zarr-metadata 0.3.0 → 0.4.1

package/dist/semantics.d.ts

@@ -8,17 +8,31 @@
  *
  * - the `regular` chunk grid's `chunk_shape` has one length per dimension
  *   of `shape`;
+ * - the `rectilinear` chunk grid's `chunk_shapes` has one entry per
+ *   dimension, and each explicit chunk list (integers and `[size, count]`
+ *   run-length pairs) sums exactly to that dimension's length (the
+ *   bare-integer uniform shorthand carries no sum constraint, like the
+ *   regular grid);
  * - a `transpose` codec's `order` is a permutation of `0..n-1`, with one
  *   entry per array dimension;
  * - a `sharding_indexed` codec's inner `chunk_shape` matches the array's
- *   dimensionality and evenly divides the shape of the chunk it shards
- *   (the regular grid's chunk at the top level, the parent shard's inner
- *   chunk when sharding nests);
+ *   dimensionality and evenly divides every chunk it shards — the grid's
+ *   chunk at the top level (each distinct per-dimension size, for
+ *   rectilinear grids), the parent shard's inner chunk when sharding
+ *   nests;
  * - `fill_value` has a JSON shape permitted for the named core data type
  *   (booleans for `bool`, ranged integers for the int types, numbers /
  *   the "NaN"-family sentinels / width-checked "0x…" strings for the
  *   float types, two-element arrays for the complex types).
  *
+ * Dimensional context is THREADED through codec pipelines rather than
+ * assumed constant (mirroring zarr-python's chunk-spec threading): a valid
+ * `transpose` permutes the per-dimension chunk sizes for the codecs after
+ * it, and any codec this layer cannot reason about — `reshape` may change
+ * a chunk's rank, and unknown codecs may do anything — invalidates the
+ * dimensional context for the rest of the pipeline instead of letting
+ * stale array-level facts produce false verdicts.
+ *
  * Unrecognized names are skipped everywhere — the extension name space is
  * open, and a rule that guessed would lie. This layer has no counterpart
  * in the Python reference implementation (which stops at structure), so it

package/dist/semantics.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"semantics.d.ts","sourceRoot":"","sources":["../src/semantics.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwCG;AAEH,OAAO,EAAU,KAAK,SAAS,EAAoB,MAAM,aAAa,CAAC;AA6OvE;;;;;GAKG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,OAAO,GAAG,SAAS,CAqFlE"}

