@talmolab/sleap-io.js 0.1.0 → 0.1.2

package/README.md

@@ -69,6 +69,21 @@ The demo in `demo/` loads the built package from `dist/`. Build first, then serv
 npm run build
 ```
 
+## Release & Publishing
+
+This package uses npm Trusted Publishing. The first publish must be done manually to unlock the npm package settings:
+
+1. First-time publish (one-time):
+
+```bash
+npm login
+npm publish --access public
+```
+
+2. Enable Trusted Publisher at `https://www.npmjs.com/package/@talmolab/sleap-io.js/access`.
+
+After that, GitHub Releases trigger the publish workflow automatically.
+
 ## Links
 
 - Python sleap-io: https://github.com/talmolab/sleap-io

package/dist/index.d.ts

@@ -433,4 +433,7 @@ declare function labelsFromNumpy(data: number[][][][], options: {
     returnConfidence?: boolean;
 }): Labels;
 
-export { Camera, CameraGroup, Edge, FrameGroup, Instance, InstanceGroup, LabeledFrame, Labels, type LabelsDict, LabelsSet, Mp4BoxVideoBackend, Node, type NodeOrIndex, type Point, type PointsArray, PredictedInstance, type PredictedPoint, type PredictedPointsArray, RecordingSession, Skeleton, SuggestionFrame, Symmetry, Track, Video, type VideoBackend, type VideoFrame, fromDict, fromNumpy, labelsFromNumpy, loadSlp, loadVideo, makeCameraFromDict, pointsEmpty, pointsFromArray, pointsFromDict, predictedPointsEmpty, predictedPointsFromArray, predictedPointsFromDict, rodriguesTransformation, saveSlp, toDict, toNumpy };
+declare function decodeYamlSkeleton(yamlData: string): Skeleton | Skeleton[];
+declare function encodeYamlSkeleton(skeletons: Skeleton | Skeleton[]): string;
+
+export { Camera, CameraGroup, Edge, FrameGroup, Instance, InstanceGroup, LabeledFrame, Labels, type LabelsDict, LabelsSet, Mp4BoxVideoBackend, Node, type NodeOrIndex, type Point, type PointsArray, PredictedInstance, type PredictedPoint, type PredictedPointsArray, RecordingSession, Skeleton, SuggestionFrame, Symmetry, Track, Video, type VideoBackend, type VideoFrame, decodeYamlSkeleton, encodeYamlSkeleton, fromDict, fromNumpy, labelsFromNumpy, loadSlp, loadVideo, makeCameraFromDict, pointsEmpty, pointsFromArray, pointsFromDict, predictedPointsEmpty, predictedPointsFromArray, predictedPointsFromDict, rodriguesTransformation, saveSlp, toDict, toNumpy };

package/dist/index.js

@@ -2578,6 +2578,81 @@ async function loadVideo(filename, options) {
   const backend = await createVideoBackend(filename, { dataset: options?.dataset });
   return new Video({ filename, backend, openBackend: options?.openBackend ?? true });
 }
+
+// src/codecs/skeleton-yaml.ts
+import YAML from "yaml";
+function getNodeName(entry) {
+  if (typeof entry === "string") return entry;
+  if (entry && typeof entry.name === "string") return entry.name;
+  throw new Error("Invalid node entry in skeleton YAML.");
+}
+function resolveName(value) {
+  if (typeof value === "string") return value;
+  if (value && typeof value.name === "string") return value.name;
+  throw new Error("Invalid name reference in skeleton YAML.");
+}
+function decodeSkeleton(data, fallbackName) {
+  if (!data?.nodes) throw new Error("Skeleton YAML missing nodes.");
+  const nodes = data.nodes.map((entry) => new Node(getNodeName(entry)));
+  const edges = (data.edges ?? []).map((edge) => {
+    if (Array.isArray(edge)) {
+      const [source2, destination] = edge;
+      return new Edge(nodes[Number(source2)], nodes[Number(destination)]);
+    }
+    const sourceName = resolveName(edge.source);
+    const destName = resolveName(edge.destination);
+    const source = nodes.find((node) => node.name === sourceName);
+    const dest = nodes.find((node) => node.name === destName);
+    if (!source || !dest) throw new Error("Edge references unknown node.");
+    return new Edge(source, dest);
+  });
+  const symmetries = (data.symmetries ?? []).map((symmetry) => {
+    if (!Array.isArray(symmetry) || symmetry.length !== 2) {
+      throw new Error("Symmetry must contain exactly 2 nodes.");
+    }
+    const [left, right] = symmetry;
+    const leftName = resolveName(left);
+    const rightName = resolveName(right);
+    const leftNode = nodes.find((node) => node.name === leftName);
+    const rightNode = nodes.find((node) => node.name === rightName);
+    if (!leftNode || !rightNode) throw new Error("Symmetry references unknown node.");
+    return new Symmetry([leftNode, rightNode]);
+  });
+  return new Skeleton({
+    name: data.name ?? fallbackName,
+    nodes,
+    edges,
+    symmetries
+  });
+}
+function decodeYamlSkeleton(yamlData) {
+  const parsed = YAML.parse(yamlData);
+  if (!parsed) throw new Error("Empty skeleton YAML.");
+  if (Object.prototype.hasOwnProperty.call(parsed, "nodes")) {
+    return decodeSkeleton(parsed);
+  }
+  return Object.entries(parsed).map(
+    ([name, skeletonData]) => decodeSkeleton(skeletonData, name)
+  );
+}
+function encodeYamlSkeleton(skeletons) {
+  const list = Array.isArray(skeletons) ? skeletons : [skeletons];
+  const payload = {};
+  list.forEach((skeleton, index) => {
+    const name = skeleton.name ?? `Skeleton-${index}`;
+    const nodes = skeleton.nodes.map((node) => ({ name: node.name }));
+    const edges = skeleton.edges.map((edge) => ({
+      source: { name: edge.source.name },
+      destination: { name: edge.destination.name }
+    }));
+    const symmetries = skeleton.symmetries.map((symmetry) => {
+      const pair = Array.from(symmetry.nodes);
+      return [{ name: pair[0].name }, { name: pair[1].name }];
+    });
+    payload[name] = { nodes, edges, symmetries };
+  });
+  return YAML.stringify(payload);
+}
 export {
   Camera,
   CameraGroup,
@@ -2597,6 +2672,8 @@ export {
   Symmetry,
   Track,
   Video,
+  decodeYamlSkeleton,
+  encodeYamlSkeleton,
   fromDict,
   fromNumpy,
   labelsFromNumpy,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@talmolab/sleap-io.js",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "private": false,
   "type": "module",
   "exports": {
@@ -12,6 +12,10 @@
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",
   "files": ["dist"],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/talmolab/sleap-io.js.git"
+  },
   "scripts": {
     "build": "tsup src/index.ts --format esm --dts",
     "test": "vitest",