Deploy 9eecba1

Give Evo 2 a place in the product, not just on a GPU

Source: https://github.com/WINTER4000/turingDNA/commit/9eecba109b5215f1a319c81fee2d9132d7f46140

dee/server.py

@@ -819,6 +819,12 @@ _RL_RULES = [
     ("/api/primers/multiplex",         (30,  60)),
     ("/api/primers/analyze",           (40,  60)),
     ("/api/crispr",                    (40,  60)),
+    # Evo 2 (7B) on a rented GPU — the most expensive call in the product by a
+    # wide margin, and unlike ESM-2's Achilles tier there is no free local path
+    # to fall back to. Tighter than every other tool bucket on purpose: this
+    # limit is about the GPU bill, not about protecting a worker thread.
+    ("/api/dna/generate",              (6,   60)),   # autoregressive — priciest
+    ("/api/dna",                       (12,  60)),
     ("/api/plasmid",                   (60,  60)),
     ("/api/ping",                      (60,  60)),   # dwell heartbeat — its own
                                                      # bucket so ~2/min never eats
@@ -864,6 +870,8 @@ _EVENT_KINDS = {
     "/api/primers/save":    "primer_save",
     "/api/align":           "sequence_align",
     "/api/de/round2":       "de_round2",
+    "/api/dna/score":       "dna_score",
+    "/api/dna/generate":    "dna_generate",
 }
 # Sort longest-prefix-first so the most specific rule matches.
 _RL_RULES.sort(key=lambda r: len(r[0]), reverse=True)
@@ -3300,6 +3308,108 @@ def create_app() -> Flask:
         resp.headers["Cache-Control"] = "no-store, max-age=0"
         return resp
 
+    # ── DNA-level scoring / generation (Evo 2) ───────────────────────────
+    # Until now the ONLY route to Evo 2 was the agent deciding to call
+    # score_or_generate_dna mid-conversation. The engine computed dna_models
+    # for /api/models and no frontend read it, so a capability that runs on a
+    # 7B genome model was, in practice, unreachable by clicking. These are the
+    # two endpoints the DNA view calls.
+    #
+    # Both are deliberately thin: dee/core/dna_scoring.py already owns tier
+    # rules, bounds and the "not configured is not the same as broken"
+    # distinction, and duplicating any of that here would give the product two
+    # answers to the same question.
+
+    def _dna_signin_gate(where: str):
+        """Same contract as CRISPR/primers: no anonymous use. Distinct from
+        the trial timer — the 403 carries kind=signin_required so auth.js
+        routes to /signin rather than showing the trial modal."""
+        auth = _auth.get_auth()
+        if auth.anonymous:
+            return jsonify({
+                "error": ("DNA scoring requires a free account. Sign in or "
+                          "create one to keep going."),
+                "kind": "signin_required",
+                "signup_url": f"https://turingdna.com/signin/?from={where}",
+            }), 403
+        return None
+
+    @app.post("/api/dna/score")
+    def dna_score() -> Response:
+        gate = _dna_signin_gate("dna")
+        if gate is not None:
+            return gate
+
+        body = request.get_json(force=True, silent=True) or {}
+        reference = "".join(str(body.get("reference") or "").split()).upper()
+        raw_variants = body.get("variants") or []
+        tier = str(body.get("tier") or "achilles").strip().lower()
+
+        if not reference:
+            return jsonify({"error": "missing 'reference'"}), 400
+        if not isinstance(raw_variants, list) or not raw_variants:
+            return jsonify({"error": "missing 'variants'"}), 400
+        variants = [str(v).strip().upper() for v in raw_variants if str(v).strip()]
+        if not variants:
+            return jsonify({"error": "missing 'variants'"}), 400
+
+        try:
+            result = _dna_scoring.score_dna_variants(reference, variants, tier=tier)
+        except _dna_scoring.DnaModelUnavailable as exc:
+            # Customer-safe by construction — dna_scoring keeps env-var names
+            # and repo paths in the log, not in this message.
+            return jsonify({"error": str(exc), "kind": "dna_unavailable"}), 503
+        except ValueError as exc:
+            return jsonify({"error": str(exc)}), 400
+        except Exception:  # noqa: BLE001
+            app.logger.exception("dna_score failed")
+            return jsonify({
+                "error": ("The DNA model didn't return a result for that "
+                          "request. Nothing was scored — try again, and if it "
+                          "keeps failing the backend is having a moment."),
+                "kind": "dna_error",
+            }), 502
+        return jsonify(result)
+
+    @app.post("/api/dna/generate")
+    def dna_generate() -> Response:
+        gate = _dna_signin_gate("dna")
+        if gate is not None:
+            return gate
+
+        body = request.get_json(force=True, silent=True) or {}
+        prompt = "".join(str(body.get("prompt") or "").split()).upper()
+        tier = str(body.get("tier") or "prometheus").strip().lower()
+        if not prompt:
+            return jsonify({"error": "missing 'prompt'"}), 400
+
+        try:
+            n_tokens = int(body.get("n_tokens") or 200)
+            temperature = float(body.get("temperature") or 1.0)
+            top_k = int(body.get("top_k") or 4)
+        except (TypeError, ValueError):
+            return jsonify({"error": "n_tokens/temperature/top_k must be numbers"}), 400
+
+        try:
+            result = _dna_scoring.generate_dna_sequence(
+                prompt, n_tokens=n_tokens, tier=tier,
+                temperature=temperature, top_k=top_k)
+        except _dna_scoring.DnaModelUnavailable as exc:
+            # Also the path for "generation is Prometheus-only" — enforced in
+            # dna_scoring AND again in modal/evo2_scoring, so a caller that
+            # skips this route still gets refused.
+            return jsonify({"error": str(exc), "kind": "dna_unavailable"}), 503
+        except ValueError as exc:
+            return jsonify({"error": str(exc)}), 400
+        except Exception:  # noqa: BLE001
+            app.logger.exception("dna_generate failed")
+            return jsonify({
+                "error": ("The DNA model didn't return a sequence for that "
+                          "prompt. Nothing was generated — try again."),
+                "kind": "dna_error",
+            }), 502
+        return jsonify(result)
+
     @app.get("/api/benchmarks")
     def benchmarks() -> Response:
         """The receipts — how well the engine's zero-shot ranking predicts

