@jbrowse/cli 5.0.0-beta.10 → 5.0.0-beta.11

package/dist/commands/add-track-utils/adapter-utils.js

@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { adapterTypesToTrackTypeMap, formats, matchFormat, resolveIndexType, sidecarCandidateNames, trackTypeForAdapter, } from '@jbrowse/add-track-core';
+import { adapterTypesToTrackTypeMap, fileNameOf, formats, matchFormat, resolveIndexType, sidecarCandidateNames, trackTypeForAdapter, } from '@jbrowse/add-track-core';
 import { isURL } from '../../types/common.js';
 import { densitySidecarPath } from '../shared/density.js';
 import { configManifest } from '../validate/configManifest.generated.js';
@@ -134,14 +134,6 @@ export function makeLocationProtocol(protocol) {
         throw new Error(`invalid protocol ${protocol}`);
     };
 }
-/**
- * The bare filename the format table matches against — the same thing
- * `@jbrowse/core`'s `getFileName` hands the guesser chain, so a path and a URL
- * with a presigned query string both reduce to what the regexes expect.
- */
-export function fileNameOf(location) {
-    return (location.replaceAll('\\', '/').split('/').at(-1)?.split(/[?#]/)[0] ?? '');
-}
 // resolves the file-layout spec that both the adapter config and the copied
 // file set derive from, honoring an explicit --adapterType. `typeOverride` is
 // the label to stamp on the adapter when the extension's layout is reused under

package/dist/commands/validate/configManifest.generated.js

@@ -2757,7 +2757,8 @@ export const configManifest = {
                 "DotplotDisplay",
                 "LinearSyntenyDisplay",
                 "LGVSyntenyDisplay",
-                "MultiWaySyntenyDisplay"
+                "MultiWaySyntenyDisplay",
+                "LinearMarkDisplay"
             ]
         },
         "GWASTrack": {
@@ -3124,7 +3125,6 @@ export const configManifest = {
                 "id",
                 "type",
                 "configuration",
-                "filterSetting",
                 "pinnedFeatureIds",
                 "soloFeatureIds",
                 "soloApplied",
@@ -5101,7 +5101,6 @@ export const configManifest = {
                 "id",
                 "type",
                 "configuration",
-                "filterSetting",
                 "pinnedFeatureIds",
                 "soloFeatureIds",
                 "soloApplied",
@@ -5346,8 +5345,7 @@ export const configManifest = {
                 "runClustering",
                 "clusterRegion",
                 "sortRowsBy",
-                "configuration",
-                "filterSetting"
+                "configuration"
             ]
         },
         "LDTrackDisplay": {
@@ -6442,7 +6440,6 @@ export const configManifest = {
                 "clusterRegion",
                 "sortRowsBy",
                 "configuration",
-                "filterSetting",
                 "indexSnp",
                 "indexSnpPinned"
             ]
@@ -6923,14 +6920,17 @@ export const configManifest = {
                 "minimalTicks",
                 "jexlFilters"
             ],
+            "aliases": [
+                "LinearArcDisplay",
+                "LinearPairedArcDisplay"
+            ],
             "stateModelProps": [
                 "id",
                 "type",
                 "runClustering",
                 "clusterRegion",
                 "sortRowsBy",
-                "configuration",
-                "filterSetting"
+                "configuration"
             ]
         }
     },
@@ -7431,6 +7431,7 @@ export const configManifest = {
                 "assemblyNames",
                 "drawCigar",
                 "showGridlines",
+                "showTickLabels",
                 "lockAspectRatio",
                 "lineWidth",
                 "minIdentity",
@@ -7558,6 +7559,9 @@ export const configManifest = {
         "*": [
             "heightPreConfig"
         ],
+        "LinearBasicDisplay": [
+            "jexlFiltersSetting"
+        ],
         "LinearAlignmentsDisplay": [
             "PileupDisplay",
             "SNPCoverageDisplay",
@@ -7568,6 +7572,9 @@ export const configManifest = {
             "hideMismatchesSetting",
             "trackMaxHeight"
         ],
+        "LinearVariantDisplay": [
+            "jexlFiltersSetting"
+        ],
         "LinearMultiSampleVariantDisplay": [
             "clusterTree",
             "jexlFilters",

