
   padding-top: 0.75rem;
-  border-top: 1px solid rgba(var(--border-color-rgb, 0, 0, 0), 0.5);
+  border-top: 1px solid color-mix(in srgb, var(--border-color) 50%, transparent);
 }
 
 .mint-timeline__description {
@@ -434,42 +434,15 @@
   width: 2rem;
 }
 
-/* Empty state */
-.mint-timeline__empty {
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-timeline__state {
   display: flex;
   align-items: center;
   justify-content: center;
-  padding: 2rem;
   border: 2px dashed var(--border-color);
   border-radius: var(--radius-md);
 }
 
-.mint-timeline__empty-content {
-  text-align: center;
-}
-
-.mint-timeline__empty-text {
-  color: var(--text-muted);
-  margin-top: 0 !important;
-  margin-bottom: 0.5rem !important;
-  padding: 0 !important;
-}
-
-.mint-timeline__empty-btn {
-  padding: 0.375rem 0.75rem;
-  font-size: 0.875rem;
-  background-color: var(--color-primary);
-  color: white;
-  border: none;
-  border-radius: var(--radius-md);
-  cursor: pointer;
-  transition: background-color 0.15s ease;
-}
-
-.mint-timeline__empty-btn:hover {
-  opacity: 0.9;
-}
-
 /* Add step button (end) */
 .mint-timeline__add-end {
   display: flex;

package/src/styles/components/form-builder.css

@@ -40,16 +40,16 @@
 }
 
 .mint-form-section__title {
-  font-size: var(--font-size-base, 0.9375rem);
+  font-size: 0.9375rem;
   font-weight: 600;
-  color: var(--color-text, #1a1a2e);
+  color: var(--text-primary);
   margin: 0;
   line-height: 1.4;
 }
 
 .mint-form-section__description {
-  font-size: var(--font-size-sm, 0.8125rem);
-  color: var(--color-text-secondary, #6b7280);
+  font-size: 0.8125rem;
+  color: var(--text-secondary);
   margin: 0;
   line-height: 1.5;
 }
@@ -65,5 +65,5 @@
   align-items: center;
   gap: 0.75rem;
   padding-top: 1rem;
-  border-top: 1px solid var(--color-border, #e5e7eb);
+  border-top: 1px solid var(--border-color);
 }

package/src/styles/components/lcms-sequence-table.css

@@ -64,7 +64,11 @@
   padding-right: 0.25rem;
 }
 
+/* The handle is a button so it can also take Alt+Arrow keyboard reordering. */
 .mint-lcms-sequence-table__drag-handle {
+  padding: 0;
+  border: 0;
+  background: none;
   color: var(--text-muted, #64748b);
   cursor: grab;
   font-family: var(--font-mono, 'Fira Code', monospace);
@@ -72,6 +76,11 @@
   letter-spacing: -0.08em;
 }
 
+.mint-lcms-sequence-table__drag-handle:focus-visible {
+  outline: none;
+  box-shadow: var(--focus-ring);
+}
+
 .mint-lcms-sequence-table__td {
   min-width: 0;
   color: var(--text-primary, #0f172a);
@@ -168,7 +177,6 @@
   background: color-mix(in srgb, var(--mint-error, #ef4444) 10%, transparent);
 }
 
-.mint-lcms-sequence-table__empty,
 .mint-lcms-sequence-table__more {
   color: var(--text-muted, #64748b);
   font-size: 0.875rem;
@@ -176,6 +184,13 @@
   text-align: center;
 }
 
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-lcms-sequence-table__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}
+
 .mint-lcms-sequence-table__more {
   border-top: 1px solid var(--border-color, #e2e8f0);
   padding: 0.625rem 1rem;

package/src/styles/components/multi-select.css

@@ -64,7 +64,7 @@
 }
 
 .mint-multi-select__chip--active:hover {
-  background-color: var(--color-primary-dark, #4338ca);
+  background-color: var(--color-primary-hover);
 }
 