dee/static/app.css

@@ -9691,3 +9691,126 @@ body.de-agent-run .dna-edit-actions { display: none; }
     font-size: 10px; line-height: 1.5; color: var(--ink-faint);
     border-top: 1px solid var(--line); padding-top: 7px;
 }
+
+/* ═══════════════════════════════════════════════════════════════════════
+   DNA Design (Evo 2) — mirrors the primer/CRISPR card idiom deliberately,
+   so the newest tool doesn't announce itself as a bolt-on.
+   Tokens: --bg-card / --bg-raised / --line-strong / --ink-*. There is no
+   --surface or --surface-raised in this stylesheet; using them renders
+   invisible components and no test catches it.
+   ═══════════════════════════════════════════════════════════════════════ */
+
+.dna-mode-row { display: flex; gap: 6px; margin-bottom: 16px; }
+.dna-mode {
+    padding: 7px 14px; border-radius: var(--r-2);
+    border: 1px solid var(--line-strong); background: var(--gray-0);
+    color: var(--ink-soft); font-size: 12.5px; cursor: pointer;
+    font-family: inherit;
+}
+.dna-mode:hover { color: var(--ink); border-color: var(--line-bold); }
+.dna-mode.is-active {
+    background: var(--ink-strong); color: var(--on-ink);
+    border-color: var(--ink-strong);
+}
+
+.dna-textarea {
+    width: 100%; box-sizing: border-box; resize: vertical;
+    font-family: var(--font-mono); font-size: 13px; line-height: 1.5;
+    padding: 12px 14px; border: 1px solid var(--line-strong); border-radius: var(--r-3);
+    background: var(--gray-0); color: var(--ink);
+}
+.dna-textarea:focus { outline: none; border-color: var(--brand); }
+
+.dna-meta { margin: 6px 0 14px; font-size: 11.5px; color: var(--ink-faint); }
+.dna-meta.is-warn { color: var(--warning); }
+
+.dna-select {
+    width: 100%; box-sizing: border-box; padding: 9px 12px;
+    border: 1px solid var(--line-strong); border-radius: var(--r-2);
+    background: var(--gray-0); color: var(--ink); font-size: 13px;
+    font-family: inherit;
+}
+.dna-select:focus { outline: none; border-color: var(--brand); }
+/* A tier that exists but isn't reachable stays visible and disabled — that
+   is a more useful statement than quietly dropping the row. */
+.dna-select option:disabled { color: var(--ink-disabled); }
+
+.dna-gen-knobs { display: flex; gap: 14px; flex-wrap: wrap; margin-bottom: 14px; }
+.dna-knob { display: flex; flex-direction: column; gap: 4px; font-size: 12px; color: var(--ink-soft); }
+.dna-knob input {
+    width: 110px; padding: 7px 10px; font-family: var(--font-mono); font-size: 13px;
+    border: 1px solid var(--line-strong); border-radius: var(--r-2);
+    background: var(--gray-0); color: var(--ink);
+}
+.dna-knob input:focus { outline: none; border-color: var(--brand); }
+
+.dna-actions { display: flex; gap: 10px; justify-content: flex-end; margin-top: 14px; }
+
+/* The wait matters: a cold 7B container is ~80s and a silent spinner over
+   that long is indistinguishable from a hang. */
+.dna-wait {
+    margin-top: 12px; font-size: 12.5px; color: var(--ink-soft);
+    background: var(--gray-1); border-left: 3px solid var(--line-bold);
+    padding: 9px 12px; border-radius: var(--r-2);
+}
+
+.dna-results-head {
+    display: flex; align-items: baseline; justify-content: space-between;
+    gap: 12px; flex-wrap: wrap; margin-bottom: 10px;
+}
+.dna-results-title { font-size: 14px; color: var(--ink-strong); font-weight: 600; }
+.dna-results-meta { font-size: 11.5px; color: var(--ink-faint); font-family: var(--font-mono); }
+
+.dna-table { width: 100%; border-collapse: collapse; font-size: 13px; margin-top: 8px; }
+.dna-table th {
+    text-align: left; font-size: 11px; text-transform: uppercase;
+    letter-spacing: .06em; color: var(--ink-faint); font-weight: 600;
+    padding: 6px 10px 6px 0; border-bottom: 1px solid var(--line);
+}
+.dna-table td { padding: 8px 10px 8px 0; border-bottom: 1px solid var(--line); vertical-align: middle; }
+.dna-table td:last-child, .dna-table th:last-child { width: 42%; padding-right: 0; }
+
+.dna-delta { white-space: nowrap; }
+.dna-delta--neg { color: var(--danger); }
+.dna-delta--pos { color: var(--success); }
+
+.dna-bar { display: block; height: 8px; border-radius: 999px; min-width: 2px; }
+.dna-bar--neg { background: color-mix(in srgb, var(--danger) 55%, transparent); }
+.dna-bar--pos { background: color-mix(in srgb, var(--success) 55%, transparent); }
+
+.dna-scale-note { margin-top: 10px; font-size: 11.5px; color: var(--ink-faint); line-height: 1.5; }
+
+/* Refused variants are an input finding, never folded into "no result". */
+.dna-skipped {
+    margin-top: 16px; padding: 12px 14px; border-radius: var(--r-2);
+    background: color-mix(in srgb, var(--warning) 8%, transparent);
+    border-left: 3px solid var(--warning);
+}
+.dna-skipped-hd { margin: 0 0 6px; font-size: 12px; font-weight: 600; color: var(--warning); }
+.dna-skipped ul { margin: 0; padding-left: 18px; font-size: 12.5px; color: var(--ink-soft); }
+.dna-skipped li { margin: 3px 0; }
+.dna-skipped-why { margin: 8px 0 0; font-size: 11.5px; color: var(--ink-faint); line-height: 1.5; }
+
+.dna-generated {
+    margin: 8px 0 0; padding: 12px 14px; border-radius: var(--r-2);
+    background: var(--gray-1); border: 1px solid var(--line);
+    font-size: 12.5px; line-height: 1.6; color: var(--ink);
+    white-space: pre-wrap; word-break: break-all; overflow-x: auto;
+}
+.dna-empty { font-size: 13px; color: var(--ink-faint); margin: 8px 0 0; }
+
+/* Mobile: the standing rule is 44px tap targets and nothing under 12px. */
+@media (max-width: 720px) {
+    .dna-mode { padding: 11px 16px; min-height: 44px; font-size: 13px; }
+    .dna-actions { flex-direction: column-reverse; }
+    .dna-actions button { width: 100%; min-height: 44px; }
+    .dna-knob input { width: 100%; min-height: 44px; }
+    .dna-gen-knobs { flex-direction: column; gap: 10px; }
+    .dna-table { font-size: 12px; }
+    .dna-table td:last-child, .dna-table th:last-child { width: 30%; }
+    /* The standing rule is nothing under 12px on a phone. Shared components
+       (<code>, <summary>) sit at 11–11.5px across every existing view and
+       are left alone here — but everything this tool owns meets it. */
+    .dna-meta, .dna-results-meta, .dna-scale-note,
+    .dna-skipped-why, .dna-table th { font-size: 12px; }
+}

dee/static/app.js

@@ -390,7 +390,9 @@ renderGutter();
 // existed): 'turing' leads the list and is the no-hash fallback. The other
 // four tools stay one click away for hands-on work — Turing just isn't a
 // nav-rail peer anymore, it's what a session starts with.
-const ROUTES = ['mission', 'turing', 'structure', 'plasmid', 'design', 'crispr', 'primers', 'docs'];
+// 'dna' (Evo 2) sits next to 'design': DE designs at the protein level, DNA
+// Design at the nucleotide level. Same phase of the loop, different molecule.
+const ROUTES = ['mission', 'turing', 'structure', 'plasmid', 'design', 'dna', 'crispr', 'primers', 'docs'];
 