package/dist/semantics.js

@@ -8,17 +8,31 @@
  *
  * - the `regular` chunk grid's `chunk_shape` has one length per dimension
  *   of `shape`;
+ * - the `rectilinear` chunk grid's `chunk_shapes` has one entry per
+ *   dimension, and each explicit chunk list (integers and `[size, count]`
+ *   run-length pairs) sums exactly to that dimension's length (the
+ *   bare-integer uniform shorthand carries no sum constraint, like the
+ *   regular grid);
  * - a `transpose` codec's `order` is a permutation of `0..n-1`, with one
  *   entry per array dimension;
  * - a `sharding_indexed` codec's inner `chunk_shape` matches the array's
- *   dimensionality and evenly divides the shape of the chunk it shards
- *   (the regular grid's chunk at the top level, the parent shard's inner
- *   chunk when sharding nests);
+ *   dimensionality and evenly divides every chunk it shards — the grid's
+ *   chunk at the top level (each distinct per-dimension size, for
+ *   rectilinear grids), the parent shard's inner chunk when sharding
+ *   nests;
  * - `fill_value` has a JSON shape permitted for the named core data type
  *   (booleans for `bool`, ranged integers for the int types, numbers /
  *   the "NaN"-family sentinels / width-checked "0x…" strings for the
  *   float types, two-element arrays for the complex types).
  *
+ * Dimensional context is THREADED through codec pipelines rather than
+ * assumed constant (mirroring zarr-python's chunk-spec threading): a valid
+ * `transpose` permutes the per-dimension chunk sizes for the codecs after
+ * it, and any codec this layer cannot reason about — `reshape` may change
+ * a chunk's rank, and unknown codecs may do anything — invalidates the
+ * dimensional context for the rest of the pipeline instead of letting
+ * stale array-level facts produce false verdicts.
+ *
  * Unrecognized names are skipped everywhere — the extension name space is
  * open, and a rule that guessed would lie. This layer has no counterpart
  * in the Python reference implementation (which stops at structure), so it
@@ -122,22 +136,39 @@ function isPermutation(order) {
 }
 /**
  * Walk one codec pipeline. `dims` is the array dimensionality at this point
- * (undefined when unknowable); `outerChunkShape` is the shape of the chunk
- * this pipeline encodes — what a sharding codec's inner chunks must divide.
+ * (undefined when unknowable); `outerChunkSizes` holds the distinct chunk
+ * lengths per dimension this pipeline may encode — what a sharding codec's
+ * inner chunks must divide. A regular grid contributes one size per
+ * dimension; a rectilinear grid may contribute several.
  */
-function pipelineIssues(pipeline, path, dims, outerChunkShape) {
+function pipelineIssues(pipeline, path, initialDims, initialChunkSizes) {
     const issues = [];
+    // The dimensional context THREADS through the pipeline: transpose permutes
+    // it, and anything this layer cannot reason about invalidates it for the
+    // remaining codecs.
+    let dims = initialDims;
+    let chunkSizes = initialChunkSizes;
+    const dropContext = () => {
+        dims = undefined;
+        chunkSizes = undefined;
+    };
     pipeline.forEach((entry, index) => {
         const parts = fieldParts(entry);
-        if (parts === undefined)
+        if (parts === undefined) {
+            dropContext(); // structurally invalid entry: no further reasoning
             return;
+        }
         const { name, configuration } = parts;
         if (name === "transpose") {
             const order = configuration?.["order"];
-            if (!isIntArray(order))
-                return; // shape errors are the schema layer's
+            if (!isIntArray(order)) {
+                dropContext(); // shape errors are the schema layer's
+                return;
+            }
             const orderPath = [...path, index, "configuration", "order"];
+            let sound = true;
             if (!isPermutation(order)) {
+                sound = false;
                 issues.push({
                     path: orderPath,
                     message: `expected a permutation of the integers 0..${order.length - 1}`,
@@ -145,17 +176,30 @@ function pipelineIssues(pipeline, path, dims, outerChunkShape) {
                 });
             }
             if (dims !== undefined && order.length !== dims) {
+                sound = false;
                 issues.push({
                     path: orderPath,
                     message: `expected one entry per array dimension (${dims})`,
                     kind: "invalid_value",
                 });
             }
+            if (!sound) {
+                dropContext();
+            }
+            else if (chunkSizes !== undefined) {
+                const sizes = chunkSizes;
+                chunkSizes =
+                    order.length === sizes.length
+                        ? order.map((axis) => sizes[axis])
+                        : undefined;
+            }
         }
         else if (name === "sharding_indexed") {
             const chunkShape = configuration?.["chunk_shape"];
-            if (!isIntArray(chunkShape))
+            if (!isIntArray(chunkShape)) {
+                dropContext();
                 return;
+            }
             const chunkShapePath = [...path, index, "configuration", "chunk_shape"];
             if (dims !== undefined && chunkShape.length !== dims) {
                 issues.push({
@@ -164,22 +208,44 @@ function pipelineIssues(pipeline, path, dims, outerChunkShape) {
                     kind: "invalid_value",
                 });
             }
-            else if (outerChunkShape !== undefined &&
-                chunkShape.length === outerChunkShape.length &&
-                chunkShape.every((length) => length > 0) &&
-                outerChunkShape.some((outer, axis) => outer % chunkShape[axis] !== 0)) {
-                issues.push({
-                    path: chunkShapePath,
-                    message: `expected ${JSON.stringify(chunkShape)} to evenly divide the outer chunk shape ${JSON.stringify(outerChunkShape)}`,
-                    kind: "invalid_value",
+            else if (chunkSizes !== undefined &&