package/dist/commands/validate/configSchema.generated.js

@@ -5,7 +5,7 @@ export const configJsonSchema = JSON.parse(`
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "$id": "https://jbrowse.org/jb2/schema/v5/config.json",
   "title": "JBrowse config.json",
-  "description": "The JBrowse 5.0.0-beta.10 config.json: assemblies, tracks, connections, site-wide configuration and a default session. Generated from the registered types by \`pnpm autogen\`.",
+  "description": "The JBrowse 5.0.0-beta.11 config.json: assemblies, tracks, connections, site-wide configuration and a default session. Generated from the registered types by \`pnpm autogen\`.",
   "type": "object",
   "properties": {
     "$schema": {
@@ -8656,7 +8656,11 @@ export const configJsonSchema = JSON.parse(`
       ],
       "properties": {
         "type": {
-          "const": "LinearMarkDisplay"
+          "enum": [
+            "LinearMarkDisplay",
+            "LinearArcDisplay",
+            "LinearPairedArcDisplay"
+          ]
         },
         "displayId": {
           "type": "string"
@@ -11907,6 +11911,9 @@ export const configJsonSchema = JSON.parse(`
                 },
                 {
                   "$ref": "#/$defs/MultiWaySyntenyDisplaySlots/properties/fetchSizeLimit"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/fetchSizeLimit"
                 }
               ]
             },
@@ -11917,6 +11924,9 @@ export const configJsonSchema = JSON.parse(`
                 },
                 {
                   "$ref": "#/$defs/MultiWaySyntenyDisplaySlots/properties/forceLoad"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/forceLoad"
                 }
               ]
             },
@@ -11927,6 +11937,9 @@ export const configJsonSchema = JSON.parse(`
                 },
                 {
                   "$ref": "#/$defs/MultiWaySyntenyDisplaySlots/properties/height"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/height"
                 }
               ]
             },
@@ -11950,10 +11963,24 @@ export const configJsonSchema = JSON.parse(`
               "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/growMaxHeight"
             },
             "densityTier": {
-              "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/densityTier"
+              "anyOf": [
+                {
+                  "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/densityTier"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/densityTier"
+                }
+              ]
             },
             "densityTierBpPerPx": {
-              "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/densityTierBpPerPx"
+              "anyOf": [
+                {
+                  "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/densityTierBpPerPx"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/densityTierBpPerPx"
+                }
+              ]
             },
             "readConnectionsLineWidth": {
               "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/readConnectionsLineWidth"
@@ -11987,13 +12014,27 @@ export const configJsonSchema = JSON.parse(`
               "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/filterBy"
             },
             "facet": {
-              "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/facet"
+              "anyOf": [
+                {
+                  "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/facet"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/facet"
+                }
+              ]
             },
             "collapseGroupRows": {
               "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/collapseGroupRows"
             },
             "scales": {
-              "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/scales"
+              "anyOf": [
+                {
+                  "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/scales"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/scales"
+                }
+              ]
             },
             "mismatchAlpha": {
               "$ref": "#/$defs/LGVSyntenyDisplaySlots/properties/mismatchAlpha"
@@ -12008,6 +12049,9 @@ export const configJsonSchema = JSON.parse(`
                 },
                 {
                   "$ref": "#/$defs/MultiWaySyntenyDisplaySlots/properties/showLegend"
+                },
+                {
+                  "$ref": "#/$defs/LinearMarkDisplaySlots/properties/showLegend"
                 }
               ]
             },
@@ -12140,6 +12184,51 @@ export const configJsonSchema = JSON.parse(`
             },
             "splitStrands": {
               "$ref": "#/$defs/MultiWaySyntenyDisplaySlots/properties/splitStrands"
+            },
+            "marks": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/marks"
+            },
+            "transform": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/transform"
+            },
+            "rows": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/rows"
+            },
+            "rowColor": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/rowColor"