 .mint-multi-select__chip--disabled {

package/src/styles/components/reagent-list.css

@@ -138,6 +138,24 @@
   color: var(--text-secondary);
 }
 
+/* Sortable headers are real buttons; strip the native chrome so the cell keeps
+   its table-header look while staying keyboard-operable. */
+.mint-reagent-list__sort-btn {
+  display: inline-flex;
+  align-items: center;
+  width: 100%;
+  margin: 0;
+  padding: 0;
+  border: 0;
+  background: none;
+  color: inherit;
+  font: inherit;
+  letter-spacing: inherit;
+  text-transform: inherit;
+  text-align: inherit;
+  cursor: inherit;
+}
+
 .mint-reagent-list__sort-icon {
   display: inline-block;
   width: 0.75rem;
@@ -332,45 +350,34 @@
   height: 1rem;
 }
 
-/* Empty state */
-.mint-reagent-list__empty {
-  padding: 2rem;
-  text-align: center;
-}
-
-.mint-reagent-list__empty-icon {
-  width: 2.5rem;
-  height: 2.5rem;
-  margin: 0 auto 0.75rem;
-  color: var(--text-muted);
-  opacity: 0.5;
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-reagent-list__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
 }
 
-.mint-reagent-list__empty-text {
-  font-size: 0.875rem;
-  color: var(--text-muted);
-  margin-top: 0 !important;
-  margin-bottom: 0.75rem !important;
-  padding: 0 !important;
+/* Drag handle */
+/* The drag handle doubles as the keyboard reorder target (Alt+Arrow). */
+.mint-reagent-list__drag-handle-btn {
+  display: inline-flex;
+  align-items: center;
+  padding: 0;
+  border: 0;
+  background: none;
+  color: inherit;
+  cursor: grab;
 }
 
-.mint-reagent-list__empty-btn {
-  padding: 0.375rem 0.75rem;
-  font-size: 0.875rem;
-  font-weight: 500;
-  color: white;
-  background-color: var(--color-primary);
-  border: none;
-  border-radius: var(--radius);
-  cursor: pointer;
-  transition: background-color 0.15s ease;
+.mint-reagent-list__drag-handle-btn:focus-visible {
+  outline: none;
+  box-shadow: var(--focus-ring);
 }
 
-.mint-reagent-list__empty-btn:hover {
-  background-color: var(--color-primary-hover);
+.mint-reagent-list__drag-handle-btn:focus-visible .mint-reagent-list__drag-handle {
+  opacity: 1;
 }
 
-/* Drag handle */
 .mint-reagent-list__drag-handle {
   width: 1rem;
   color: var(--text-muted);

package/src/styles/components/sample-hierarchy-tree.css

@@ -288,23 +288,9 @@
   }
 }
 
-/* Empty state */
-.mint-sample-tree__empty {
-  padding: 1rem;
-  text-align: center;
-  color: var(--text-muted);
-}
-
-.mint-sample-tree__empty-icon {
-  width: 2rem;
-  height: 2rem;
-  margin: 0 auto 0.5rem;
-  opacity: 0.5;
-}
-
-.mint-sample-tree__empty-text {
-  font-size: 0.875rem;
-  margin-top: 0 !important;
-  margin-bottom: 0 !important;
-  padding: 0 !important;
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-sample-tree__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
 }

package/src/styles/components/sample-selector.css

@@ -468,14 +468,21 @@
   height: 0.625rem;
 }
 
-/* Empty State */
-.mint-sample-selector__empty {
+/* Inline hint shown inside the grouped/flat sub-lists */
+.mint-sample-selector__hint {
   text-align: center;
   padding: 1rem;
   font-size: 0.875rem;
   color: var(--text-muted);
 }
 
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-sample-selector__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}
+
 /* Ungrouped Section */
 .mint-sample-selector__ungrouped {
   margin-top: 0.75rem;

package/src/styles/components/schedule-calendar.css

@@ -470,3 +470,11 @@
 .mint-schedule__month-more:hover {
   text-decoration: underline;
 }
+
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-schedule__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  min-height: 12rem;
+}

package/src/styles/components/scientific-number.css

@@ -59,5 +59,5 @@
 }
 
 .mint-sci-number__copy-btn--copied {
-  color: var(--color-success, #10b981);
+  color: var(--mint-success);
 }

