@jbrowse/cli 5.0.0-beta.1 → 5.0.0-beta.11

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

@@ -0,0 +1,573 @@
+// 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, 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
+ * refer to it by.
+ */
+export const MARK_RULES = {
+    /** A bar, point or rule naming no `y`, with no step before it writing one it reads by default. */
+    'mark-without-value': 'error',
+    /** A channel the mark's type does not read, such as `y` on a `span` or a size field on a point. */
+    'unread-channel': 'warning',
+    /** An `encoding.size` on a mark that draws no point or rule and strokes no link. */
+    'unread-size': 'warning',
+    /** A `linkShape` on a mark that draws no link. */
+    'unread-link-shape': 'warning',
+    /** An `interpolate` on a mark that draws no line. */
+    'unread-interpolate': 'warning',
+    /** A `rowProportion` on a mark that draws no span. */
+    'unread-row-proportion': 'warning',
+    /** `source: "density"` on a `span`, a `text` or a `link`, which cannot draw the sidecar's bins. */
+    'span-density-source': 'warning',
+    /** Threshold cuts that repeat, leaving an interval no value falls in. */
+    '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`. */
+    'ramp-domain': 'warning',
+    /** A scale's `domainMax` below its `domainMin`: a colour ramp's, a width's or `scales.y`'s. */
+    'domain-ends': 'warning',
+    /** A colour ramp's or `scales.y`'s `domainQuantile` outside 0.5 to 1, a percent among them. */
+    'domain-quantile': 'warning',
+    /** A colour's or a shape's `field` spelling a CSS colour or a shape name, which is a constant written `{ value }`. */
+    '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 `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. */
+    'step-expression': 'error',
+    /** A `bin` whose `step` is neither `"auto"` nor a positive width. */
+    'bin-width': 'error',
+    /** A `bin`'s `as` or `fields`, or a `pileup`'s `fields`, naming other than two fields, so the step reads its defaults. */
+    'step-pair': 'warning',
+    /** A `bin` naming a `field` beside the `fields` it cuts at the bin edges, which leaves the `field` unread. */
+    'bin-field-and-fields': 'warning',
+    /** A `sum`, `mean`, `min` or `max` naming no `field`. */
+    'op-field': 'error',
+    /** A `weight` on a `min` or a `max`, which no weight moves. */
+    'unread-weight': 'warning',
+    /** A step's field written as a `jexl:` expression, where a step reads a name or a dotted path. */
+    '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. */
+    'two-packings': 'warning',
+    /** A `pileup` in the display's `transform` under a `facet`, packing across every section. */
+    'cross-section-packing': 'warning',
+    /** A second mark standing in for the density sidecar at a zoom where one already does. */
+    'second-density-mark': 'warning',
+    /** `rows` beside a `facet` on another field, where the facet draws alone. */
+    'rows-beside-facet': 'warning',
+    /** A `pileup` or a `row` field under `rows`, whose packed rows share their value's one row. */
+    'packing-under-rows': 'warning',
+};
+function found(rule, slot, message) {
+    return { rule, level: MARK_RULES[rule], slot, message };
+}
+function markTypeOf(mark) {
+    return mark.mark ?? DEFAULT_MARK_TYPE;
+}
+// Whether a slot holds nothing a reader could act on: unset, empty text, an
+// empty list, or an object none of whose members holds anything.
+function unwritten(value) {
+    return (value === undefined ||
+        value === '' ||
+        (Array.isArray(value) && value.length === 0) ||
+        (typeof value === 'object' &&
+            value !== null &&
+            Object.values(value).every(unwritten)));
+}
+// Whether a channel is written as its default, which a display's snapshot
+// leaves off and a file may spell out: the two read alike, so a slot at its
+// default is no channel for a rule to find unread.