+            },
+            "showTree": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/showTree"
+            },
+            "showBranchLength": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/showBranchLength"
+            },
+            "showRowLabels": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/showRowLabels"
+            },
+            "treeAreaWidth": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/treeAreaWidth"
+            },
+            "rowHeight": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/rowHeight"
+            },
+            "origin": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/origin"
+            },
+            "minWidthPx": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/minWidthPx"
+            },
+            "filter": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/filter"
+            },
+            "displayCrossHatches": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/displayCrossHatches"
+            },
+            "minimalTicks": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/minimalTicks"
+            },
+            "jexlFilters": {
+              "$ref": "#/$defs/LinearMarkDisplaySlots/properties/jexlFilters"
             }
           },
           "patternProperties": {
@@ -14268,7 +14357,11 @@ export const configJsonSchema = JSON.parse(`
             "type": "object",
             "properties": {
               "type": {
-                "const": "LinearMarkDisplay"
+                "enum": [
+                  "LinearMarkDisplay",
+                  "LinearArcDisplay",
+                  "LinearPairedArcDisplay"
+                ]
               }
             },
             "required": [
@@ -15073,12 +15166,6 @@ export const configJsonSchema = JSON.parse(`
     "LinearBasicDisplayState": {
       "type": "object",
       "properties": {
-        "filterSetting": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "pinnedFeatureIds": {
           "type": "array",
           "items": {
@@ -15136,6 +15223,10 @@ export const configJsonSchema = JSON.parse(`
         "heightPreConfig": {
           "deprecated": true,
           "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
+        },
+        "jexlFiltersSetting": {
+          "deprecated": true,
+          "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
         }
       }
     },
@@ -15659,12 +15750,6 @@ export const configJsonSchema = JSON.parse(`
     "LinearVariantDisplayState": {
       "type": "object",
       "properties": {
-        "filterSetting": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "pinnedFeatureIds": {
           "type": "array",
           "items": {
@@ -15722,6 +15807,10 @@ export const configJsonSchema = JSON.parse(`
         "heightPreConfig": {
           "deprecated": true,
           "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
+        },
+        "jexlFiltersSetting": {
+          "deprecated": true,
+          "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
         }
       }
     },
@@ -15770,12 +15859,6 @@ export const configJsonSchema = JSON.parse(`
           "type": "string"
         },
         "sortRowsBy": {},
-        "filterSetting": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "heightPreConfig": {
           "deprecated": true,
           "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
@@ -16126,12 +16209,6 @@ export const configJsonSchema = JSON.parse(`
           "type": "string"
         },
         "sortRowsBy": {},
-        "filterSetting": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "indexSnp": {
           "type": "string"
         },
@@ -16189,12 +16266,6 @@ export const configJsonSchema = JSON.parse(`
           "type": "string"
         },
         "sortRowsBy": {},
-        "filterSetting": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "heightPreConfig": {
           "deprecated": true,
           "description": "Legacy display-instance key: a migration lifts it onto the setting that replaced it."
@@ -16212,7 +16283,11 @@ export const configJsonSchema = JSON.parse(`
       ],
       "properties": {
         "type": {
-          "const": "LinearMarkDisplay"
+          "enum": [
+            "LinearMarkDisplay",
+            "LinearArcDisplay",
+            "LinearPairedArcDisplay"
+          ]
         },
         "id": {
           "type": "string"
@@ -17075,7 +17150,11 @@ export const configJsonSchema = JSON.parse(`
             "type": "object",
             "properties": {
               "type": {
-                "const": "LinearMarkDisplay"
+                "enum": [
+                  "LinearMarkDisplay",
+                  "LinearArcDisplay",
+                  "LinearPairedArcDisplay"
+                ]
               }
             },
             "required": [
@@ -18979,6 +19058,9 @@ export const configJsonSchema = JSON.parse(`
         "showGridlines": {
           "type": "boolean"
         },
+        "showTickLabels": {
+          "type": "boolean"
+        },
         "lockAspectRatio": {
           "type": "boolean"
         },