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

@@ -284,3 +284,11 @@
   font-size: 0.75rem;
   color: var(--text-muted);
 }
+
+/* Empty / loading / error placeholder host (content comes from EmptyState) */
+.mint-well-plate__state {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  min-height: 12rem;
+}

package/src/styles/index.css

@@ -57,6 +57,7 @@
 @import './components/dropdown-button.css';
 @import './components/calendar.css';
 @import './components/dataframe.css';
+@import './components/data-state.css';
 @import './components/well-edit-popup.css';
 @import './components/rack-editor.css';
 @import './components/loading-spinner.css';
@@ -92,3 +93,10 @@
 @import './components/artifact-save-dialog.css';
 @import './components/experiment-popover.css';
 @import './components/fit-panel.css';
+@import './components/app-avatar-menu.css';
+@import './components/app-page-selector.css';
+@import './components/app-pill-nav.css';
+@import './components/app-plugin-switcher.css';
+@import './components/mobile-support-gate.css';
+@import './components/plugin-icon.css';
+@import './components/reagent-editor.css';

package/src/styles/variables.css

@@ -66,6 +66,32 @@
   /* The MINT 1.1 card system uses exactly one shadow for every card. */
   --card-shadow: 0 1px 2px 0 rgb(0 0 0 / 0.04), 0 1px 3px 0 rgb(0 0 0 / 0.06);
 
+  /* Categorical sample scale — mirrored by SAMPLE_COLOR_SCALE in
+     src/utils/color.ts. The JS constant carries the same hexes as a
+     canvas/SVG/persistence-safe fallback; change both together. */
+  --mint-sample-1: #3B82F6;
+  --mint-sample-2: #10B981;
+  --mint-sample-3: #EF4444;
+  --mint-sample-4: #F59E0B;
+  --mint-sample-5: #8B5CF6;
+  --mint-sample-6: #F97316;
+  --mint-sample-7: #06B6D4;
+  --mint-sample-8: #14B8A6;
+  --mint-sample-9: #6B7280;
+
+  /* Rack / plate slot positions — mirrored by SLOT_COLORS in
+     src/utils/color.ts. */
+  --mint-slot-r: #ef4444;
+  --mint-slot-g: #22c55e;
+  --mint-slot-b: #3b82f6;
+  --mint-slot-y: #eab308;
+
+  /* Motion — the SDK's standard easing curve. */
+  --mint-ease-out-quart: cubic-bezier(0.25, 1, 0.5, 1);
+
+  /* Typography — Fira Code for data, code and routes. */
+  --font-mono: 'Fira Code', ui-monospace, SFMono-Regular, Menlo, monospace;
+
   /* Border radius */
   --radius-sm: 0.25rem;
   --radius: 0.375rem;
@@ -90,6 +116,8 @@
   --mint-warning-hover: #D97706;
   --mint-warning-bg: rgba(245, 158, 11, 0.1);
   --mint-warning-border: rgba(245, 158, 11, 0.3);
+  /* Readable warning label on --mint-warning-bg (amber-700, 5.9:1). */
+  --mint-warning-text: #B45309;
   --mint-info: #3B82F6;
   --mint-info-bg: rgba(59, 130, 246, 0.1);
   --mint-info-border: rgba(59, 130, 246, 0.3);
@@ -178,6 +206,7 @@ html.dark {
   --mint-success-bg: rgba(16, 185, 129, 0.15);
   --mint-error-bg: rgba(239, 68, 68, 0.15);
   --mint-warning-bg: rgba(245, 158, 11, 0.15);
+  --mint-warning-text: #FCD34D;
   --mint-info-bg: rgba(59, 130, 246, 0.15);
 
   /* Focus ring - dark mode offset uses bg-primary instead of white */

package/src/templates/builderPresetControls.ts

@@ -7,7 +7,7 @@ import {
   readString,
   readStringList,
 } from './builderReadUtils'
-import { readPlateFormat } from './plateGeometry'
+import { readPlateFormat } from '../components/WellPlate.geometry'
 import { getBioTemplatePresetInfo } from './presets'
 import type {
   CreateElisaAssayCollectionOptions,

package/src/templates/componentPlateHelpers.ts

@@ -2,6 +2,7 @@ import type {
   PlateMapEditorState,
   WellLegendItem,
 } from '../types'
+import { SAMPLE_COLOR_SCALE } from '../utils/color'
 
 export function activePlateFromState(state: PlateMapEditorState) {
   return state.plates.find(plate => plate.id === state.activePlateId) ?? state.plates[0]
@@ -24,6 +25,7 @@ export function legendItemsFromPlateState(state: PlateMapEditorState): WellLegen
 }
 