 // ── UI mode flag (Mission-Control-+-Bench re-architecture, 2026-07-13) ──
 // 'bench' is now the default UI; ?ui=classic remains as a rollback escape
@@ -10311,6 +10313,7 @@ function runOracle(opts){
     // The tools, for the ⌘K command palette (verbs on the current work).
     const TOOLS = [
         { label: 'Evolve a sequence', hint: 'Directed evolution', route: 'design' },
+        { label: 'Score a DNA change', hint: 'Promoters, splice sites, UTRs', route: 'dna' },
         { label: 'Build a plasmid', hint: 'Map & annotate a construct', route: 'plasmid' },
         { label: 'Design CRISPR guides', hint: 'Guides + specificity', route: 'crispr' },
         { label: 'Check primers', hint: 'Tm, dimers, specificity', route: 'primers' },
@@ -10348,6 +10351,10 @@ function runOracle(opts){
         { route: 'plasmid', label: 'Build a plasmid',      kw: ['plasmid','vector','clone','clonin','annotate','assembl','gibson','golden','backbone','insert','map '] },
         { route: 'crispr',  label: 'Design CRISPR guides', kw: ['crispr','guide','grna','sgrna','knockout','knock out','cas9','base edit','base-edit','excis','disrupt'] },
         { route: 'primers', label: 'Check primers',        kw: ['primer',' pcr','anneal','dimer','amplif','oligo','melting'] },
+        // DNA-level, so the vocabulary is regulatory/non-coding rather than
+        // protein. Deliberately LAST: 'design'/'crispr' above own the terms a
+        // protein or editing question would use, and matching is first-hit.
+        { route: 'dna',     label: 'Score a DNA change',   kw: ['promoter','enhancer','splice','utr',' rbs','ribosome binding','non-coding','noncoding','regulatory','intron','terminator','operator','evo 2','evo2','nucleotide'] },
     ];
     function matchIntent(q) {
         const s = ' ' + String(q || '').toLowerCase() + ' ';
@@ -10944,7 +10951,11 @@ function runOracle(opts){
 // keep working. Only ever active in the opt-in bench UI.
 // ═══════════════════════════════════════════════════════════════════════
 (function () {
-    const TAB_ROUTES = ['structure', 'design', 'plasmid', 'crispr', 'primers'];
+    // 'dna' sits next to 'design' for the same reason it does in the nav:
+    // both are the Design phase, one at the protein level and one at the
+    // nucleotide level. Bench is the DEFAULT UI — a route missing from this
+    // list has a nav entry that goes nowhere.
+    const TAB_ROUTES = ['structure', 'design', 'dna', 'plasmid', 'crispr', 'primers'];
     let current = null;   // { name, sub, phaseIdx, route }
 
