Add restart dialog with state cleanup and pre-filled settings

- Replace simple "Start" button with restart modal that pre-fills all
  project settings (idea, venue, model, telegram, iterations)
- User can modify any setting before restarting
- Deep research checkbox: keep existing report or redo from scratch
- Backend cleans state (auto_research/state/, results/, experiments/,
  paper generated files) while preserving venue templates and uploaded PDF
- Rewrite config.yaml with updated settings before resubmitting job
- Add venue_format, venue_pages, telegram_token, telegram_chat_id,
  has_deep_research to project detail API response
- Fix subprocess.run UTF-8 decode in compile_latex (handle both bytes
  and str for mock compatibility)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: JihaoXin

ark/compiler.py

@@ -201,8 +201,8 @@ def compile_latex(self) -> bool:
                     timeout=120,
                     cwd=self.latex_dir,
                 )
-                stderr = result.stderr.decode("utf-8", errors="replace")
-                stdout = result.stdout.decode("utf-8", errors="replace")
+                stderr = result.stderr.decode("utf-8", errors="replace") if isinstance(result.stderr, bytes) else (result.stderr or "")
+                stdout = result.stdout.decode("utf-8", errors="replace") if isinstance(result.stdout, bytes) else (result.stdout or "")
                 if result.returncode != 0 and "main.tex" in cmd:
                     self._last_compile_stderr = stderr[:1000] or stdout[-1000:]
                     self.log(f"LaTeX compilation warning: {stderr[:500]}")

ark/webapp/routes.py

@@ -175,6 +175,57 @@ def _write_config_yaml(project_dir: Path, project: Project, model: str = "claude
     config_path.write_text(yaml.dump(config, default_flow_style=False, allow_unicode=True))
 