package/dist/commands/validate/markRules/markProblems.js

@@ -1,8 +1,8 @@
 // Generated by scripts/generateMarkRules.ts from plugins/marks/src/LinearMarkDisplay/markProblems.ts: do not edit, `pnpm autogen` rewrites it.
 import { AUTO_BIN } from './autoBin.js';
 import { FEATURE_FIELD_PRESETS, aggregateFieldName, colorProblems, fieldScaleOf, isJexl, SHAPE_NAMES, isNamedColor, paintedScale, scaleEndProblems, universalPresetOf, } from './markRuleFacts.js';
-import { MARK_SPECS, rampResolvesPerRegion, readsValue } from './markSpecs.js';
-import { DEFAULT_AGGREGATE_OP, BIN_OVERLAP_FIELD, DEFAULT_BIN_AS, DEFAULT_BIN_FIELD, DEFAULT_COVERAGE_AS, DEFAULT_FORMULA_AS, DEFAULT_LINE_INTERPOLATE, DEFAULT_ROW_PROPORTION, DEFAULT_LINK_SHAPE, DEFAULT_MARK_TYPE, CELLS_FIELDS, DEFAULT_PILEUP_AS, DEFAULT_PILEUP_FIELDS, DEFAULT_TEXT_FIELD, DEFAULT_X2, MATE_FIELDS, } from './markVocabulary.js';
+import { MARK_SPECS, readsValue } from './markSpecs.js';
+import { DEFAULT_AGGREGATE_OP, BIN_OVERLAP_FIELD, DEFAULT_BIN_AS, DEFAULT_BIN_FIELD, DEFAULT_COVERAGE_AS, DEFAULT_FORMULA_AS, DEFAULT_LINE_INTERPOLATE, DEFAULT_ROW_PROPORTION, DEFAULT_LINK_SHAPE, DEFAULT_MARK_TYPE, CELLS_FIELDS, DEFAULT_PILEUP_AS, DEFAULT_PILEUP_FIELDS, DEFAULT_TEXT_FIELD, DEFAULT_X2, MATE_FIELDS, MAX_THRESHOLD_CUTS, } from './markVocabulary.js';
 import { stepChannels } from './stepChannels.js';
 /**
  * The level of every rule of the list, by the stable id a report and a test
@@ -27,6 +27,8 @@ export const MARK_RULES = {
     'threshold-cuts': 'warning',
     /** A threshold colour naming no cut, so every value paints one colour. */
     'threshold-no-cuts': 'warning',
+    /** A threshold colour naming more cuts than it paints, so a value past the eighth takes the ninth colour. */
+    'threshold-cut-count': 'warning',
     /** A threshold `range` not one colour longer than its cuts. */
     'threshold-range': 'warning',
     /** A `domain` on a linear or log colour, whose ends are `domainMin` and `domainMax`. */
@@ -39,8 +41,6 @@ export const MARK_RULES = {
     'field-spells-constant': 'warning',
     /** A colour's or a shape's `labels` naming values its `domain` does not list, or no categorical scale's. */
     'labels-domain': 'warning',
-    /** A text's colour ramp with an open end, whose colours then differ from one region to the next. */
-    'unpinned-text-ramp': 'warning',
     /** A `minBpPerPx` not below the mark's `maxBpPerPx`, so the mark never draws. */
     'empty-zoom-range': 'error',
     /** A `filter` or `formula` whose `expr` is not a `jexl:` expression. */
@@ -59,6 +59,8 @@ export const MARK_RULES = {
     'step-field-expression': 'error',
     /** A `y` naming a field that no `aggregate` or `coverage` step before it writes. */
     'unwritten-y': 'error',
+    /** Another channel naming a field that no `aggregate` or `coverage` step before it writes, so it reads no value; the field a `facet` or `rows` splits on counts as written. */
+    'unwritten-field': 'warning',
     /** A mark other than a span drawn beside one that stacks rows, standing in the first of them. */
     'value-beside-rows': 'warning',
     /** Two `pileup` steps packing one plot, whose rows share numbers. */
@@ -120,11 +122,6 @@ function stepsOf(mark) {
 function colorScaleOf({ scale, field = '' }) {
     return paintedScale({ scale, field }, fieldScaleOf(FEATURE_FIELD_PRESETS, field));
 }
-function rampColor(mark) {
-    const color = mark.encoding?.color ?? {};
-    const painted = colorScaleOf(color);
-    return painted === 'linear' || painted === 'log' ? color : undefined;
-}
 function sizeFieldOf(size) {
     return typeof size === 'string'
         ? size
@@ -381,7 +378,34 @@ function stepProblems(steps, list = 'transform') {
     }
     return problems;
 }
-function ownProblems(mark, display, section) {
+// Each field a mark's channels read besides `y`, by the slot naming it: the
+// channels its type reads, a colour's or a shape's field where it is a scale,
+// a text's field as its default leaves it, and a link's size field.
+function channelFields(mark, spec) {
+    const encoding = mark.encoding ?? {};
+    const { x, x2, row, color = {}, shape, text = DEFAULT_TEXT_FIELD } = encoding;
+    const reads = (channel) => spec.channels.includes(channel);
+    const named = [
+        ['encoding.x', x],
+        ['encoding.x2', typeof x2 === 'string' ? x2 : x2?.pos],
+        ['encoding.x2.chrom', typeof x2 === 'object' ? x2.chrom : undefined],
+        ['encoding.row', reads('row') ? row : undefined],
+        [
+            'encoding.color.field',
+            reads('color') && colorScaleOf(color) !== 'none'
+                ? fieldOf(color)
+                : undefined,
+        ],