     function el(id) { return document.getElementById(id); }
@@ -11894,3 +11905,373 @@ if (document.readyState === 'loading') {
 } else {
     initModelPicker();
 }
+
+
+// ═══════════════════════════════════════════════════════════════════════
+// DNA Design — Evo 2 (7B) scoring and generation
+// ═══════════════════════════════════════════════════════════════════════
+// The DNA-level counterpart to Directed Evolution. Before this view, the only
+// way to reach Evo 2 was for Turing to decide to call score_or_generate_dna
+// mid-conversation: /api/models computed `dna_models` and NOTHING in the
+// frontend read it, so the one capability that understands non-coding and
+// regulatory sequence was unreachable by clicking.
+//
+// Two things this file is careful about, both learned the hard way elsewhere
+// in this codebase:
+//
+//   · Availability is what the SERVER says, per tier. A tier whose backend
+//     isn't reachable is disabled with its reason shown, never offered and
+//     then failed. (/api/models' `available` is a live probe now — see
+//     dee/core/modal_client.reachable.)
+//   · A cold 7B container takes ~80s (warm ~23s, both measured). A spinner
+//     with no elapsed time over that long is indistinguishable from a hang,
+//     which is the exact complaint the Interaction Radar's elapsed-time work
+//     already answered once.
+// ═══════════════════════════════════════��═══════════════════════════════
+(function () {
+    const $ = (id) => document.getElementById(id);
+    const esc = (s) => (typeof escapeHtml === 'function' ? escapeHtml(String(s)) : String(s));
+
+    // The E. coli lac promoter / operator region — the same fragment used to
+    // verify the backend end to end, with substitutions whose WT bases are
+    // real. An example that gets refused would teach the wrong lesson.
+    const EXAMPLE_REF =
+        'TTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCA' +
+        'CACAGGAAACAGCTATGACCATGATTACGGATTCACTGGCCGTCGTTTTACAA';
+    const EXAMPLE_VARIANTS = 'T10G\nG20C\nT30A\nG45C';
+
+    let mode = 'score';
+    let tiers = [];
+    let busy = false;
+    let timerId = null;
+
+    function view() { return document.querySelector('[data-view="dna"]'); }
+
+    // ── tier picker, driven by what the server says is reachable ─────────
+    async function loadTiers() {
+        const sel = $('dnaTier');
+        if (!sel) return;
+        try {
+            const res = await fetch('/api/models');
+            const data = await res.json();
+            tiers = (data && data.dna_models) || [];
+        } catch (_) {
+            tiers = [];
+        }
+        if (!tiers.length) {
+            sel.innerHTML = '<option value="">DNA scoring isn\'t available here</option>';
+            sel.disabled = true;
+            setTierNote('');
+            return;
+        }
+        sel.disabled = false;
+        sel.innerHTML = tiers.map((t) => {
+            // Disabled rather than hidden: "this tier exists but isn't running
+            // right now" is a different, more useful statement than silence.
+            const off = t.available ? '' : ' disabled';
+            const suffix = t.available ? '' : ' — unavailable';
+            return `<option value="${esc(t.id)}"${off}>${esc(t.label)}${suffix}</option>`;
+        }).join('');
+        const firstUp = tiers.find((t) => t.available);
+        if (firstUp) sel.value = firstUp.id;
+        syncTier();
+    }
+
+    function currentTier() {
+        const sel = $('dnaTier');
+        return tiers.find((t) => t.id === (sel && sel.value)) || null;
+    }
+
+    function setTierNote(text) {
+        const el = $('dnaTierNote');
+        if (el) el.textContent = text || '';
+    }
+
+    function syncTier() {
+        const t = currentTier();
+        const runBtn = $('dnaRun');
+        if (!t) {
+            setTierNote('');
+            if (runBtn) runBtn.disabled = true;
+            return;
+        }
+        let note = t.note || '';
+        if (mode === 'generate' && !t.generation) {
+            // Say it here rather than letting the server 503 after a click.
+            note += ' Generation is Prometheus-only — the checkpoint is the '
+                  + 'same on both tiers, generation access is the difference.';
+        }
+        if (t.max_reference_nt) {
+            note += ` Up to ${Number(t.max_reference_nt).toLocaleString()} nt per call.`;
+        }
+        setTierNote(note.trim());
+        if (runBtn) {
+            runBtn.disabled = busy || !t.available
+                || (mode === 'generate' && !t.generation);
+        }
+    }
+
+    // ── mode ─────────────────────────────────────────────────────────────
+    function setMode(next) {
+        mode = next;
+        const scoreBtn = $('dnaModeScore');
+        const genBtn = $('dnaModeGenerate');
+        if (scoreBtn) {
+            scoreBtn.classList.toggle('is-active', mode === 'score');
+            scoreBtn.setAttribute('aria-selected', String(mode === 'score'));
+        }
+        if (genBtn) {
+            genBtn.classList.toggle('is-active', mode === 'generate');
+            genBtn.setAttribute('aria-selected', String(mode === 'generate'));
+        }
+        const sp = $('dnaScorePane');
+        const gp = $('dnaGeneratePane');
+        if (sp) sp.hidden = mode !== 'score';
+        if (gp) gp.hidden = mode !== 'generate';
+        const run = $('dnaRun');
+        if (run) run.textContent = mode === 'score' ? 'Score variants' : 'Generate sequence';
+        // Generation needs Prometheus; jump there if the current pick can't.
+        if (mode === 'generate') {
+            const t = currentTier();
+            if (t && !t.generation) {
+                const gen = tiers.find((x) => x.generation && x.available);
+                if (gen) $('dnaTier').value = gen.id;
+            }
+        }
+        hideResults();
+        syncTier();
+    }
+
+    // ── input helpers ────────────────────────────────────────────────────
+    function cleanSeq(raw) {
+        // Tolerate FASTA headers and whitespace — people paste what they have.
+        return String(raw || '')
+            .split('\n').filter((l) => !l.trim().startsWith('>')).join('')
+            .replace(/\s+/g, '').toUpperCase();
+    }
+
+    function refMeta() {
+        const el = $('dnaRefMeta');
+        if (!el) return;
+        const seq = cleanSeq($('dnaReference') && $('dnaReference').value);
+        if (!seq) { el.hidden = true; return; }
+        const bad = seq.replace(/[ACGT]/g, '');
+        const gc = seq ? Math.round(100 * (seq.match(/[GC]/g) || []).length / seq.length) : 0;
+        el.hidden = false;
+        el.textContent = bad
+            ? `${seq.length.toLocaleString()} nt · ${gc}% GC · ${new Set(bad).size} non-ACGT character(s) — those will be rejected`
+            : `${seq.length.toLocaleString()} nt · ${gc}% GC`;
+        el.classList.toggle('is-warn', Boolean(bad));
+    }
+
+    function showError(msg) {
+        const el = $('dnaError');
+        if (!el) return;
+        el.hidden = false;
+        el.textContent = msg;
+    }
+    function clearError() {
+        const el = $('dnaError');
+        if (el) { el.hidden = true; el.textContent = ''; }
+    }
+    function hideResults() {
+        const c = $('dnaResultsCard');
+        if (c) c.hidden = true;
+    }
+
+    // ── the wait ─────────────────────────────────────────────────────────
+    function startWait() {
+        const el = $('dnaWait');
+        if (!el) return;
+        const t0 = Date.now();
+        el.hidden = false;
+        const tick = () => {
+            const s = Math.round((Date.now() - t0) / 1000);
+            // Honest, and specific about WHY it might be slow. "Loading…" for
+            // 80 seconds reads as broken; naming the cold start does not.
+            el.textContent = s < 25
+                ? `Scoring on the GPU — ${s}s`
+                : `Still going — ${s}s. A cold container loads a 7B checkpoint `
+                  + `before its first pass; that's usually under 90s.`;
+        };
+        tick();