+function atDefault(channel, value) {
+    switch (channel) {
+        case 'x':
+            return value === DEFAULT_BIN_AS[0];
+        case 'x2':
+            return (value === DEFAULT_X2 ||
+                (typeof value === 'object' &&
+                    value !== null &&
+                    unwritten(value.chrom) &&
+                    (value.pos === DEFAULT_X2 ||
+                        unwritten(value.pos))));
+        case 'text':
+            return value === DEFAULT_TEXT_FIELD;
+        default:
+            return false;
+    }
+}
+/** The channels a mark's encoding writes, less those at their default. */
+function writtenChannels(encoding) {
+    return Object.entries(encoding ?? {})
+        .filter(([channel, value]) => !unwritten(value) && !atDefault(channel, value))
+        .map(([channel]) => channel);
+}
+function stepsOf(mark) {
+    return mark.transform ?? [];
+}
+function colorScaleOf({ scale, field = '' }) {
+    return paintedScale({ scale, field }, fieldScaleOf(FEATURE_FIELD_PRESETS, field));
+}
+function sizeFieldOf(size) {
+    return typeof size === 'string'
+        ? size
+        : typeof size === 'object'
+            ? (size.field ?? '')
+            : '';
+}
+// A shape's labels name its domain values in order, as a colour's do, and a
+// constant shape names none.
+// What a reader writes as a colour, without the colour parser the rule list
+// cannot carry into `jbrowse validate`.
+function spellsColor(text) {
+    return (/^(#[\da-f]{3,8}|(rgb|hsl|hwb|lab|lch|oklab|oklch|color)a?\(.*\)|transparent)$/i.test(text) || isNamedColor(text.toLowerCase()));
+}
+function fieldOf(channel) {
+    const field = typeof channel === 'object' && channel !== null
+        ? channel.field
+        : channel;
+    return typeof field === 'string' && !isJexl(field) ? field : '';
+}
+// Inside `encoding` a bare string is a field, so a constant written the way a
+// display-level colour takes one reads as a field no feature holds.
+function constantAsFieldProblems(encoding) {
+    const color = fieldOf(encoding?.color);
+    const shape = fieldOf(encoding?.shape);
+    return [
+        ...(color && spellsColor(color)
+            ? [
+                found('field-spells-constant', 'encoding.color.field', `${JSON.stringify(color)} is a colour, and a string in encoding is a field: a constant colour is { "value": ${JSON.stringify(color)} }`),
+            ]
+            : []),
+        ...(shape && SHAPE_NAMES.includes(shape)
+            ? [
+                found('field-spells-constant', 'encoding.shape.field', `${JSON.stringify(shape)} is a shape, and a string in encoding is a field: a constant shape is { "value": ${JSON.stringify(shape)} }`),
+            ]
+            : []),
+    ];
+}
+function shapeLabelProblems(shape) {
+    if (typeof shape !== 'object' || shape === null) {
+        return [];
+    }
+    const { field = '', scale, domain = [], labels = [] } = shape;
+    // an unwritten domain pairs the labels with the field's own order, as the
+    // key and the worker do
+    const order = domain.length > 0 ? domain : (universalPresetOf(field)?.domain ?? []);
+    const named = paintedScale({ scale, field }, 'categorical') === 'categorical'
+        ? order.length
+        : 0;
+    return labels.length > named
+        ? [
+            found('labels-domain', 'encoding.shape.labels', `labels names one domain value each, and ${labels.length} ${labels.length === 1 ? 'label names' : 'labels name'} ${named}: a label past them names nothing`),
+        ]
+        : [];
+}
+function drawsDensity(mark) {
+    return mark.source === 'density' && readsValue(markTypeOf(mark));
+}
+function drawTogether(a, b) {
+    const upper = (m) => m.maxBpPerPx || Infinity;
+    const lower = (m) => m.minBpPerPx ?? 0;
+    return lower(a) < upper(b) && lower(b) < upper(a);
+}
+// The field names a step reads, by the slot each is written in.
+function fieldRefs(step) {
+    const list = (slot, refs = []) => refs.map((ref, k) => [`${slot}.${k}`, ref]);
+    switch (step.type) {
+        case 'bin':
+            return [['field', step.field], ...list('fields', step.fields)];
+        case 'flatten':
+        case 'cells':
+            return [['field', step.field]];
+        case 'pileup':
+            return list('fields', step.fields);
+        case 'aggregate':
+            return [
+                ...list('groupby', step.groupby),
+                ...(step.ops ?? []).flatMap((o, k) => [
+                    [`ops.${k}.field`, o.field],
+                    [`ops.${k}.weight`, o.weight],
+                ]),
+            ];
+        default:
+            return [];
+    }
+}
+// The slots naming two fields, and what each reads as when it names another
+// number of them: a bin's `fields` left empty is a bin by `field`.