+                chunkShape.length === chunkSizes.length &&
+                chunkShape.every((length) => length > 0)) {
+                let violation;
+                chunkSizes.forEach((sizes, axis) => {
+                    if (violation !== undefined)
+                        return;
+                    const bad = sizes.find((size) => size % chunkShape[axis] !== 0);
+                    if (bad !== undefined)
+                        violation = { axis, size: bad };
                 });
+                if (violation !== undefined) {
+                    const { axis, size } = violation;
+                    const sizesNow = chunkSizes;
+                    const uniform = sizesNow.every((sizes) => sizes.length === 1);
+                    issues.push({
+                        path: chunkShapePath,
+                        message: uniform
+                            ? `expected ${JSON.stringify(chunkShape)} to evenly divide the outer chunk shape ${JSON.stringify(sizesNow.map((sizes) => sizes[0]))}`
+                            : `expected ${JSON.stringify(chunkShape)} to evenly divide every chunk size of the grid (dimension ${axis} has chunk size ${size})`,
+                        kind: "invalid_value",
+                    });
+                }
             }
             const inner = configuration?.["codecs"];
             if (Array.isArray(inner)) {
-                issues.push(...pipelineIssues(inner, [...path, index, "configuration", "codecs"], dims, chunkShape));
+                issues.push(...pipelineIssues(inner, [...path, index, "configuration", "codecs"], chunkShape.length, chunkShape.map((length) => [length])));
             }
             // index_codecs encode the shard index, whose shape differs from the
-            // array's — no dimensional context applies there.
+            // array's — no dimensional context applies there. After the
+            // array -> bytes boundary the dimensional context is spent.
+            dropContext();
+        }
+        else {
+            // A codec this layer cannot reason about (reshape may change a
+            // chunk's rank; unknown codecs may do anything): stale array-level
+            // facts must not judge the codecs after it.
+            dropContext();
         }
     });
     return issues;
@@ -197,18 +263,72 @@ export function validateArraySemanticsV3(value) {
     const shape = isIntArray(value["shape"]) ? value["shape"] : undefined;
     const dims = shape?.length;
     const grid = fieldParts(value["chunk_grid"]);
-    let chunkShape;
+    let chunkSizes;
     if (grid?.name === "regular") {
         const configured = grid.configuration?.["chunk_shape"];
         if (isIntArray(configured)) {
-            chunkShape = configured;
             if (dims !== undefined && configured.length !== dims) {
                 issues.push({
                     path: ["chunk_grid", "configuration", "chunk_shape"],
                     message: `expected one length per dimension of shape (${dims})`,
                     kind: "invalid_value",
                 });
-                chunkShape = undefined; // wrong arity: unusable as division context
+                // wrong arity: unusable as division context
+            }
+            else {
+                chunkSizes = configured.map((length) => [length]);
+            }
+        }
+    }
+    else if (grid?.name === "rectilinear") {
+        const specs = grid.configuration?.["chunk_shapes"];
+        if (Array.isArray(specs)) {
+            if (dims !== undefined && specs.length !== dims) {
+                issues.push({
+                    path: ["chunk_grid", "configuration", "chunk_shapes"],
+                    message: `expected one entry per dimension of shape (${dims})`,
+                    kind: "invalid_value",
+                });
+            }
+            else {
+                const perDim = specs.map((spec, dim) => {
+                    // Bare integer: uniform shorthand, no sum constraint (edge chunks
+                    // are permitted, as with the regular grid).
+                    if (Number.isInteger(spec))
+                        return spec > 0 ? [spec] : undefined;
+                    if (!Array.isArray(spec))
+                        return undefined; // registry schema's problem
+                    const sizes = new Set();
+                    let total = 0;
+                    for (const entry of spec) {
+                        if (Number.isInteger(entry)) {
+                            sizes.add(entry);
+                            total += entry;
+                        }
+                        else if (Array.isArray(entry) &&
+                            entry.length === 2 &&
+                            Number.isInteger(entry[0]) &&
+                            Number.isInteger(entry[1])) {
+                            sizes.add(entry[0]);
+                            total += entry[0] * entry[1];
+                        }
+                        else {
+                            return undefined; // malformed entry: registry schema's problem
+                        }
+                    }
+                    const extent = shape?.[dim];
+                    if (extent !== undefined && total !== extent) {
+                        issues.push({
+                            path: ["chunk_grid", "configuration", "chunk_shapes", dim],
+                            message: `expected chunk sizes summing to ${extent} along dimension ${dim}, got ${total}`,
+                            kind: "invalid_value",
+                        });
+                    }
+                    return [...sizes];
+                });
+                if (perDim.every((sizes) => sizes !== undefined)) {
+                    chunkSizes = perDim;
+                }
             }
         }
     }
@@ -221,7 +341,7 @@ export function validateArraySemanticsV3(value) {
     }
     const codecs = value["codecs"];
     if (Array.isArray(codecs)) {
-        issues.push(...pipelineIssues(codecs, ["codecs"], dims, chunkShape));
+        issues.push(...pipelineIssues(codecs, ["codecs"], dims, chunkSizes));
     }
     return treeOf(issues);
 }