 export function colorForIndex(index: number): string {
-  const colors = ['#3B82F6', '#10B981', '#EF4444', '#F59E0B', '#8B5CF6', '#F97316', '#06B6D4', '#14B8A6']
+  // The gray tail of the scale is reserved for "other"; component plates cycle the eight hues.
+  const colors = SAMPLE_COLOR_SCALE.slice(0, 8)
   return colors[index % colors.length]
 }

package/src/templates/doseResponseAdapters.ts

@@ -2,6 +2,7 @@ import type {
   PlateCondition,
   PlateMapEditorState,
 } from '../types'
+import { SAMPLE_COLOR_SCALE } from '../utils/color'
 import { toPlateMapEditorState } from './plateMapAdapters'
 import { getTemplateData } from './templateEnvelopes'
 import { validateDoseResponseData } from './templateValidators'
@@ -11,18 +12,6 @@ import type {
   DoseResponseTemplateData,
 } from './types'
 
-const CONDITION_COLORS = [
-  '#3B82F6',
-  '#10B981',
-  '#EF4444',
-  '#F59E0B',
-  '#8B5CF6',
-  '#F97316',
-  '#06B6D4',
-  '#14B8A6',
-  '#6B7280',
-]
-
 export function toDoseConditions(
   template: DoseResponseTemplate | DoseResponseTemplateData
 ): DoseConditionsAdapterResult {
@@ -30,7 +19,7 @@ export function toDoseConditions(
   validateDoseResponseData(data)
   return data.compounds.map((compound, index): PlateCondition => ({
     label: compound.name,
-    color: String(compound.metadata?.color ?? CONDITION_COLORS[index % CONDITION_COLORS.length]),
+    color: String(compound.metadata?.color ?? SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length]),
     concentrations: compound.concentrations,
     unit: data.unit,
   }))

package/src/templates/elisaAssayCollectionBuilder.ts

@@ -1,5 +1,5 @@
 import { createAssayMatrixTemplate } from './assayMatrixBuilder'
-import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'
+import { SAMPLE_COLOR_SCALE } from '../utils/color'
 import { idFromName } from './builderIdUtils'
 import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
 import { createPlateMapTemplate } from './plateMapBuilder'
@@ -27,7 +27,7 @@ export function createElisaAssayCollection(
       ...sampleRecords.map((sample, index) => ({
         id: sample.sampleId,
         name: sample.name ?? sample.sampleId,
-        color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],
+        color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
       })),
     ],
   })

package/src/templates/plateMapBuilder.ts

@@ -1,4 +1,4 @@
-import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'
+import { SAMPLE_COLOR_SCALE } from '../utils/color'
 import { sampleIdFromName } from './builderIdUtils'
 import { createTemplateEnvelope } from './templateEnvelopes'
 import type {
@@ -23,7 +23,7 @@ export function createPlateMapTemplate(
     return {
       id: sampleIdFromName(sample, index),
       name: sample,
-      color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],
+      color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
     }
   })
 

package/src/templates/qpcrPlateBuilder.ts

@@ -1,5 +1,5 @@
 import { idFromName } from './builderIdUtils'
-import { wellIdsForFormat } from './plateGeometry'
+import { wellIdsForFormat } from '../components/WellPlate.geometry'
 import {
   normalizeQpcrSample,
   normalizeQpcrTarget,

package/src/templates/templateValidators.ts

@@ -12,7 +12,7 @@ import type {
   SampleSheetTemplateData,
   TimeCourseTemplateData,
 } from './types'
-import { assertWellInFormat } from './plateGeometry'
+import { assertWellInFormat } from '../components/WellPlate.geometry'
 
 export function validatePlateMapData(data: PlateMapTemplateData): void {
   if (!Array.isArray(data.plates) || data.plates.length === 0) {

package/src/templates/timeCourseBuilder.ts

@@ -1,4 +1,4 @@
-import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'
+import { SAMPLE_COLOR_SCALE } from '../utils/color'
 import {
   idFromName,
   timepointId,
@@ -36,7 +36,7 @@ export function createTimeCourseTemplate(
     return {
       id: idFromName(condition, `condition-${index + 1}`),
       name: condition,
-      color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],
+      color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
       metadata: {},
     }
   })