+function pairSlots(step) {
+    return step.type === 'bin'
+        ? [
+            { slot: 'as', names: step.as, reads: DEFAULT_BIN_AS.join(' and ') },
+            {
+                slot: 'fields',
+                names: step.fields?.length ? step.fields : undefined,
+                reads: `its field alone, ${step.field || DEFAULT_BIN_FIELD}`,
+            },
+        ]
+        : step.type === 'pileup'
+            ? [
+                {
+                    slot: 'fields',
+                    names: step.fields,
+                    reads: DEFAULT_PILEUP_FIELDS.join(' and '),
+                },
+            ]
+            : [];
+}
+function readable(steps) {
+    return steps.filter(s => s !== undefined);
+}
+function packsIn(steps) {
+    return steps.some(s => s?.type === 'pileup');
+}
+function packs(mark) {
+    return packsIn(stepsOf(mark));
+}
+function named(field) {
+    return typeof field === 'string' && field !== '';
+}
+const ONE_ROW_PER_VALUE = "rows draws one row per value, so the rows a pileup packs share their value's row; a facet gives each value a section as deep as its pileup";
+// Where a display drawing one row per value packs more than one.
+function packingsUnderRows(marks, transform, section) {
+    const pileups = (steps, list) => steps.flatMap((step, i) => step?.type === 'pileup'
+        ? [found('packing-under-rows', `${list}.${i}`, ONE_ROW_PER_VALUE)]
+        : []);
+    return [
+        ...pileups(transform, 'transform'),
+        ...pileups(section, 'facet.transform'),
+        ...marks.flatMap((mark, i) => mark
+            ? [
+                ...pileups(stepsOf(mark), 'transform'),
+                ...(mark.encoding?.row
+                    ? [found('packing-under-rows', 'encoding.row', ONE_ROW_PER_VALUE)]
+                    : []),
+            ].map(p => ({ mark: i, ...p }))
+            : []),
+    ];
+}
+function banded(mark, shared) {
+    return (!!mark.encoding?.row ||
+        stepChannels([...shared, ...stepsOf(mark)]).row !== undefined);
+}
+// The fields the last step that makes its features from nothing leaves behind,
+// with what the steps after it add, over the display's steps and then the
+// mark's; undefined where no step does, and every field of the file is still
+// there.
+function madeFields(steps) {
+    const made = steps.findLastIndex(s => s.type === 'aggregate' || s.type === 'coverage');
+    const last = steps[made];
+    if (!last) {
+        return undefined;
+    }
+    const fields = new Set(['refName', 'start', 'end']);
+    if (last.type === 'coverage') {
+        fields.add(last.as ?? DEFAULT_COVERAGE_AS);
+    }
+    else if (last.type === 'aggregate') {
+        const bin = steps
+            .slice(0, made)
+            .findLast((s) => s.type === 'bin');
+        const edges = bin?.as ?? DEFAULT_BIN_AS;
+        for (const field of last.groupby?.length
+            ? last.groupby
+            : edges.length === 2
+                ? edges
+                : []) {
+            fields.add(field);
+        }
+        for (const { op = DEFAULT_AGGREGATE_OP, field, as } of last.ops ?? []) {
+            fields.add(aggregateFieldName({ op, field, as }));
+        }
+    }
+    for (const step of steps.slice(made + 1)) {
+        if (step.type === 'formula') {
+            fields.add(step.as ?? DEFAULT_FORMULA_AS);
+        }
+        else if (step.type === 'pileup') {
+            fields.add(step.as ?? DEFAULT_PILEUP_AS);
+        }
+        else if (step.type === 'flatten') {
+            for (const field of [step.index, step.key]) {
+                if (field) {
+                    fields.add(field);
+                }
+            }
+        }
+        else if (step.type === 'mate') {
+            for (const field of MATE_FIELDS) {
+                fields.add(field);
+            }
+        }
+        else if (step.type === 'cells') {
+            for (const field of CELLS_FIELDS) {
+                fields.add(field);
+            }
+        }
+        else if (step.type === 'bin') {
+            for (const edge of step.as?.length === 2 ? step.as : DEFAULT_BIN_AS) {
+                fields.add(edge);
+            }
+            if (step.fields?.length === 2) {
+                fields.add(BIN_OVERLAP_FIELD);
+            }
+        }
+    }
+    return fields;
+}
+// What a list of steps cannot run as written, a mark's, the facet's or the
+// display's, each slot under the list's own name.