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "zarr-metadata",
-  "version": "0.3.0",
+  "version": "0.4.1",
   "description": "Spec-defined metadata types and validators for Zarr v2 and v3.",
   "license": "MIT",
   "type": "module",

package/src/semantics.ts

@@ -8,17 +8,31 @@
  *
  * - the `regular` chunk grid's `chunk_shape` has one length per dimension
  *   of `shape`;
+ * - the `rectilinear` chunk grid's `chunk_shapes` has one entry per
+ *   dimension, and each explicit chunk list (integers and `[size, count]`
+ *   run-length pairs) sums exactly to that dimension's length (the
+ *   bare-integer uniform shorthand carries no sum constraint, like the
+ *   regular grid);
  * - a `transpose` codec's `order` is a permutation of `0..n-1`, with one
  *   entry per array dimension;
  * - a `sharding_indexed` codec's inner `chunk_shape` matches the array's
- *   dimensionality and evenly divides the shape of the chunk it shards
- *   (the regular grid's chunk at the top level, the parent shard's inner
- *   chunk when sharding nests);
+ *   dimensionality and evenly divides every chunk it shards — the grid's
+ *   chunk at the top level (each distinct per-dimension size, for
+ *   rectilinear grids), the parent shard's inner chunk when sharding
+ *   nests;
  * - `fill_value` has a JSON shape permitted for the named core data type
  *   (booleans for `bool`, ranged integers for the int types, numbers /
  *   the "NaN"-family sentinels / width-checked "0x…" strings for the
  *   float types, two-element arrays for the complex types).
  *
+ * Dimensional context is THREADED through codec pipelines rather than
+ * assumed constant (mirroring zarr-python's chunk-spec threading): a valid
+ * `transpose` permutes the per-dimension chunk sizes for the codecs after
+ * it, and any codec this layer cannot reason about — `reshape` may change
+ * a chunk's rank, and unknown codecs may do anything — invalidates the
+ * dimensional context for the rest of the pipeline instead of letting
+ * stale array-level facts produce false verdicts.
+ *
  * Unrecognized names are skipped everywhere — the extension name space is
  * open, and a rule that guessed would lie. This layer has no counterpart
  * in the Python reference implementation (which stops at structure), so it
@@ -140,25 +154,44 @@ function isPermutation(order: number[]): boolean {
 