+        ['encoding.shape.field', reads('shape') ? fieldOf(shape) : undefined],
+        ['encoding.text', reads('text') ? text : undefined],
+        [
+            'encoding.size.field',
+            spec.size === 'channel' ? sizeFieldOf(encoding.size) : undefined,
+        ],
+    ];
+    return named.flatMap(([slot, field]) => field && !isJexl(field) ? [[slot, field]] : []);
+}
+function ownProblems(mark, display, section, split) {
     const type = markTypeOf(mark);
     const problems = [];
     const y = mark.encoding?.y;
@@ -430,6 +454,10 @@ function ownProblems(mark, display, section) {
         (color.domain ?? []).length === 0) {
         problems.push(found('threshold-no-cuts', 'encoding.color.domain', 'a threshold names its cut points in domain, and with none every value paints the first colour'));
     }
+    const cutCount = (color.domain ?? []).filter(cut => Number.isFinite(Number(cut))).length;
+    if (colorScaleOf(color) === 'threshold' && cutCount > MAX_THRESHOLD_CUTS) {
+        problems.push(found('threshold-cut-count', 'encoding.color.domain', `a threshold paints ${MAX_THRESHOLD_CUTS} cuts, and these ${cutCount} leave a value past the ${MAX_THRESHOLD_CUTS}th in the ${MAX_THRESHOLD_CUTS + 1}th colour`));
+    }
     problems.push(...shapeLabelProblems(mark.encoding?.shape));
     problems.push(...constantAsFieldProblems(mark.encoding));
     if (typeof size === 'object') {
@@ -437,14 +465,6 @@ function ownProblems(mark, display, section) {
             problems.push(found(rule, `encoding.size.${slot}`, message));
         }
     }
-    const ramp = rampColor(mark);
-    if (ramp) {
-        const { domainMin, domainMax } = ramp;
-        if (rampResolvesPerRegion(type) &&
-            (domainMin === undefined || domainMax === undefined)) {
-            problems.push(found('unpinned-text-ramp', `encoding.color.${domainMin === undefined ? 'domainMin' : 'domainMax'}`, `a ${type}'s ramp resolves an open end against each region's own extremes, so its colours agree across regions only with domainMin and domainMax both pinned`));
-        }
-    }
     const { minBpPerPx = 0, maxBpPerPx = 0 } = mark;
     if (minBpPerPx > 0 && maxBpPerPx > 0 && minBpPerPx >= maxBpPerPx) {
         problems.push(found('empty-zoom-range', 'minBpPerPx', `never draws: minBpPerPx ${minBpPerPx} is not below maxBpPerPx ${maxBpPerPx}`));
@@ -454,8 +474,19 @@ function ownProblems(mark, display, section) {
         problems.push(found('two-packings', 'transform', `packs rows of its own over the ${packsIn(section) ? "facet's" : "display's"} pileup, and the two share row numbers; one pileup packs every mark`));
     }
     const fields = madeFields([...display, ...section, ...stepsOf(mark)]);
-    if (fields && y && !isJexl(y) && !fields.has(y)) {
-        problems.push(found('unwritten-y', 'encoding.y', `reads "${y}", which no step before it writes; they leave ${[...fields].join(', ')}`));
+    if (fields) {
+        if (split) {
+            fields.add(split);
+        }
+        const leaves = `which no step before it writes; they leave ${[...fields].join(', ')}`;
+        if (y && !isJexl(y) && !fields.has(y)) {
+            problems.push(found('unwritten-y', 'encoding.y', `reads "${y}", ${leaves}`));
+        }
+        for (const [slot, field] of channelFields(mark, spec)) {
+            if (!fields.has(field)) {
+                problems.push(found('unwritten-field', slot, `reads "${field}", ${leaves}`));
+            }
+        }
     }
     return problems;
 }
@@ -468,6 +499,13 @@ function ownProblems(mark, display, section) {
 export function markProblems({ marks, facet, transform = [], rows, scales, }) {
     const faceted = named(facet?.field);
     const drawsRows = named(rows?.field) && !faceted;
+    // the field the sections or rows are split on, which every section's rows
+    // keep through the steps that make rows
+    const split = faceted
+        ? String(facet?.field)
+        : drawsRows
+            ? String(rows?.field)
+            : undefined;
     const section = readable(facet?.transform ?? []);
     const display = readable(transform);
     const shared = [...display, ...section];
@@ -489,7 +527,10 @@ export function markProblems({ marks, facet, transform = [], rows, scales, }) {
             : []),
         ...(drawsRows ? packingsUnderRows(marks, transform, section) : []),
         ...marks.flatMap((mark, i) => mark
-            ? ownProblems(mark, display, section).map(p => ({ mark: i, ...p }))
+            ? ownProblems(mark, display, section, split).map(p => ({
+                mark: i,
+                ...p,
+            }))
             : []),
     ];
     for (const [i, mark] of marks.entries()) {