+function stepProblems(steps, list = 'transform') {
+    const problems = [];
+    for (const [i, step] of steps.entries()) {
+        if (!step) {
+            continue;
+        }
+        const { type } = step;
+        const at = `${list}.${i}`;
+        if ((type === 'filter' || type === 'formula') && !isJexl(step.expr ?? '')) {
+            problems.push(found('step-expression', `${at}.expr`, `a ${type} reads a jexl: expression`));
+        }
+        if (type === 'bin' &&
+            step.step !== undefined &&
+            step.step !== AUTO_BIN &&
+            !(Number(step.step) > 0)) {
+            problems.push(found('bin-width', `${at}.step`, 'a bin is a positive width in bp'));
+        }
+        for (const pair of pairSlots(step)) {
+            if (pair.names && pair.names.length !== 2) {
+                problems.push(found('step-pair', `${at}.${pair.slot}`, `a ${type} reads two field names from ${pair.slot} and this names ${pair.names.length}, so it reads ${pair.reads}`));
+            }
+        }
+        if (type === 'bin' &&
+            step.fields?.length === 2 &&
+            step.field &&
+            step.field !== DEFAULT_BIN_FIELD) {
+            problems.push(found('bin-field-and-fields', `${at}.field`, `a bin over fields cuts each interval at the bin edges and reads no field, so ${step.field} is unread`));
+        }
+        if (type === 'aggregate') {
+            for (const [k, { op = DEFAULT_AGGREGATE_OP, field, weight }] of (step.ops ?? []).entries()) {
+                if (op !== 'count' && !field) {
+                    problems.push(found('op-field', `${at}.ops.${k}.field`, `${op} reads a field and names none`));
+                }
+                if ((op === 'min' || op === 'max') && weight) {
+                    problems.push(found('unread-weight', `${at}.ops.${k}.weight`, `a weight moves no ${op === 'min' ? 'minimum' : 'maximum'}, so the ${op} reads its field alone`));
+                }
+            }
+        }
+        for (const [slot, ref] of fieldRefs(step)) {
+            if (ref && isJexl(ref)) {
+                problems.push(found('step-field-expression', `${at}.${slot}`, `the ${type} step reads a field name or a dotted path; a formula step in front computes one`));
+            }
+        }
+    }
+    return problems;
+}
+// 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;
+    if (readsValue(type) &&
+        !y &&
+        !stepChannels([...display, ...section, ...stepsOf(mark)]).y) {
+        problems.push(found('mark-without-value', 'encoding.y', `a ${type} stands at a value, and names no y field while no step before it writes one — a coverage, or an aggregate with one op — so it draws nothing`));
+    }
+    const spec = MARK_SPECS[type];
+    const channels = new Set(['x', 'x2', 'size', ...spec.channels]);
+    for (const channel of writtenChannels(mark.encoding)) {
+        if (!channels.has(channel)) {
+            problems.push(found('unread-channel', `encoding.${channel}`, `a ${type} does not read ${channel}`));
+        }
+    }
+    const size = mark.encoding?.size;
+    if (!unwritten(size) && spec.size === undefined) {
+        problems.push(found('unread-size', 'encoding.size', `a ${type} draws no point or rule and strokes no link, so it reads no size`));
+    }
+    else if (spec.size === 'constant' && sizeFieldOf(size)) {
+        problems.push(found('unread-channel', 'encoding.size.field', `a ${type} reads its size as a number, and only a link maps a field to it`));
+    }
+    if (mark.linkShape !== undefined &&
+        mark.linkShape !== DEFAULT_LINK_SHAPE &&
+        type !== 'link') {
+        problems.push(found('unread-link-shape', 'linkShape', `a ${type} draws no link, so it reads no linkShape`));
+    }
+    if (mark.interpolate !== undefined &&
+        mark.interpolate !== DEFAULT_LINE_INTERPOLATE &&
+        type !== 'line') {
+        problems.push(found('unread-interpolate', 'interpolate', `a ${type} draws no line, so it reads no interpolate`));
+    }
+    if (mark.rowProportion !== undefined &&
+        mark.rowProportion !== DEFAULT_ROW_PROPORTION &&
+        type !== 'span') {
+        problems.push(found('unread-row-proportion', 'rowProportion', `a ${type} draws no span, so it reads no rowProportion`));
+    }
+    if (!readsValue(type) && mark.source === 'density') {
+        problems.push(found('span-density-source', 'source', `a ${type} does not draw the density sidecar`));
+    }
+    const color = mark.encoding?.color ?? {};
+    for (const { rule, slot, message } of colorProblems(color, FEATURE_FIELD_PRESETS)) {
+        problems.push(found(rule, `encoding.color.${slot}`, message));