 /**
  * Walk one codec pipeline. `dims` is the array dimensionality at this point
- * (undefined when unknowable); `outerChunkShape` is the shape of the chunk
- * this pipeline encodes — what a sharding codec's inner chunks must divide.
+ * (undefined when unknowable); `outerChunkSizes` holds the distinct chunk
+ * lengths per dimension this pipeline may encode — what a sharding codec's
+ * inner chunks must divide. A regular grid contributes one size per
+ * dimension; a rectilinear grid may contribute several.
  */
 function pipelineIssues(
   pipeline: unknown[],
   path: Path,
-  dims: number | undefined,
-  outerChunkShape: number[] | undefined,
+  initialDims: number | undefined,
+  initialChunkSizes: number[][] | undefined,
 ): PathedIssue[] {
   const issues: PathedIssue[] = [];
+  // The dimensional context THREADS through the pipeline: transpose permutes
+  // it, and anything this layer cannot reason about invalidates it for the
+  // remaining codecs.
+  let dims = initialDims;
+  let chunkSizes = initialChunkSizes;
+  const dropContext = (): void => {
+    dims = undefined;
+    chunkSizes = undefined;
+  };
   pipeline.forEach((entry, index) => {
     const parts = fieldParts(entry);
-    if (parts === undefined) return;
+    if (parts === undefined) {
+      dropContext(); // structurally invalid entry: no further reasoning
+      return;
+    }
     const { name, configuration } = parts;
     if (name === "transpose") {
       const order = configuration?.["order"];
-      if (!isIntArray(order)) return; // shape errors are the schema layer's
+      if (!isIntArray(order)) {
+        dropContext(); // shape errors are the schema layer's
+        return;
+      }
       const orderPath = [...path, index, "configuration", "order"];
+      let sound = true;
       if (!isPermutation(order)) {
+        sound = false;
         issues.push({
           path: orderPath,
           message: `expected a permutation of the integers 0..${order.length - 1}`,
@@ -166,15 +199,28 @@ function pipelineIssues(
         });
       }
       if (dims !== undefined && order.length !== dims) {
+        sound = false;
         issues.push({
           path: orderPath,
           message: `expected one entry per array dimension (${dims})`,
           kind: "invalid_value",
         });
       }
+      if (!sound) {
+        dropContext();
+      } else if (chunkSizes !== undefined) {
+        const sizes = chunkSizes;
+        chunkSizes =
+          order.length === sizes.length
+            ? order.map((axis) => sizes[axis] as number[])
+            : undefined;
+      }
     } else if (name === "sharding_indexed") {
       const chunkShape = configuration?.["chunk_shape"];
-      if (!isIntArray(chunkShape)) return;
+      if (!isIntArray(chunkShape)) {
+        dropContext();
+        return;
+      }
       const chunkShapePath = [...path, index, "configuration", "chunk_shape"];
       if (dims !== undefined && chunkShape.length !== dims) {
         issues.push({
@@ -183,25 +229,49 @@ function pipelineIssues(
           kind: "invalid_value",
         });
       } else if (
-        outerChunkShape !== undefined &&
-        chunkShape.length === outerChunkShape.length &&
-        chunkShape.every((length) => length > 0) &&
-        outerChunkShape.some((outer, axis) => outer % (chunkShape[axis] as number) !== 0)
+        chunkSizes !== undefined &&
+        chunkShape.length === chunkSizes.length &&
+        chunkShape.every((length) => length > 0)
       ) {
-        issues.push({
-          path: chunkShapePath,
-          message: `expected ${JSON.stringify(chunkShape)} to evenly divide the outer chunk shape ${JSON.stringify(outerChunkShape)}`,
-          kind: "invalid_value",
+        let violation: { axis: number; size: number } | undefined;
+        chunkSizes.forEach((sizes, axis) => {
+          if (violation !== undefined) return;
+          const bad = sizes.find((size) => size % (chunkShape[axis] as number) !== 0);
+          if (bad !== undefined) violation = { axis, size: bad };
         });
+        if (violation !== undefined) {
+          const { axis, size } = violation;
+          const sizesNow = chunkSizes;
+          const uniform = sizesNow.every((sizes) => sizes.length === 1);
+          issues.push({
+            path: chunkShapePath,
+            message: uniform
+              ? `expected ${JSON.stringify(chunkShape)} to evenly divide the outer chunk shape ${JSON.stringify(sizesNow.map((sizes) => sizes[0]))}`
+              : `expected ${JSON.stringify(chunkShape)} to evenly divide every chunk size of the grid (dimension ${axis} has chunk size ${size})`,
+            kind: "invalid_value",
+          });
+        }
       }
       const inner = configuration?.["codecs"];
       if (Array.isArray(inner)) {
         issues.push(
-          ...pipelineIssues(inner, [...path, index, "configuration", "codecs"], dims, chunkShape),
+          ...pipelineIssues(
+            inner,
+            [...path, index, "configuration", "codecs"],
+            chunkShape.length,
+            chunkShape.map((length) => [length]),
+          ),
         );
       }
       // index_codecs encode the shard index, whose shape differs from the
-      // array's — no dimensional context applies there.
+      // array's — no dimensional context applies there. After the
+      // array -> bytes boundary the dimensional context is spent.
+      dropContext();
+    } else {
+      // A codec this layer cannot reason about (reshape may change a
+      // chunk's rank; unknown codecs may do anything): stale array-level
+      // facts must not judge the codecs after it.
+      dropContext();
     }
   });
   return issues;
@@ -220,18 +290,67 @@ export function validateArraySemanticsV3(value: unknown): ErrorTree {
   const dims = shape?.length;
 
