sciogen 0.1.2__tar.gz → 0.1.3__tar.gz

{sciogen-0.1.2 → sciogen-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciogen
-Version: 0.1.2
+Version: 0.1.3
 Summary: Codebase intelligence layer — a queryable knowledge graph over your code.
 Project-URL: Homepage, https://ayanbag.github.io/sciogen/
 Project-URL: Repository, https://github.com/ayanbag/sciogen
@@ -34,7 +34,13 @@ Requires-Dist: einops; extra == 'embeddings'
 Requires-Dist: sentence-transformers>=3.0; extra == 'embeddings'
 Description-Content-Type: text/markdown
 
-<img src="site/public/logo.png" alt="Image" width="100%" />
+<img src="https://github.com/user-attachments/assets/1f736f23-c647-4838-8901-5db0edb91616" alt="Image" width="100%" />
+
+
+
+
+
+
 
 <div align="center">
   <p>

{sciogen-0.1.2 → sciogen-0.1.3}/README.md

@@ -1,4 +1,10 @@
-<img src="site/public/logo.png" alt="Image" width="100%" />
+<img src="https://github.com/user-attachments/assets/1f736f23-c647-4838-8901-5db0edb91616" alt="Image" width="100%" />
+
+
+
+
+
+
 
 <div align="center">
   <p>

{sciogen-0.1.2 → sciogen-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sciogen"
-version = "0.1.2"
+version = "0.1.3"
 description = "Codebase intelligence layer — a queryable knowledge graph over your code."
 readme = "README.md"
 requires-python = ">=3.10"

{sciogen-0.1.2 → sciogen-0.1.3}/sciogen/__init__.py

@@ -19,6 +19,6 @@ Public entry point::
 
 from sciogen.api import SciogenGraph, open  # noqa: A004 - deliberate, mirrors sqlite3.connect ergonomics
 
-__version__ = "0.1.1"
+__version__ = "0.1.3"
 
 __all__ = ["SciogenGraph", "open", "__version__"]

{sciogen-0.1.2 → sciogen-0.1.3}/sciogen/cli/explore/template.html

@@ -284,7 +284,8 @@ GRAPH.edges.forEach(e => {
   if (adjacency.has(e.dst)) adjacency.get(e.dst).push(e);
 });
 const degree = id => GRAPH.in_degrees[id] || 0;
-const maxDegree = Math.max(1, ...Object.values(GRAPH.in_degrees));
+let maxDegree = 1;
+for (const v of Object.values(GRAPH.in_degrees)) if (v > maxDegree) maxDegree = v;
 const nodeSize = id => 22 + 36 * Math.sqrt(degree(id) / maxDegree);
 const shortLabel = n => n.kind === "FileNode" ? n.name.split("/").pop() : (n.name.split(".").pop() || n.name);
 
@@ -293,6 +294,8 @@ const visible = new Set(GRAPH.nodes.filter(n => n.kind === "FileNode").map(n =>
 const revealedBy = new Map();
 const expanded = new Set();
 const hiddenKinds = new Set();
+const savedPos = new Map();          // id → {x,y}; lets nodes reappear where they were
+const LAYOUT_ANIM_MAX = 700;         // above this many visible nodes, layout runs without animation
 let minConf = 0;
 let currentLayout = "force";
 let shownEdges = 0;
@@ -374,45 +377,129 @@ const cy = cytoscape({
   wheelSensitivity: 0.25,
 });
 