package/dist/commands/validate/markRules/markSpecs.js

@@ -12,46 +12,39 @@ export const MARK_SPECS = {
     bar: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
     },
     point: {
         channels: ['y', 'row', 'color', 'shape'],
         value: 'required',
-        ramp: 'display',
         hit: 'index',
         size: 'constant',
     },
     rule: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
         size: 'constant',
     },
     line: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
         size: 'constant',
     },
     span: {
         channels: ['row', 'color'],
         value: 'none',
-        ramp: 'display',
         hit: 'rows',
     },
     text: {
         channels: ['y', 'row', 'color', 'text'],
         value: 'optional',
-        ramp: 'worker',
         hit: false,
     },
     link: {
         channels: ['y', 'row', 'color', 'size'],
         value: 'optional',
-        ramp: 'display',
         hit: 'index',
         farFoot: true,
         size: 'channel',
@@ -72,23 +65,18 @@ export function plotsValue(type) {
 export function hitsByIndex(type) {
     return specOf(type).hit === 'index';
 }
-/** Whether a mark type's ramp colour resolves per region, in the worker. */
-export function rampResolvesPerRegion(type) {
-    return specOf(type).ramp === 'worker';
-}
 /**
- * The lanes a mark asks the worker to fill: its type's channels, a ramp's raw
- * values beside the colour where the display resolves the ramp, and the hit
- * index where the mark answers a hover through one. The encoder fills whichever of
- * `color` and `colorValue` the colour declaration calls for.
+ * The lanes a mark asks the worker to fill: its type's channels, the colour
+ * lanes `colorLanesOf` chose for its declaration, and the hit index where the
+ * mark answers a hover through one.
  */
-export function markLanes(type) {
+export function markLanes(type, colorLanes) {
     const spec = specOf(type);
     return [
         ...spec.channels.flatMap((channel) => channel === 'shape'
             ? ['glyph']
-            : channel === 'color' && spec.ramp === 'display'
-                ? [channel, 'colorValue']
+            : channel === 'color'
+                ? colorLanes
                 : [channel]),
         ...(spec.farFoot ? ['x2Ref'] : []),
         ...(hitsByIndex(type) ? ['index'] : []),