+        timerId = setInterval(tick, 1000);
+    }
+    function stopWait() {
+        if (timerId) { clearInterval(timerId); timerId = null; }
+        const el = $('dnaWait');
+        if (el) { el.hidden = true; el.textContent = ''; }
+    }
+
+    // ── results ──────────────────────────────────────────────────────────
+    function renderScores(data) {
+        const card = $('dnaResultsCard');
+        const body = $('dnaResultsBody');
+        const meta = $('dnaResultsMeta');
+        if (!card || !body) return;
+
+        const scores = (data.scores || []).slice().sort(
+            (a, b) => (a.delta_ll || 0) - (b.delta_ll || 0));
+        const skipped = data.skipped || [];
+
+        const bits = [];
+        if (typeof data.reference_ll === 'number') {
+            bits.push(`reference log-likelihood ${data.reference_ll.toFixed(4)}`);
+        }
+        if (data.checkpoint) bits.push(esc(data.checkpoint));
+        if (typeof data.elapsed_s === 'number') bits.push(`${data.elapsed_s}s`);
+        if (meta) meta.textContent = bits.join(' · ');
+
+        let html = '';
+        if (scores.length) {
+            // Scale bars against the largest |delta| in THIS result set, and
+            // say so — a bar with an unstated scale invites reading it as an
+            // absolute effect size.
+            const max = Math.max.apply(null, scores.map((s) => Math.abs(s.delta_ll || 0))) || 1;
+            html += '<table class="dna-table"><thead><tr>'
+                 + '<th>Variant</th><th>&Delta; log-likelihood</th><th>Effect</th>'
+                 + '</tr></thead><tbody>';
+            scores.forEach((s) => {
+                const d = Number(s.delta_ll || 0);
+                const pct = Math.round(100 * Math.abs(d) / max);
+                const dir = d < 0 ? 'neg' : 'pos';
+                html += `<tr><td class="mono">${esc(s.label)}</td>`
+                     + `<td class="mono dna-delta dna-delta--${dir}">${d.toFixed(4)}</td>`
+                     + `<td><span class="dna-bar dna-bar--${dir}" style="width:${pct}%"></span></td></tr>`;
+            });
+            html += '</tbody></table>';
+            html += '<p class="dna-scale-note">Bars are relative to the largest '
+                 + 'effect in this set, not an absolute scale. Negative = the '
+                 + 'model finds the change less likely than what\'s there now.</p>';
+        }
+
+        if (skipped.length) {
+            // Never fold these into "no result". A refused variant is a
+            // statement about the INPUT, and hiding it would let a typo look
+            // like a shorter answer.
+            html += '<div class="dna-skipped"><p class="dna-skipped-hd">'
+                 + `Not scored (${skipped.length})</p><ul>`;
+            skipped.forEach((s) => {
+                const label = esc(s.label || s.variant || s);
+                const why = s.why || s.reason || 'the reference base at that position does not match';
+                html += `<li><span class="mono">${label}</span> — ${esc(why)}</li>`;
+            });
+            html += '</ul><p class="dna-skipped-why">These were refused rather than '
+                 + 'scored: positions are 1-based against the reference above, and '
+                 + 'a mismatched WT base usually means an off-by-one or the wrong '
+                 + 'strand.</p></div>';
+        }
+
+        if (!scores.length && !skipped.length) {
+            html = '<p class="dna-empty">The model returned no scores for that request.</p>';
+        }
+
+        body.innerHTML = html;
+        card.hidden = false;
+    }
+
+    function renderGenerated(data) {
+        const card = $('dnaResultsCard');
+        const body = $('dnaResultsBody');
+        const meta = $('dnaResultsMeta');
+        if (!card || !body) return;
+        const seq = String(data.sequence || data.generated || '');
+        const bits = [];
+        if (seq) bits.push(`${seq.length.toLocaleString()} nt generated`);
+        if (data.checkpoint) bits.push(esc(data.checkpoint));
+        if (typeof data.elapsed_s === 'number') bits.push(`${data.elapsed_s}s`);
+        if (meta) meta.textContent = bits.join(' · ');
+        body.innerHTML = seq
+            ? `<pre class="dna-generated mono">${esc(seq.replace(/(.{60})/g, '$1\n'))}</pre>`
+              + '<p class="dna-scale-note">Sampled sequence — plausible to the model, '
+              + 'not validated. Nothing here has been checked for function, '
+              + 'synthesisability, or anything else.</p>'
+            : '<p class="dna-empty">The model returned no sequence.</p>';
+        card.hidden = false;
+    }
+
+    // ── run ──────────────────────────────────────────────────────────────
+    async function run() {
+        if (busy) return;
+        clearError();
+        hideResults();
+
+        const tier = ($('dnaTier') && $('dnaTier').value) || '';
+        if (!tier) { showError('No DNA model tier is available on this deployment.'); return; }
+
+        let url, payload;
+        if (mode === 'score') {
+            const reference = cleanSeq($('dnaReference') && $('dnaReference').value);
+            const variants = String(($('dnaVariants') && $('dnaVariants').value) || '')
+                .split(/[\n,;]+/).map((v) => v.trim().toUpperCase()).filter(Boolean);
+            if (!reference) { showError('Paste a reference sequence first.'); return; }
+            if (!variants.length) { showError('Add at least one variant, like T10G.'); return; }
+            url = '/api/dna/score';
+            payload = { reference, variants, tier };
+        } else {
+            const prompt = cleanSeq($('dnaPrompt') && $('dnaPrompt').value);
+            if (!prompt) { showError('Paste a starting sequence first.'); return; }
+            url = '/api/dna/generate';
+            payload = {
+                prompt, tier,
+                n_tokens: Number(($('dnaNTokens') || {}).value || 200),
+                temperature: Number(($('dnaTemperature') || {}).value || 1.0),
+                top_k: Number(($('dnaTopK') || {}).value || 4),
+            };
+        }
+
+        const btn = $('dnaRun');
+        busy = true;
+        if (btn) btn.disabled = true;
+        startWait();
+        try {
+            const res = await fetch(url, {
+                method: 'POST',
+                headers: { 'Content-Type': 'application/json' },
+                body: JSON.stringify(payload),
+            });
+            const data = await res.json();
+            if (!res.ok) {
+                if (data && data.kind === 'signin_required') {
+                    window.dispatchEvent(new Event('td:signin-required'));
+                    return;   // the modal IS the message
+                }
+                throw new Error(data.error || 'The DNA model call failed.');
+            }
+            if (mode === 'score') renderScores(data);
+            else renderGenerated(data);
+        } catch (err) {
+            showError((err && err.message) || String(err));
+        } finally {
+            busy = false;
+            stopWait();
+            syncTier();
+        }
+    }
+
+    // ── wire ─────────────────────────────────────────────────────────────
+    function init() {
+        if (!view()) return;
+        const on = (id, ev, fn) => { const el = $(id); if (el) el.addEventListener(ev, fn); };
+        on('dnaModeScore', 'click', () => setMode('score'));
+        on('dnaModeGenerate', 'click', () => setMode('generate'));
+        on('dnaTier', 'change', syncTier);
+        on('dnaRun', 'click', run);
+        on('dnaReference', 'input', refMeta);
+        on('dnaExample', 'click', () => {
+            setMode('score');
+            const r = $('dnaReference'), v = $('dnaVariants');
+            if (r) r.value = EXAMPLE_REF;
+            if (v) v.value = EXAMPLE_VARIANTS;
+            refMeta();
+            clearError();
+        });
+        loadTiers();
+    }
+
+    if (document.readyState === 'loading') {
+        document.addEventListener('DOMContentLoaded', init);
+    } else {
+        init();
+    }
+}());