+    }
+    if (colorScaleOf(color) === 'threshold' &&
+        (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 ${MAX_THRESHOLD_CUTS + 1}th colour`));
+    }
+    problems.push(...shapeLabelProblems(mark.encoding?.shape));
+    problems.push(...constantAsFieldProblems(mark.encoding));
+    if (typeof size === 'object') {
+        for (const { rule, slot, message } of scaleEndProblems(size)) {
+            problems.push(found(rule, `encoding.size.${slot}`, message));
+        }
+    }
+    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}`));
+    }
+    problems.push(...stepProblems(stepsOf(mark)));
+    if (packs(mark) && (packsIn(section) || packsIn(display))) {
+        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) {
+        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}", ${leaves}`));
+            }
+        }
+    }
+    return problems;
+}
+/**
+ * Every rule a plot breaks. The display's step lists are checked as a mark's
+ * are and reported with no mark, under `transform` and `facet.transform`, and
+ * so are `scales.y`'s ends. A file's own spelling goes through the schema's
+ * lift first, which `jbrowse validate` does from the generated manifest.
+ */
+export function markProblems({ marks, facet, transform = [], rows, scales, }) {
+    const faceted = named(facet?.field);
+    const drawsRows = named(rows?.field) && !faceted;
+    // the field the sections or rows are split on, which every section's rows
+    // keep through the steps that make rows
+    const split = faceted
+        ? String(facet?.field)
+        : drawsRows
+            ? String(rows?.field)
+            : undefined;
+    const section = readable(facet?.transform ?? []);
+    const display = readable(transform);
+    const shared = [...display, ...section];
+    const problems = [
+        ...stepProblems(transform),
+        ...stepProblems(facet?.transform ?? [], 'facet.transform'),
+        ...scaleEndProblems(scales?.y ?? {}).map(({ rule, slot, message }) => found(rule, `scales.y.${slot}`, message)),
+        ...(faceted
+            ? transform.flatMap((step, i) => step?.type === 'pileup'
+                ? [
+                    found('cross-section-packing', `transform.${i}`, 'runs before the facet splits the features, so it packs across every section and leaves each section the rows the others fill; the same pileup in facet.transform packs each section on its own'),
+                ]
+                : [])
+            : []),
+        ...(faceted && named(rows?.field) && rows?.field !== facet?.field
+            ? [
+                found('rows-beside-facet', 'rows.field', 'facet stacks a labelled section per value and rows one row per value; bands of rows over two fields are not drawn yet, so the facet draws alone'),
+            ]
+            : []),
+        ...(drawsRows ? packingsUnderRows(marks, transform, section) : []),
+        ...marks.flatMap((mark, i) => mark
+            ? ownProblems(mark, display, section, split).map(p => ({
+                mark: i,
+                ...p,
+            }))
+            : []),
+    ];
+    for (const [i, mark] of marks.entries()) {
+        for (const [j, other] of marks.entries()) {
+            if (i === j || !mark || !other || !drawTogether(mark, other)) {
+                continue;
+            }
+            if (!faceted &&
+                !drawsRows &&
+                markTypeOf(mark) !== 'span' &&
+                !banded(mark, shared) &&
+                banded(other, shared)) {
+                problems.push({
+                    mark: i,
+                    ...found('value-beside-rows', 'encoding.row', `stands in the first of the rows mark ${j} bands the plot into, its axis repeated per row`),
+                });
+            }
+            if (i > j && packs(mark) && packs(other)) {
+                problems.push({
+                    mark: i,
+                    ...found('two-packings', 'transform', `packs rows of its own, as mark ${j} does, and the two share row numbers; one pileup in the ${faceted ? "facet's transform packs them together per section" : "display's transform packs them together"}`),
+                });
+            }
+            if (i > j && drawsDensity(mark) && drawsDensity(other)) {
+                problems.push({
+                    mark: i,
+                    ...found('second-density-mark', 'source', `mark ${j} already stands in for the density sidecar here`),
+                });
+            }
+        }
+    }
+    return problems;
+}
+/**
+ * A problem as one line of a notice: `mark 0 encoding.y: …`, or
+ * `transform.0.step: …` for the display's own step.