package/dist/commands/validate/markRules/markVocabulary.js

@@ -26,6 +26,8 @@ export const DEFAULT_LINK_SHAPE = 'dome';
 export const DEFAULT_LINK_STROKE_PX = 2;
 /** The fraction of its row a span fills where its `rowProportion` is left unwritten. */
 export const DEFAULT_ROW_PROPORTION = 1;
+/** The cuts a threshold colour paints, render-core's `MAX_COLOR_CUTS`. */
+export const MAX_THRESHOLD_CUTS = 8;
 export const SIZE_SCALES = ['linear', 'log'];
 export const MARK_SOURCES = ['features', 'density'];
 export const DEFAULT_MARK_SOURCE = 'features';

package/dist/commands/validate/validateConfig.js

@@ -8,6 +8,7 @@
 // loading normally with the setting doing nothing.
 //
 // Pure: no filesystem, no process exit. The command wrapper owns both.
+import { fileNameOf, isLooseTrackConfig, matchFormat, } from '@jbrowse/add-track-core';
 import { configManifest } from './configManifest.generated.js';
 import { displayDefaultsForTrackType } from './displayDefaultKeys.js';
 import { isRecord, liftToSnapshot } from './liftConfig.js';
@@ -103,7 +104,7 @@ function checkPluggable(obj, group, groupLabel, where, report) {
 }
 function checkTrack(track, index, manifest, report, ctx) {
     const where = `tracks[${index}]`;
-    const loose = typeof track.uri === 'string' && !('adapter' in track);
+    const loose = isLooseTrackConfig(track);
     const trackId = track.trackId;
     if (typeof trackId === 'string' && trackId) {
         if (ctx.seenTrackIds.has(trackId)) {
@@ -129,6 +130,19 @@ function checkTrack(track, index, manifest, report, ctx) {
             }
         }
     }
+    if (loose) {
+        const file = fileNameOf(track.uri);
+        const spec = matchFormat(file)?.spec;
+        if (!spec || !('adapterType' in spec)) {
+            const message = `JBrowse infers no track from "${file}", so the track fails to load: give it an "adapter"`;
+            if (ctx.declaresPlugins) {
+                report.warn(`${where}.uri`, `${message}, unless a plugin it declares guesses this extension`);
+            }
+            else {
+                report.error(`${where}.uri`, message);
+            }
+        }
+    }
     checkPluggable(track, manifest.tracks, 'track', where, report);
     if (!loose) {
         checkPluggable(track.adapter, manifest.adapters, 'adapter', `${where}.adapter`, report);

package/dist/version.js

@@ -1 +1 @@
-export const version = '5.0.0-beta.10';
+export const version = '5.0.0-beta.11';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.11",
   "type": "module",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
@@ -31,9 +31,9 @@
     "cli-progress": "^3.12.0",
     "serve-handler": "^6.1.7",
     "tmp": "^0.2.7",
-    "@jbrowse/add-track-core": "^5.0.0-beta.10",
-    "@jbrowse/cigar-utils": "^5.0.0-beta.10",
-    "@jbrowse/text-indexing-core": "^5.0.0-beta.10"
+    "@jbrowse/add-track-core": "^5.0.0-beta.11",
+    "@jbrowse/text-indexing-core": "^5.0.0-beta.11",
+    "@jbrowse/cigar-utils": "^5.0.0-beta.11"
   },
   "publishConfig": {
     "access": "public"