-/* stagger-fade the initial file nodes in */
+/* persist node positions after any layout or manual drag, so incremental
+   updates never re-simulate — reappearing nodes land where they were */
+cy.on("layoutstop", () => {
+  cy.nodes().forEach(n => savedPos.set(n.id(), { x: n.position("x"), y: n.position("y") }));
+});
+cy.on("dragfree", "node", e =>
+  savedPos.set(e.target.id(), { x: e.target.position("x"), y: e.target.position("y") }));
+
+/* fade the initial file nodes in as one group (not one timer per node) */
 if (!reduce) {
-  cy.nodes().forEach((n, i) => {
-    n.style("opacity", 0);
-    setTimeout(() => n.animate({ style: { opacity: 1 } }, { duration: 260, easing: "ease-out" }), 24 * i);
+  const first = cy.nodes();
+  first.style("opacity", 0);
+  first.animate({ style: { opacity: 1 } }, { duration: 300, easing: "ease-out" });
+}
+
+/* Desired on-screen sets. Edges are collected by walking only the adjacency
+   of visible nodes — never the full GRAPH.edges array — so cost scales with
+   what's shown, not with the size of the whole codebase. */
+function computeWanted() {
+  const wantNodes = new Set();
+  for (const id of visible) {
+    const n = nodesById.get(id);
+    if (n && !hiddenKinds.has(n.kind)) wantNodes.add(id);
+  }
+  const wantEdges = new Map();
+  for (const id of wantNodes) {
+    const adj = adjacency.get(id);
+    if (!adj) continue;
+    for (const e of adj) {
+      if (e.kind === "DEFINES" || e.kind === "PART_OF") continue;
+      if (e.confidence < minConf) continue;
+      if (!wantNodes.has(e.src) || !wantNodes.has(e.dst)) continue;
+      const key = e.src + "→" + e.dst + "→" + e.kind;
+      if (!wantEdges.has(key)) wantEdges.set(key, e);
+    }
+  }
+  shownEdges = wantEdges.size;
+  return { wantNodes, wantEdges };
+}
+
+/* Place freshly-revealed nodes in a ring around whatever expanded them —
+   no physics, no global relayout, existing nodes never move. */
+function positionNew(added, curNodes) {
+  const groups = new Map();
+  added.forEach(n => {
+    const id = n.id();
+    if (savedPos.has(id)) { n.position(savedPos.get(id)); return; }
+    const by = revealedBy.get(id) || "__root";
+    (groups.get(by) || groups.set(by, []).get(by)).push(n);
   });
+  // position groups whose anchor already existed first, so anchors added in
+  // this same batch are themselves placed before their children reference them
+  const order = [...groups.keys()].sort((a, b) =>
+    (curNodes.has(a) ? 0 : 1) - (curNodes.has(b) ? 0 : 1));
+  for (const by of order) {
+    const members = groups.get(by);
+    const anchor = by !== "__root" ? cy.getElementById(by) : null;
+    const has = anchor && anchor.nonempty();
+    const cx = has ? anchor.position("x") : cy.width() / 2;
+    const cyy = has ? anchor.position("y") : cy.height() / 2;
+    const r = 55 + members.length * 7;
+    members.forEach((m, i) => {
+      const a = (2 * Math.PI * i) / members.length - Math.PI / 2;
+      m.position({ x: cx + r * Math.cos(a), y: cyy + r * Math.sin(a) });
+      savedPos.set(m.id(), { x: m.position("x"), y: m.position("y") });
+    });
+  }
 }
 
+/* Incremental reconciliation: diff current vs wanted, add/remove only the
+   delta inside one batched frame. No cy.json() teardown, no relayout. */
 function refresh(opts) {
   opts = opts || {};
-  const before = new Set(cy.nodes().map(n => n.id()));
-  const els = buildElements();
-  const after = new Set(els.filter(e => !e.data.source).map(e => e.data.id));
-
-  const doUpdate = () => {
-    cy.json({ elements: els });
-    cy.style(cyStyle());
-    if (!reduce) {
-      cy.nodes().forEach(n => {
-        if (!before.has(n.id())) {
-          n.style("opacity", 0);
-          n.animate({ style: { opacity: 1 } }, { duration: 240, easing: "ease-out" });
-        }
-      });
+  const { wantNodes, wantEdges } = computeWanted();
+  const curNodes = new Set(cy.nodes().map(n => n.id()));
+  const curEdges = new Set(cy.edges().map(e => e.id()));
+
+  let remove = cy.collection();
+  cy.nodes().forEach(n => {
+    if (!wantNodes.has(n.id())) {
+      savedPos.set(n.id(), { x: n.position("x"), y: n.position("y") });
+      remove = remove.union(n);
     }
-    cy.layout(LAYOUTS[currentLayout]).run();
-    if (opts.fit) cy.animate({ fit: { padding: 40 }, duration: reduce ? 0 : 350, easing: "ease-out" });
-    updateStats();
-    if (opts.then) opts.then();
-  };
+  });
+  cy.edges().forEach(e => { if (!wantEdges.has(e.id())) remove = remove.union(e); });
+
+  const addNodes = [], addEdges = [];
+  for (const id of wantNodes) {
+    if (curNodes.has(id)) continue;
+    const n = nodesById.get(id);
+    addNodes.push({ group: "nodes", data: { id, label: shortLabel(n), kind: n.kind, size: nodeSize(id) } });
+  }
+  for (const [key, e] of wantEdges) {
+    if (curEdges.has(key)) continue;
+    addEdges.push({ group: "edges", data: { id: key, source: e.src, target: e.dst, kind: e.kind, confidence: e.confidence }, classes: edgeClass(e.confidence) });
+  }
+
+  let added = cy.collection();
+  cy.batch(() => {
+    if (remove.nonempty()) cy.remove(remove);
+    if (addNodes.length) { added = cy.add(addNodes); positionNew(added, curNodes); }
+    if (addEdges.length) cy.add(addEdges);
+  });
 