dee/static/index.html

@@ -112,7 +112,7 @@
     <!-- ?v= query bumps invalidate browser + iframe asset caches when app.css /
          app.js change. Bump these numbers whenever you ship a frontend update —
          without them, users keep getting the stale file for up to a week. -->
-    <link rel="stylesheet" href="/static/app.css?v=20260811-buildC" />
+    <link rel="stylesheet" href="/static/app.css?v=20260812-dna" />
     <!-- The work catalog + the draggable rail. Kept out of app.css so two new
          self-contained surfaces stay reviewable; every colour is an app.css
          token, so both themes work with nothing added. -->
@@ -250,10 +250,11 @@
                 </a>
 
                 <!--
-                    THE LOOP — the four tools as one ordered workflow, not a
+                    THE LOOP — the tools as one ordered workflow, not a
                     scattered tab-list. A hairline spine (.nav-loop::before) ties
                     them together; each name carries its loop phase on the right.
                       · Directed Evolution — ESM-2 zero-shot variant libraries  (Design)
+                      · DNA Design         — Evo 2 zero-shot nucleotide scoring (Design)
                       · Plasmid Editor      — map / annotate / clone a construct (Build)
                       · CRISPR              — knockout & base-edit guide design  (Edit)
                       · Primer Analysis     — score & rank candidate primers     (Verify)
@@ -273,6 +274,26 @@
                         <span class="nav-step-nm">Directed Evolution</span>
                         <span class="nav-step-ph">Design</span>
                     </a>
+                    <!--
+                        DNA Design sits BESIDE Directed Evolution, not as a
+                        fifth phase: DE designs at the PROTEIN level (ESM-2),
+                        this designs at the DNA level (Evo 2). Both are the
+                        loop's "Design" step, which is why they share a phase
+                        label — inventing a fifth phase here would break the
+                        Design/Build/Edit/Verify story the landing page and the
+                        Start Here router are both built on.
+                    -->
+                    <a class="nav-item nav-step" href="#dna" data-analytics="nav-dna" title="DNA Design">
+                        <span class="nav-icon" aria-hidden="true">
+                            <svg viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="1.7" stroke-linecap="round" stroke-linejoin="round">
+                                <path d="M5 3c0 5 14 6 14 9s-14 4-14 9"/>
+                                <path d="M19 3c0 5-14 6-14 9s14 4 14 9"/>
+                                <path d="M8 6h8M7 9.6h10M7 14.4h10M8 18h8"/>
+                            </svg>
+                        </span>
+                        <span class="nav-step-nm">DNA Design</span>
+                        <span class="nav-step-ph">Design</span>
+                    </a>
                     <a class="nav-item nav-step" href="#plasmid" data-analytics="nav-plasmid" title="Plasmid Editor">
                         <span class="nav-icon" aria-hidden="true">
                             <svg viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="1.7" stroke-linecap="round" stroke-linejoin="round">
@@ -507,6 +528,7 @@
               <nav class="bench-tabs" id="benchTabs" aria-label="Construct artifacts">
                 <button class="bench-tab" data-route="structure" data-analytics="bench-tab-structure" type="button">Structure</button>
                 <button class="bench-tab" data-route="design"  data-analytics="bench-tab-design" type="button">Library</button>
+                <button class="bench-tab" data-route="dna"     data-analytics="bench-tab-dna" type="button">DNA</button>
                 <button class="bench-tab" data-route="plasmid" data-analytics="bench-tab-plasmid" type="button">Map</button>
                 <button class="bench-tab" data-route="crispr"  data-analytics="bench-tab-crispr" type="button">Guides</button>
                 <button class="bench-tab" data-route="primers" data-analytics="bench-tab-primers" type="button">Primers</button>
@@ -1104,6 +1126,119 @@
                    by the per-user /dashboard/ page on the landing site
                    (task #98). See sidebar comment above for context. -->
 
+              <!-- ═════════════════════════════ DNA Design (Evo 2) ════════════
+                   The DNA-level counterpart to Directed Evolution. DE scores
+                   amino-acid substitutions with ESM-2; this scores NUCLEOTIDE
+                   substitutions with Evo 2 (7B), which is the only thing in
+                   this product that understands non-coding and regulatory
+                   sequence at all — promoters.py is a curated lookup table and
+                   exon.py is coordinate arithmetic, neither is a model.
+
+                   Every call here is a metered GPU call: unlike protein's
+                   Achilles tier (35M on the Space's own CPU) there is no free
+                   local path for a 7B model. Hence the account gate, the
+                   tighter rate-limit bucket, and the honest wait copy — a cold
+                   container is ~80s, warm ~23s, and a dead spinner over that
+                   long reads as a hang.
+                   ════════════════════════════════════════════════════════ -->
+              <section class="view view--dna" data-view="dna" hidden>
+                  <header class="view-head">
+                      <h1 class="view-title"><em>DNA Design</em></h1>
+                      <p class="view-sub">Score changes to DNA itself — promoters, splice sites, UTRs,
+                          any non-coding stretch — against a genome foundation model. Directed Evolution
+                          asks whether a protein change is tolerated; this asks whether a
+                          <em>sequence</em> change is, in the context it actually sits in.</p>
+                  </header>
+
+                  <section class="card dna-input-card">
+                      <div class="dna-mode-row" role="tablist" aria-label="What to do">
+                          <button class="dna-mode is-active" type="button" id="dnaModeScore"
+                                  role="tab" aria-selected="true">Score variants</button>
+                          <button class="dna-mode" type="button" id="dnaModeGenerate"
+                                  role="tab" aria-selected="false">Generate sequence</button>
+                      </div>
+
+                      <!-- ── Score ── -->
+                      <div id="dnaScorePane">
+                          <label class="field-label" for="dnaReference">Reference sequence</label>
+                          <p class="field-hint">The stretch of DNA your change sits in — a promoter, a
+                              splice junction, a UTR. Context is the point: the same substitution scores
+                              differently depending on what surrounds it, which is exactly what a lookup
+                              table cannot tell you.</p>
+                          <textarea id="dnaReference" class="dna-textarea mono" rows="5" spellcheck="false"
+                              placeholder="Paste DNA (A/C/G/T)…"></textarea>
+                          <p class="dna-meta" id="dnaRefMeta" hidden></p>
+
+                          <label class="field-label" for="dnaVariants">Variants to score</label>
+                          <p class="field-hint">One per line, as <code>&lt;WT base&gt;&lt;position&gt;&lt;new base&gt;</code>
+                              — e.g. <code>T10G</code>. Positions are 1-based against the reference above.
+                              A variant whose WT base doesn't match the reference is <strong>refused, not
+                              scored</strong>, and listed separately so a typo can't quietly shrink your table.</p>
+                          <textarea id="dnaVariants" class="dna-textarea mono" rows="4" spellcheck="false"
+                              placeholder="T10G&#10;G20C&#10;T30A"></textarea>
+                      </div>
+
+                      <!-- ── Generate ── -->
+                      <div id="dnaGeneratePane" hidden>
+                          <label class="field-label" for="dnaPrompt">Starting sequence</label>
+                          <p class="field-hint">The model continues from what you paste. Prometheus tier only —
+                              generation is the one real capability difference between the DNA tiers
+                              (the checkpoint is identical).</p>
+                          <textarea id="dnaPrompt" class="dna-textarea mono" rows="5" spellcheck="false"
+                              placeholder="Paste the DNA to continue from (A/C/G/T)…"></textarea>
+                          <div class="dna-gen-knobs">
+                              <label class="dna-knob">Bases to generate
+                                  <input type="number" id="dnaNTokens" value="200" min="1" max="2000" />
+                              </label>
+                              <label class="dna-knob">Temperature
+                                  <input type="number" id="dnaTemperature" value="1.0" min="0.1" max="2" step="0.1" />
+                                  <span class="field-hint">Lower = more conservative.</span>
+                              </label>
+                              <label class="dna-knob">Top-k
+                                  <input type="number" id="dnaTopK" value="4" min="1" max="4" />
+                                  <span class="field-hint">There are only 4 bases.</span>
+                              </label>
+                          </div>
+                      </div>
+
+                      <label class="field-label" for="dnaTier">Model tier</label>
+                      <select id="dnaTier" class="dna-select"></select>
+                      <p class="field-hint" id="dnaTierNote"></p>
+
+                      <div class="dna-actions">
+                          <button class="ghost" type="button" id="dnaExample"
+                                  title="Loads the E. coli lac promoter / operator region and three real substitutions">Try an example</button>
+                          <button class="primary primary-lg" type="button" id="dnaRun">Score variants</button>
+                      </div>
+                      <p class="dna-wait" id="dnaWait" hidden></p>
+                      <div class="error-banner" id="dnaError" hidden></div>
+                  </section>
+
+                  <section class="card dna-results-card" id="dnaResultsCard" hidden>
+                      <div class="dna-results-head">
+                          <span class="dna-results-title">Predicted effect</span>
+                          <span class="dna-results-meta" id="dnaResultsMeta"></span>
+                      </div>
+                      <details class="how-to-read">
+                          <summary>How to read this</summary>
+                          <div class="how-to-read-body">
+                              <p><strong>&Delta; log-likelihood</strong> &mdash; how much more, or less, likely the
+                                  model finds your sequence after the change. <strong>Negative</strong> means the
+                                  model is more surprised by the variant than by the reference: the change breaks a
+                                  pattern the model learned from real genomes. <strong>Near zero</strong> means
+                                  it's unremarkable. <strong>Positive</strong> means the variant looks
+                                  <em>more</em> typical than what's there now.</p>
+                              <p>This is <strong>zero-shot</strong> — no training on your system, no measured data.
+                                  It ranks candidates; it does not predict expression level, and it is not a
+                                  substitute for a reporter assay. Treat it as a prior for what to test first.</p>
+                              <p><strong>Reference log-likelihood</strong> is the model's score for your unchanged
+                                  sequence, shown so the deltas have something to sit against.</p>
+                          </div>
+                      </details>
+                      <div id="dnaResultsBody"></div>
+                  </section>
+              </section>
+
               <!-- ═════════════════════════════ CRISPR view (Cas9 knockout) ═══
                    Paste a gene → ranked SpCas9 sgRNAs with on-target
                    scoring. Sign-in gated server-side; anonymous users
@@ -2128,6 +2263,35 @@
                               </ul>
                           </section>
 
