@genome-spy/app 0.69.1 → 0.71.0

package/package.json

@@ -8,7 +8,7 @@
   "contributors": [],
   "license": "MIT",
   "homepage": "https://genomespy.app/",
-  "version": "0.69.1",
+  "version": "0.71.0",
   "main": "dist/index.js",
   "type": "module",
   "exports": {
@@ -27,7 +27,9 @@
     "dev": "node dev-server.mjs",
     "build": "rm -rf dist && mkdir -p dist && vite build && npm run build:schema",
     "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.d.ts' --type AppRootSpec > dist/schema.json",
-    "test:tsc": "tsc -p tsconfig.json --noEmit",
+    "test:tsc": "npm run test:tsc:src && npm run test:tsc:tests",
+    "test:tsc:src": "tsc -p tsconfig.json --noEmit",
+    "test:tsc:tests": "tsc -p tsconfig.tests.json --noEmit",
     "storybook": "storybook dev -p 6006",
     "build-storybook": "storybook build",
     "prepublishOnly": "npm run build"
@@ -37,7 +39,7 @@
     "@fortawesome/fontawesome-free": "^6.4.2",
     "@fortawesome/fontawesome-svg-core": "^6.4.2",
     "@fortawesome/free-solid-svg-icons": "^6.4.2",
-    "@genome-spy/core": "^0.69.1",
+    "@genome-spy/core": "^0.71.0",
     "@reduxjs/toolkit": "^2.11.0",
     "d3-color": "^3.1.0",
     "idb": "^7.1.1",
@@ -45,7 +47,8 @@
     "lz-string": "^1.4.4",
     "mapsort": "^1.0.5",
     "micromark": "^4.0.0",
-    "redux-undo": "^1.0.1"
+    "redux-undo": "^1.0.1",
+    "zarrita": "^0.6.1"
   },
-  "gitHead": "bbbc1860a0730070d0a7c1ca7a9923d4a5d25366"
+  "gitHead": "ee14df5ba7218882d48a1674916304ac6f0a4549"
 }

package/dist/index-ByuE8dvu.js

@@ -1,332 +0,0 @@
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-var F = (n, e, t) => e in n ? v(n, e, { enumerable: !0, configurable: !0, writable: !0, value: t }) : n[e] = t;
-var f = (n, e, t) => F(n, typeof e != "symbol" ? e + "" : e, t);
-const y = /%([0-9A-Fa-f]{2})/g, R = /^\s*##\s*(\S+)\s*(.*)/, g = /\r?\n$/, b = /\s+/, C = /\D/g;
-function p(n) {
-  return n.includes("%") ? n.replaceAll(y, (e, t) => String.fromCharCode(parseInt(t, 16))) : n;
-}
-function k(n) {
-  if (!n.length || n === ".")
-    return {};
-  const e = {};
-  let t = n;
-  t.endsWith(`
-`) && (t = t.slice(0, t.endsWith(`\r
-`) ? -2 : -1));
-  for (const r of t.split(";")) {
-    const s = r.indexOf("=");
-    if (s === -1)
-      continue;
-    const c = r.slice(s + 1);
-    if (!c.length)
-      continue;
-    const i = r.slice(0, s).trim();
-    let o = e[i];
-    o || (o = [], e[i] = o);
-    for (const l of c.split(","))
-      o.push(p(l.trim()));
-  }
-  return e;
-}
-function I(n) {
-  if (!n.length || n === ".")