-  // fade out nodes that are leaving before the graph snaps
-  const leaving = cy.nodes().filter(n => !after.has(n.id()));
-  if (!reduce && leaving.length && leaving.length < 80) {
-    leaving.animate({ style: { opacity: 0 } }, { duration: 150, easing: "ease-in" });
-    setTimeout(doUpdate, 160);
-  } else {
-    doUpdate();
+  if (!reduce && added.nonempty()) {
+    added.style("opacity", 0);
+    added.animate({ style: { opacity: 1 } }, { duration: 240, easing: "ease-out" });
   }
+  if (opts.fit) cy.animate({ fit: { padding: 40 }, duration: reduce ? 0 : 350, easing: "ease-out" });
+  updateStats();
+  if (opts.then) opts.then();
+}
+
+/* Explicit, user-triggered global relayout (layout buttons, expand-all).
+   Skips animation past LAYOUT_ANIM_MAX so big graphs snap instead of grind. */
+function runLayout(opts) {
+  opts = opts || {};
+  const big = cy.nodes().length > LAYOUT_ANIM_MAX;
+  const cfg = Object.assign({}, LAYOUTS[currentLayout], {
+    animate: (reduce || big) ? false : (currentLayout === "force" ? "end" : true),
+    fit: !!opts.fit,
+  });
+  cy.layout(cfg).run();
 }
 
 function updateStats() {
@@ -497,8 +584,7 @@ function esc(s) { const d = document.createElement("div"); d.textContent = s; re
 cy.on("mouseover", "node", evt => {
   const n = evt.target;
   const hood = n.closedNeighborhood();
-  cy.elements().not(hood).addClass("dim");
-  hood.addClass("hot");
+  cy.batch(() => { cy.elements().not(hood).addClass("dim"); hood.addClass("hot"); });
   tip.innerHTML = nodeTip(n);
   tip.classList.add("show");
   moveTip(evt);
@@ -506,15 +592,17 @@ cy.on("mouseover", "node", evt => {
 });
 cy.on("mouseover", "edge", evt => {
   const e = evt.target;
-  cy.elements().not(e.connectedNodes().union(e)).addClass("dim");
-  e.addClass("hot"); e.connectedNodes().addClass("hot");
+  cy.batch(() => {
+    cy.elements().not(e.connectedNodes().union(e)).addClass("dim");
+    e.addClass("hot"); e.connectedNodes().addClass("hot");
+  });
   tip.innerHTML = edgeTip(e);
   tip.classList.add("show");
   moveTip(evt);
 });
 cy.on("mousemove", "node, edge", moveTip);
 cy.on("mouseout", "node, edge", () => {
-  cy.elements().removeClass("dim hot");
+  cy.batch(() => cy.elements().removeClass("dim hot"));
   tip.classList.remove("show");
   document.getElementById("cy").style.cursor = "";
 });
@@ -651,15 +739,15 @@ searchInput.addEventListener("blur", () => setTimeout(closeSug, 150));
 
 /* ---------------------------------------------------- toolbar controls */
 document.getElementById("btn-expand").onclick = () => {
-  GRAPH.nodes.forEach(n => visible.add(n.id));
-  GRAPH.nodes.forEach(n => expanded.add(n.id));
-  refresh({ fit: true });
+  GRAPH.nodes.forEach(n => { visible.add(n.id); expanded.add(n.id); });
+  refresh();                 // add the full delta incrementally (no layout inside)
+  runLayout({ fit: true });  // one explicit relayout to arrange the whole graph
 };
 document.getElementById("btn-collapse").onclick = () => {
   visible.clear(); revealedBy.clear(); expanded.clear();
   GRAPH.nodes.filter(n => n.kind === "FileNode").forEach(n => visible.add(n.id));
   hidePanel();
-  refresh({ fit: true });
+  refresh({ fit: true });    // file nodes stay put on their saved positions
 };
 document.getElementById("btn-fit").onclick = () =>
   cy.animate({ fit: { padding: 40 }, duration: reduce ? 0 : 350, easing: "ease-out" });
@@ -669,16 +757,18 @@ function setLayout(name) {
   currentLayout = name;
   btnForce.classList.toggle("active", name === "force");
   btnHier.classList.toggle("active", name === "hier");
-  refresh({ fit: true });
+  runLayout({ fit: true });  // relayout existing nodes in place — no rebuild
 }
 btnForce.onclick = () => setLayout("force");
 btnHier.onclick = () => setLayout("hier");
 
 const confSlider = document.getElementById("conf"), confVal = document.getElementById("conf-val");
+let confTimer = null;
 confSlider.addEventListener("input", () => {
   minConf = parseFloat(confSlider.value);
   confVal.textContent = minConf.toFixed(2);
-  refresh();
+  clearTimeout(confTimer);
+  confTimer = setTimeout(refresh, 90);  // debounce; only edges change, nodes never move
 });
 