+                          <section>
+                              <h3>DNA Design</h3>
+                              <p>The DNA-level counterpart to Directed Evolution. Everything else here works on
+                                  protein (ESM-2) or on deterministic sequence bookkeeping; this is the only tool
+                                  that reads <em>nucleotides</em> with a learned model — <strong>Evo 2</strong>
+                                  (Arc Institute, 7B, Apache&nbsp;2.0), trained autoregressively on genomes.</p>
+                              <ul class="docs-list">
+                                  <li><strong>Scoring.</strong> Δ log-likelihood for each point substitution against
+                                      a reference you supply: how much more, or less, likely the model finds the
+                                      sequence after your change. Negative = the change breaks a pattern the model
+                                      learned from real genomes.</li>
+                                  <li><strong>Context is the point.</strong> The same substitution scores differently
+                                      depending on what surrounds it. That is what a curated parts table cannot do,
+                                      and it is why this works on non-coding sequence — promoters, splice sites,
+                                      UTRs, terminators — that the rest of the toolkit only annotates.</li>
+                                  <li><strong>Generation.</strong> Continues a sequence you paste. Prometheus tier
+                                      only; the checkpoint is identical on both tiers, generation access is the
+                                      difference.</li>
+                                  <li><strong>Refusals are shown.</strong> A variant whose wild-type base disagrees
+                                      with your reference is listed as not scored, with the reason — never folded
+                                      into a quietly shorter table.</li>
+                              </ul>
+                              <p class="docs-callout">Zero-shot: no training on your system and no measured data. It
+                                  ranks candidates and gives you a prior for what to test first — it does
+                                  <strong>not</strong> predict expression level and does not replace a reporter
+                                  assay. Every call runs on a rented GPU; unlike protein's Achilles tier there is no
+                                  free local path for a 7B model, so DNA scoring needs an account.</p>
+                          </section>
+
                           <section>
                               <h3>Directed Evolution</h3>
                               <p>Design a smart mutation library for an existing protein using ESM-2 zero-shot scoring. Provide a wild-type sequence (or send a CDS from the Plasmid Editor); receive a library of multi-mutant variants ranked by predicted evolutionary fitness, codon-optimized for your host, ready to order.</p>
@@ -2561,7 +2725,7 @@
     <!-- Cloning reference data must load before app.js so the Designer
          can read VECTORS / ENZYMES / CLONING_METHODS / TAGS / LINKERS. -->
     <script src="/static/cloning_db.js?v=20260530-ui-polish" defer></script>
-    <script src="/static/app.js?v=20260811-buildC" defer></script>
+    <script src="/static/app.js?v=20260812-dna" defer></script>
     <!-- The decision trace, BEFORE cockpit.js: applyEvent calls TDTrace.push
          on the very first event, and both are `defer`, so document order is
          load order. Loading it after would drop the opening events of a