+ */
+export function problemText({ mark, slot, message }) {
+    return `${mark === undefined ? '' : `mark ${mark} `}${slot}: ${message}`;
+}

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

@@ -0,0 +1,6 @@
+// Generated by scripts/generateMarkRules.ts from plugins/marks/src/LinearMarkDisplay/markRuleFacts.ts: do not edit, `pnpm autogen` rewrites it.
+export { aggregateFieldName } from './aggregateFieldName.js';
+export { isNamedColor } from './cssColorsLevel4.js';
+export { isJexl } from './jexlStrings.js';
+export { FEATURE_FIELD_PRESETS, colorProblems, fieldScaleOf, paintedScale, scaleEndProblems, universalPresetOf, } from './colorScale.js';
+export { SHAPE_NAMES } from './shapeNameList.js';

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

@@ -0,0 +1,84 @@
+/**
+ * What each mark type reads: the one statement the lane request, the rule list and
+ * the model's value tests derive theirs from.
+ *
+ * Its own module, reaching only the vocabulary beside it: the rule list reads
+ * it and `jbrowse validate` carries a copy, and markList.ts takes render-core's
+ * marks barrel — shader sources included — which the examples sites' eager
+ * budget then pays for. `layerRequests` in model.ts is where each lane is
+ * checked to be one the encoder fills.
+ */
+export const MARK_SPECS = {
+    bar: {
+        channels: ['y', 'row', 'color'],
+        value: 'required',
+        hit: 'rows',
+    },
+    point: {
+        channels: ['y', 'row', 'color', 'shape'],
+        value: 'required',
+        hit: 'index',
+        size: 'constant',
+    },
+    rule: {
+        channels: ['y', 'row', 'color'],
+        value: 'required',
+        hit: 'rows',
+        size: 'constant',
+    },
+    line: {
+        channels: ['y', 'row', 'color'],
+        value: 'required',
+        hit: 'rows',
+        size: 'constant',
+    },
+    span: {
+        channels: ['row', 'color'],
+        value: 'none',
+        hit: 'rows',
+    },
+    text: {
+        channels: ['y', 'row', 'color', 'text'],
+        value: 'optional',
+        hit: false,
+    },
+    link: {
+        channels: ['y', 'row', 'color', 'size'],
+        value: 'optional',
+        hit: 'index',
+        farFoot: true,
+        size: 'channel',
+    },
+};
+function specOf(type) {
+    return MARK_SPECS[type];
+}
+/** Whether a mark type stands at a `y` value, so a mark of it naming none draws nothing. */
+export function readsValue(type) {
+    return specOf(type).value === 'required';
+}
+/** Whether a mark type may plot a `y`, and so folds its values into the axis. */
+export function plotsValue(type) {
+    return specOf(type).value !== 'none';
+}
+/** Whether a mark type answers a hover through the hit index the worker builds. */
+export function hitsByIndex(type) {
+    return specOf(type).hit === 'index';
+}
+/**
+ * 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, colorLanes) {
+    const spec = specOf(type);
+    return [
+        ...spec.channels.flatMap((channel) => channel === 'shape'
+            ? ['glyph']
+            : channel === 'color'
+                ? colorLanes
+                : [channel]),
+        ...(spec.farFoot ? ['x2Ref'] : []),
+        ...(hitsByIndex(type) ? ['index'] : []),
+    ];
+}