   const grid = fieldParts(value["chunk_grid"]);
-  let chunkShape: number[] | undefined;
+  let chunkSizes: number[][] | undefined;
   if (grid?.name === "regular") {
     const configured = grid.configuration?.["chunk_shape"];
     if (isIntArray(configured)) {
-      chunkShape = configured;
       if (dims !== undefined && configured.length !== dims) {
         issues.push({
           path: ["chunk_grid", "configuration", "chunk_shape"],
           message: `expected one length per dimension of shape (${dims})`,
           kind: "invalid_value",
         });
-        chunkShape = undefined; // wrong arity: unusable as division context
+        // wrong arity: unusable as division context
+      } else {
+        chunkSizes = configured.map((length) => [length]);
+      }
+    }
+  } else if (grid?.name === "rectilinear") {
+    const specs = grid.configuration?.["chunk_shapes"];
+    if (Array.isArray(specs)) {
+      if (dims !== undefined && specs.length !== dims) {
+        issues.push({
+          path: ["chunk_grid", "configuration", "chunk_shapes"],
+          message: `expected one entry per dimension of shape (${dims})`,
+          kind: "invalid_value",
+        });
+      } else {
+        const perDim: (number[] | undefined)[] = specs.map((spec, dim) => {
+          // Bare integer: uniform shorthand, no sum constraint (edge chunks
+          // are permitted, as with the regular grid).
+          if (Number.isInteger(spec)) return spec as number > 0 ? [spec as number] : undefined;
+          if (!Array.isArray(spec)) return undefined; // registry schema's problem
+          const sizes = new Set<number>();
+          let total = 0;
+          for (const entry of spec) {
+            if (Number.isInteger(entry)) {
+              sizes.add(entry as number);
+              total += entry as number;
+            } else if (
+              Array.isArray(entry) &&
+              entry.length === 2 &&
+              Number.isInteger(entry[0]) &&
+              Number.isInteger(entry[1])
+            ) {
+              sizes.add(entry[0] as number);
+              total += (entry[0] as number) * (entry[1] as number);
+            } else {
+              return undefined; // malformed entry: registry schema's problem
+            }
+          }
+          const extent = shape?.[dim];
+          if (extent !== undefined && total !== extent) {
+            issues.push({
+              path: ["chunk_grid", "configuration", "chunk_shapes", dim],
+              message: `expected chunk sizes summing to ${extent} along dimension ${dim}, got ${total}`,
+              kind: "invalid_value",
+            });
+          }
+          return [...sizes];
+        });
+        if (perDim.every((sizes) => sizes !== undefined)) {
+          chunkSizes = perDim as number[][];
+        }
       }
     }
   }
@@ -246,7 +365,7 @@ export function validateArraySemanticsV3(value: unknown): ErrorTree {
 
   const codecs = value["codecs"];
   if (Array.isArray(codecs)) {
-    issues.push(...pipelineIssues(codecs, ["codecs"], dims, chunkShape));
+    issues.push(...pipelineIssues(codecs, ["codecs"], dims, chunkSizes));
   }
   return treeOf(issues);
 }