tests/test_dna_endpoints.py

@@ -0,0 +1,176 @@
+"""/api/dna/score and /api/dna/generate — the DNA view's only way in.
+
+Before these existed, the ONLY route to Evo 2 was the agent choosing to call
+score_or_generate_dna mid-conversation: /api/models computed `dna_models` and
+no frontend read it, so a 7B genome model was unreachable by clicking.
+
+What these pin is the same contract the rest of the tool endpoints keep:
+never run anonymously, never pretend a tier can do something it cannot, and
+never dress an unavailable backend as a scientific result.
+"""
+import pytest
+
+from dee import server
+from dee.core import dna_scoring
+
+
+@pytest.fixture
+def client():
+    app = server.create_app()
+    app.config.update(TESTING=True)
+    return app.test_client()
+
+
+@pytest.fixture
+def signed_in(monkeypatch):
+    """Every DNA call is a metered GPU call, so both routes are account-gated
+    the same way CRISPR and primers are."""
+    class _Auth:
+        anonymous = False
+        user_id = "11111111-1111-1111-1111-111111111111"
+    monkeypatch.setattr(server._auth, "get_auth", lambda *a, **k: _Auth())
+
+
+REF = "TTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCA"
+
+
+# ── the account gate ─────────────────────────────────────────────────────
+def test_scoring_refuses_anonymous_callers(client, monkeypatch):
+    class _Anon:
+        anonymous = True
+        user_id = None
+    monkeypatch.setattr(server._auth, "get_auth", lambda *a, **k: _Anon())
+    r = client.post("/api/dna/score", json={"reference": REF, "variants": ["T10G"]})
+    assert r.status_code == 403
+    assert r.get_json()["kind"] == "signin_required"
+
+
+def test_generation_refuses_anonymous_callers(client, monkeypatch):
+    class _Anon:
+        anonymous = True
+        user_id = None
+    monkeypatch.setattr(server._auth, "get_auth", lambda *a, **k: _Anon())
+    r = client.post("/api/dna/generate", json={"prompt": REF})
+    assert r.status_code == 403
+
+
+# ── input validation, before anything is billed ──────────────────────────
+def test_a_missing_reference_is_a_400_not_a_gpu_call(client, signed_in, monkeypatch):
+    def boom(*a, **k):
+        raise AssertionError("called the GPU for an empty request")
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", boom)
+    assert client.post("/api/dna/score", json={"variants": ["T10G"]}).status_code == 400
+
+
+def test_empty_variants_is_a_400_not_a_gpu_call(client, signed_in, monkeypatch):
+    def boom(*a, **k):
+        raise AssertionError("called the GPU for an empty request")
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", boom)
+    r = client.post("/api/dna/score", json={"reference": REF, "variants": []})
+    assert r.status_code == 400
+
+
+def test_whitespace_and_case_are_normalised(client, signed_in, monkeypatch):
+    """Users paste FASTA-ish text with newlines; the model wants bases."""
+    seen = {}
+
+    def fake(reference, variants, tier="achilles"):
+        seen["reference"] = reference
+        seen["variants"] = variants
+        return {"ok": True, "scores": [], "skipped": [], "reference_ll": -1.0}
+
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", fake)
+    client.post("/api/dna/score", json={
+        "reference": "ttta cact\ntta", "variants": [" t10g "]})
+    assert seen["reference"] == "TTTACACTTTA"
+    assert seen["variants"] == ["T10G"]
+
+
+# ── the honesty contract ─────────────────────────────────────────────────
+def test_an_unavailable_backend_is_a_503_not_an_empty_result(client, signed_in,
+                                                             monkeypatch):
+    """The failure this whole module exists to prevent: reporting "no variants
+    scored" when the truth is "nothing was asked"."""
+    def unavailable(*a, **k):
+        raise dna_scoring.DnaModelUnavailable("DNA scoring isn't switched on.")
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", unavailable)
+    r = client.post("/api/dna/score", json={"reference": REF, "variants": ["T10G"]})
+    assert r.status_code == 503
+    assert r.get_json()["kind"] == "dna_unavailable"
+
+
+def test_generation_on_the_achilles_tier_is_refused(client, signed_in):
+    """Prometheus-only, enforced here AND in dna_scoring AND again in
+    modal/evo2_scoring — a caller that skips a layer still gets refused."""
+    r = client.post("/api/dna/generate", json={"prompt": REF, "tier": "achilles"})
+    assert r.status_code == 503
+    assert "Prometheus" in r.get_json()["error"]
+
+
+def test_a_backend_crash_never_reports_a_scientific_result(client, signed_in,
+                                                           monkeypatch):
+    def boom(*a, **k):
+        raise RuntimeError("connection reset")
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", boom)
+    r = client.post("/api/dna/score", json={"reference": REF, "variants": ["T10G"]})
+    assert r.status_code == 502
+    body = r.get_json()
+    assert body["kind"] == "dna_error"
+    assert "connection reset" not in body["error"], "no raw exception text to users"
+
+
+def test_a_successful_score_is_passed_through_whole(client, signed_in, monkeypatch):
+    """Including `skipped`. A variant whose WT base disagrees with the
+    reference is REFUSED, not scored — dropping that list would turn a
+    refusal into a silently shorter table."""
+    payload = {"ok": True, "reference_ll": -147.9081,
+               "scores": [{"label": "T10G", "delta_ll": -5.5079}],
+               "skipped": [{"label": "A10G", "why": "reference base is T"}],
+               "tier": "achilles", "checkpoint": "evo2_7b"}
+    monkeypatch.setattr(dna_scoring, "score_dna_variants", lambda *a, **k: payload)
+    r = client.post("/api/dna/score",
+                    json={"reference": REF, "variants": ["T10G", "A10G"]})
+    assert r.status_code == 200
+    got = r.get_json()
+    assert got["scores"][0]["delta_ll"] == -5.5079
+    assert got["skipped"], "the refusal list must survive to the UI"
+    assert got["reference_ll"] == -147.9081
+
+
+def test_generation_forwards_its_sampling_knobs(client, signed_in, monkeypatch):
+    seen = {}
+
+    def fake(prompt, n_tokens=200, tier="prometheus", temperature=1.0, top_k=4):
+        seen.update(prompt=prompt, n_tokens=n_tokens, tier=tier,
+                    temperature=temperature, top_k=top_k)
+        return {"ok": True, "sequence": "ACGT"}
+
+    monkeypatch.setattr(dna_scoring, "generate_dna_sequence", fake)
+    client.post("/api/dna/generate", json={
+        "prompt": REF, "n_tokens": 64, "temperature": 0.8, "top_k": 3})
+    assert seen["n_tokens"] == 64 and seen["top_k"] == 3
+    assert seen["temperature"] == 0.8
+    assert seen["tier"] == "prometheus"
+
+
+def test_non_numeric_sampling_knobs_are_a_400(client, signed_in, monkeypatch):
+    def boom(*a, **k):
+        raise AssertionError("called the GPU with junk parameters")
+    monkeypatch.setattr(dna_scoring, "generate_dna_sequence", boom)
+    r = client.post("/api/dna/generate", json={"prompt": REF, "n_tokens": "lots"})
+    assert r.status_code == 400
+
+
+# ── the cost guard ───────────────────────────────────────────────────────
+def test_dna_routes_carry_their_own_tighter_rate_limits():
+    """Evo 2 7B on a rented GPU is the most expensive call in the product and
+    has no free local path. Its bucket must be tighter than the tool default,
+    and generation tighter still."""
+    rules = dict(server._RL_RULES)
+    assert rules["/api/dna/generate"][0] < rules["/api/dna"][0]
+    assert rules["/api/dna"][0] < rules["/api/crispr"][0]
+
+
+def test_dna_calls_are_logged_as_their_own_event_kinds():
+    assert server._EVENT_KINDS["/api/dna/score"] == "dna_score"
+    assert server._EVENT_KINDS["/api/dna/generate"] == "dna_generate"