 /* ------------------------------------------------------ legend filters */

{sciogen-0.1.2 → sciogen-0.1.3}/site/docs.html

@@ -367,6 +367,10 @@
       <a href="#cli">CLI reference</a>
       <a href="#configuration">Configuration</a>
     </div>
+    <div class="group">
+      <div class="group-label">Community</div>
+      <a href="#contributing">Contributing</a>
+    </div>
   </aside>
 
   <main class="doc">
@@ -817,10 +821,41 @@
           <tr><td><code>SCIOGEN_DATA_DIR</code></td><td>Override the index location (default <code>&lt;project&gt;/.sciogen</code>)</td></tr>
         </tbody>
       </table></div>
+    </section>
+
+    <!-- ============================ CONTRIBUTING ============================ -->
+    <section class="block" id="contributing">
+      <h2 class="reveal">Contributing <a class="hash" href="#contributing">#</a></h2>
+      <p class="reveal">sciogen is open source and contributions are welcome — bug reports, language-normalizer improvements, docs, and features all move it forward. The complete guide lives in <a href="https://github.com/ayanbag/sciogen/blob/master/CONTRIBUTING.md" target="_blank" rel="noopener">CONTRIBUTING.md</a>; the essentials are below.</p>
+
+      <h3 class="reveal">Set up a dev environment</h3>
+      <p class="reveal">sciogen targets <b>Python 3.10+</b> and builds with hatchling. Install it <b>editable</b> (<code>-e</code>) so source edits — including the version and CLI banner — take effect immediately, with no reinstall:</p>
+      <div class="code reveal"><span class="lang">shell</span><button class="copy" type="button" data-copy='git clone https://github.com/ayanbag/sciogen && cd sciogen && pip install -e ".[dev,embeddings]"' aria-label="Copy"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><rect x="9" y="9" width="12" height="12" rx="2"/><path d="M5 15V5a2 2 0 0 1 2-2h10"/></svg></button>
+<pre><span class="g">$</span> git clone https://github.com/ayanbag/sciogen
+<span class="g">$</span> cd sciogen
+<span class="g">$</span> pip install -e ".[dev,embeddings]"</pre></div>
+      <p class="reveal">Then confirm your environment is live — both must print the <b>same</b> version; if they disagree you're running a stale install:</p>
+      <div class="code reveal"><span class="lang">shell</span><button class="copy" type="button" data-copy='python -c "import sciogen; print(sciogen.__version__)" && python -m sciogen --version' aria-label="Copy"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><rect x="9" y="9" width="12" height="12" rx="2"/><path d="M5 15V5a2 2 0 0 1 2-2h10"/></svg></button>
+<pre><span class="g">$</span> python -c "import sciogen; print(sciogen.__version__)"
+<span class="g">$</span> python -m sciogen --version</pre></div>
+
+      <h3 class="reveal">Run the tests</h3>
+      <p class="reveal">Every change should keep the suite green. New behavior needs a test; a bug fix should add a regression test that fails before and passes after.</p>
+      <div class="code reveal"><span class="lang">shell</span><button class="copy" type="button" data-copy="pytest" aria-label="Copy"><svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><rect x="9" y="9" width="12" height="12" rx="2"/><path d="M5 15V5a2 2 0 0 1 2-2h10"/></svg></button>
+<pre><span class="g">$</span> pytest                <span class="mut"># full suite</span>
+<span class="g">$</span> pytest -p no:randomly <span class="mut"># deterministic order</span></pre></div>
+
+      <div class="callout reveal">
+        <span class="t">What belongs in sciogen</span>
+        <p>sciogen is a static index, not a generative tool. A few constraints are non-negotiable, and a PR that breaks one will be asked to change: <b>no LLM calls</b> anywhere; <b>no token counting or context-window logic</b>; query methods return <b>typed nodes, never raw source</b>; the pipeline <b>writes every edge</b> and confidence is filtered at query time, not at write time. Language-specific logic lives in exactly one place — the <b>AST normalizer</b> — so everything downstream stays language-agnostic.</p>
+      </div>
+
+      <h3 class="reveal">Versioning</h3>
+      <p class="reveal">The version lives in a <b>single place</b> — <code>__version__</code> in <code>sciogen/__init__.py</code>. <code>pyproject.toml</code> reads it via hatchling and the CLI banner imports the same constant, so bump that one line and everything stays in lockstep. Never add a second version string.</p>
 
       <div class="doc-nav reveal">
         <a href="index.html"><span class="lbl">← Back</span><div class="ttl">sciogen home</div></a>
-        <a class="next" href="https://github.com/ayanbag/sciogen" target="_blank" rel="noopener"><span class="lbl">Source →</span><div class="ttl">GitHub repository</div></a>
+        <a class="next" href="https://github.com/ayanbag/sciogen/blob/master/CONTRIBUTING.md" target="_blank" rel="noopener"><span class="lbl">Full guide →</span><div class="ttl">CONTRIBUTING.md</div></a>
       </div>
     </section>
   </main>