-    return {};
-  const e = {};
-  let t = n;
-  t.endsWith(`
-`) && (t = t.slice(0, t.endsWith(`\r
-`) ? -2 : -1));
-  for (const r of t.split(";")) {
-    const s = r.indexOf("=");
-    if (s === -1)
-      continue;
-    const c = r.slice(s + 1);
-    if (!c.length)
-      continue;
-    const i = r.slice(0, s).trim();
-    let o = e[i];
-    o || (o = [], e[i] = o);
-    for (const l of c.split(","))
-      o.push(l.trim());
-  }
-  return e;
-}
-function L(n) {
-  return _(n.split("	"));
-}
-function a(n) {
-  return n === "." || n === "" || n === void 0 ? null : n;
-}
-function _(n) {
-  const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
-  return {
-    seq_id: e ? p(e) : null,
-    source: t ? p(t) : null,
-    type: r ? p(r) : null,
-    start: s === null ? null : parseInt(s, 10),
-    end: c === null ? null : parseInt(c, 10),
-    score: i === null ? null : parseFloat(i),
-    strand: o,
-    phase: l,
-    attributes: u === null ? null : k(u)
-  };
-}
-function D(n) {
-  const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
-  return {
-    seq_id: e,
-    source: t,
-    type: r,
-    start: s === null ? null : parseInt(s, 10),
-    end: c === null ? null : parseInt(c, 10),
-    score: i === null ? null : parseFloat(i),
-    strand: o,
-    phase: l,
-    attributes: u === null ? null : I(u)
-  };
-}
-function A(n) {
-  var c, i;
-  const e = R.exec(n);
-  if (!e)
-    return null;
-  const [, t] = e;
-  let [, , r] = e;
-  const s = { directive: t };
-  if (r.length && (r = r.replace(g, ""), s.value = r), t === "sequence-region") {
-    const o = r.split(b, 3);
-    return {
-      ...s,
-      seq_id: o[0],
-      start: (c = o[1]) == null ? void 0 : c.replaceAll(C, ""),
-      end: (i = o[2]) == null ? void 0 : i.replaceAll(C, "")
-    };
-  } else if (t === "genome-build") {
-    const [o, l] = r.split(b, 2);
-    return {
-      ...s,
-      source: o,
-      buildName: l
-    };
-  }
-  return s;
-}
-const x = /^\s*[^#\s>]/, w = /^\s*(#+)(.*)/, S = /^\s*$/, E = /^\s*>/, P = /\r?\n?$/g;
-class m {
-  constructor(e) {
-    f(this, "featureCallback");
-    f(this, "endCallback");
-    f(this, "commentCallback");
-    f(this, "errorCallback");
-    f(this, "disableDerivesFromReferences");
-    f(this, "directiveCallback");
-    f(this, "bufferSize");
-    f(this, "eof", !1);
-    f(this, "lineNumber", 0);
-    // features that we have to keep on hand for now because they
-    // might be referenced by something else
-    f(this, "_underConstructionTopLevel", []);
-    // index of the above by ID
-    f(this, "_underConstructionById", {});
-    f(this, "_completedReferences", {});
-    // features that reference something we have not seen yet
-    // structured as:
-    // {  'some_id' : {
-    //     'Parent' : [ orphans that have a Parent attr referencing it ],
-    //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],
-    //    }
-    // }
-    f(this, "_underConstructionOrphans", {});
-    const t = () => {
-    };
-    this.featureCallback = e.featureCallback || t, this.endCallback = e.endCallback || t, this.commentCallback = e.commentCallback || t, this.errorCallback = e.errorCallback || t, this.directiveCallback = e.directiveCallback || t, this.disableDerivesFromReferences = e.disableDerivesFromReferences || !1, this.bufferSize = e.bufferSize === void 0 ? 1 / 0 : e.bufferSize;
-  }
-  addLine(e) {
-    if (this.eof)
-      return;
-    if (this.lineNumber += 1, x.test(e)) {
-      this._bufferLine(e);
-      return;
-    }
-    const t = w.exec(e);
-    if (t) {
-      const [, r] = t;
-      let [, , s] = t;
-      if (r.length === 3)
-        this._emitAllUnderConstructionFeatures();
-      else if (r.length === 2) {
-        const c = A(e);
-        c && (c.directive === "FASTA" ? (this._emitAllUnderConstructionFeatures(), this.eof = !0) : this._emitItem(c));
-      } else
-        this._emitItem({ comment: s.trimStart() });
-    } else if (!S.test(e)) if (E.test(e))
-      this._emitAllUnderConstructionFeatures(), this.eof = !0;
-    else {
-      const r = e.replaceAll(P, "");
-      throw new Error(`GFF3 parse error.  Cannot parse '${r}'.`);
-    }
-  }
-  addParsedFeatureLine(e) {
-    this.eof || (this.lineNumber += 1, this._bufferParsedLine(e));
-  }
-  finish() {
-    this._emitAllUnderConstructionFeatures(), this.endCallback();
-  }
-  _emitItem(e) {
-    Array.isArray(e) ? this.featureCallback(e) : "directive" in e ? this.directiveCallback(e) : "comment" in e && this.commentCallback(e);
-  }
-  _enforceBufferSizeLimit(e = 0) {
-    const t = (r) => {
-      var s, c;
-      r && Array.isArray(r) && ((c = (s = r[0].attributes) == null ? void 0 : s.ID) != null && c[0]) && (r[0].attributes.ID.forEach((o) => {
-        delete this._underConstructionById[o], delete this._completedReferences[o];
-      }), r.forEach((o) => {
-        o.child_features && o.child_features.forEach((l) => {
-          t(l);
-        }), o.derived_features && o.derived_features.forEach((l) => {
-          t(l);
-        });
-      }));
-    };
-    for (; this._underConstructionTopLevel.length + e > this.bufferSize; ) {
-      const r = this._underConstructionTopLevel.shift();
-      r && (this._emitItem(r), t(r));
-    }
-  }
-  /**
-   * return all under-construction features, called when we know
-   * there will be no additional data to attach to them
-   */
-  _emitAllUnderConstructionFeatures() {
-    this._underConstructionTopLevel.forEach(this._emitItem.bind(this)), this._underConstructionTopLevel = [], this._underConstructionById = {}, this._completedReferences = {};
-    const e = Object.keys(this._underConstructionOrphans);
-    if (e.length)
-      throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${e.join(",")}`);
-  }
-  _bufferLine(e) {
-    this._bufferParsedLine(L(e));
-  }
-  _bufferParsedLine(e) {
-    var o, l, u;
-    const t = e;
-    t.child_features = [], t.derived_features = [];
-    const r = ((o = t.attributes) == null ? void 0 : o.ID) || [], s = ((l = t.attributes) == null ? void 0 : l.Parent) || [], c = this.disableDerivesFromReferences ? [] : ((u = t.attributes) == null ? void 0 : u.Derives_from) || [];
-    if (!r.length && !s.length && !c.length) {
-      this._emitItem([t]);
-      return;
-    }
-    let i;
-    r.forEach((d) => {
-      const h = this._underConstructionById[d];
-      h ? (h[h.length - 1].type !== t.type && this._parseError(`multi-line feature "${d}" has inconsistent types: "${t.type}", "${h[h.length - 1].type}"`), h.push(t), i = h) : (i = [t], this._enforceBufferSizeLimit(1), !s.length && !c.length && this._underConstructionTopLevel.push(i), this._underConstructionById[d] = i, this._resolveReferencesTo(i, d));
-    }), this._resolveReferencesFrom(
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-      i || [t],
-      { Parent: s, Derives_from: c },
-      r
-    );
-  }
-  _resolveReferencesTo(e, t) {
-    const r = this._underConstructionOrphans[t];
-    if (r) {
-      for (const s of e)
-        s.child_features.push(...r.Parent), s.derived_features.push(...r.Derives_from);
-      delete this._underConstructionOrphans[t];
-    }
-  }
-  _parseError(e) {
-    this.eof = !0, this.errorCallback(`${this.lineNumber}: ${e}`);
-  }
-  _resolveReferencesFrom(e, t, r) {
-    for (const s of t.Parent) {
-      const c = this._underConstructionById[s];
-      if (c) {
-        let i = !1;
-        for (const o of r) {
-          const l = `Parent,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
-          u[l] && (i = !0), u[l] = !0;
-        }
-        if (!i)
-          for (const o of c)
-            o.child_features.push(e);
-      } else {
-        let i = this._underConstructionOrphans[s];
-        i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Parent.push(e);
-      }
-    }
-    for (const s of t.Derives_from) {
-      const c = this._underConstructionById[s];
-      if (c) {
-        let i = !1;
-        for (const o of r) {
-          const l = `Derives_from,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
-          u[l] && (i = !0), u[l] = !0;
-        }
-        if (!i)
-          for (const o of c)
-            o.derived_features.push(e);
-      } else {
-        let i = this._underConstructionOrphans[s];
-        i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Derives_from.push(e);
-      }
-    }
-  }
-}
-function $(n) {
-  const e = [], t = new m({
-    featureCallback: (r) => e.push(r),
-    disableDerivesFromReferences: !0,
-    errorCallback: (r) => {
-      throw new Error(r);
-    }
-  });
-  for (const r of n.split(/\r?\n/))
-    t.addLine(r);
-  return t.finish(), e;
-}
-function B(n) {
-  const e = [], t = new m({
-    featureCallback: (r) => e.push(r),
-    disableDerivesFromReferences: !0,
-    errorCallback: (r) => {
-      throw new Error(r);
-    }
-  });
-  for (const r of n)
-    t.addLine(r);
-  return t.finish(), e;
-}
-function T(n) {
-  const e = [], t = new m({
-    featureCallback: (r) => e.push(r),
-    disableDerivesFromReferences: !0,
-    errorCallback: (r) => {
-      throw new Error(r);
-    }
-  });
-  for (const r of n) {
-    const s = _(r.fields);
-    r.lineHash !== void 0 && (s.attributes || (s.attributes = {}), s.attributes._lineHash = [String(r.lineHash)]), t.addParsedFeatureLine(s);
-  }
-  return t.finish(), e;
-}
-function q(n, e) {
-  const t = [], r = new m({
-    featureCallback: (c) => t.push(c),
-    disableDerivesFromReferences: !0,
-    errorCallback: (c) => {
-      throw new Error(c);
-    }
-  }), s = e ? _ : D;
-  for (const c of n) {
-    const i = s(c.fields);
-    c.lineHash !== void 0 && (i.attributes || (i.attributes = {}), i.attributes._lineHash = [String(c.lineHash)]), r.addParsedFeatureLine(i);
-  }
-  return r.finish(), t;
-}
-export {
-  B as parseArraySync,
-  T as parseRecordsSync,
-  q as parseRecordsSyncFast,
-  $ as parseStringSync
-};