 
+def _clean_project_state(project_dir: Path, keep_deep_research: bool = True):
+    """Remove all generated state/results for a fresh restart.
+
+    Preserves: config.yaml, uploaded.pdf, venue template files (.cls/.sty/.bst),
+    agent prompts, and optionally deep_research.md/pdf.
+    """
+    # Clean auto_research/state/
+    state_dir = project_dir / "auto_research" / "state"
+    if state_dir.exists():
+        for f in state_dir.iterdir():
+            if keep_deep_research and f.name.startswith("deep_research"):
+                continue
+            if f.is_file():
+                f.unlink()
+
+    # Clean auto_research/logs/
+    logs_dir = project_dir / "auto_research" / "logs"
+    if logs_dir.exists():
+        shutil.rmtree(logs_dir, ignore_errors=True)
+        logs_dir.mkdir(exist_ok=True)
+
+    # Clean results/ and experiments/
+    for dirname in ("results", "experiments"):
+        d = project_dir / dirname
+        if d.exists():
+            shutil.rmtree(d, ignore_errors=True)
+            d.mkdir(exist_ok=True)
+
+    # Clean paper/ — keep venue template files, remove generated content
+    paper_dir = project_dir / "paper"
+    if paper_dir.exists():
+        keep_exts = {".cls", ".sty", ".bst"}
+        for f in paper_dir.iterdir():
+            if f.is_dir():
+                if f.name == "figures":
+                    shutil.rmtree(f, ignore_errors=True)
+                    f.mkdir(exist_ok=True)
+            elif f.suffix not in keep_exts:
+                f.unlink()
+
+    # Clean scripts/ (generated figure scripts)
+    scripts_dir = project_dir / "scripts"
+    if scripts_dir.exists():
+        shutil.rmtree(scripts_dir, ignore_errors=True)
+
+    # Remove .git (will be re-initialized)
+    git_dir = project_dir / ".git"
+    if git_dir.exists():
+        shutil.rmtree(git_dir, ignore_errors=True)
+
+
 def _write_user_instructions(project_dir: Path, message: str, source: str = "webapp_create"):
     """Write a persistent instruction to user_instructions.yaml."""
     state_dir = project_dir / "auto_research" / "state"
@@ -703,6 +754,8 @@ async def api_get_project(project_id: str, request: Request):
             "title": project.title,
             "idea": project.idea,
             "venue": project.venue,
+            "venue_format": project.venue_format,
+            "venue_pages": project.venue_pages,
             "mode": project.mode,
             "status": project.status,
             "score": score,
@@ -715,6 +768,9 @@ async def api_get_project(project_id: str, request: Request):
             "queue_position": _queue_position(project_id, session),
             "user_email": owner.email if owner else "",
             "model": _read_project_model(pdir),
+            "telegram_token": project.telegram_token,
+            "telegram_chat_id": project.telegram_chat_id,
+            "has_deep_research": (pdir / "auto_research" / "state" / "deep_research.md").exists(),
             "environment": "ROCS Testbed" if project.slurm_job_id and project.slurm_job_id != "local" else "Local",
             "created_at": project.created_at.isoformat(),
             "updated_at": project.updated_at.isoformat(),
@@ -745,6 +801,13 @@ async def api_restart_project(project_id: str, request: Request):
     user = _require_user(request)
     _check_webapp_enabled()
     settings = get_settings()
+
+    # Parse JSON body (new restart dialog sends settings)
+    try:
+        body = await request.json()
+    except Exception:
+        body = {}
+
     with get_session(settings.db_path) as session:
         project = get_project(session, project_id)
         if not project or not _can_access_project(user, project):
@@ -756,6 +819,41 @@ async def api_restart_project(project_id: str, request: Request):
         if active:
             raise HTTPException(400, "You already have an active project.")
         pdir = _project_dir(settings, project.user_id, project_id)
+
+        # Update project fields from request body
+        if body.get("idea"):
+            project.idea = body["idea"]
+        if body.get("venue"):
+            project.venue = body["venue"]
+        if body.get("venue_format"):
+            project.venue_format = body["venue_format"]
+        if "venue_pages" in body:
+            project.venue_pages = int(body["venue_pages"])
+        if "max_iterations" in body:
+            project.max_iterations = max(1, min(3, int(body["max_iterations"])))
+        if "telegram_token" in body:
+            project.telegram_token = body["telegram_token"]
+        if "telegram_chat_id" in body:
+            project.telegram_chat_id = body["telegram_chat_id"]
+        project.score = 0.0
+
+        # Clean up project state for fresh restart
+        redo_deep_research = body.get("redo_deep_research", False)
+        _clean_project_state(pdir, keep_deep_research=not redo_deep_research)
+
+        # Rewrite config.yaml with updated settings
+        model = body.get("model", "claude-sonnet-4-6")
+        _write_config_yaml(pdir, project, model=model)
+
+        # Write instructions if provided
+        comment = body.get("comment", "").strip()
+        if comment:
+            _write_user_instructions(pdir, comment, source="webapp_restart")
+
+        session.add(project)
+        session.commit()
+        session.refresh(project)
+
         final_status = _try_submit_or_pending(project, pdir, session, settings)
         send_telegram_notify(
             f"🔄 <b>{project.name}</b> restarted ({final_status})",

ark/webapp/static/app.html

@@ -907,6 +907,72 @@ <h3 data-i18n="continue_project">Continue Project</h3>
   </div>
 </div>
 
+<!-- RESTART MODAL -->
+<div class="modal-backdrop" id="modal-restart">
+  <div class="modal" style="max-width:620px">
+    <h3>Restart Project</h3>
+    <div class="form-group">
+      <label>Research Idea</label>
+      <textarea id="restart-idea" rows="4" style="width:100%"></textarea>
+    </div>
+    <div class="form-group">
+      <label>Instructions <span style="font-weight:400;color:var(--text-muted)">(optional)</span></label>
+      <textarea id="restart-comment" rows="3" style="width:100%"
+        placeholder="e.g. Focus on a different baseline, change experiment setup..."></textarea>
+    </div>
+    <div class="form-row">
+      <div class="form-group" style="flex:2">
+        <label>Venue</label>
+        <select id="restart-venue" onchange="restartVenueChanged(this)"></select>
+      </div>
+      <div class="form-group" style="flex:1">
+        <label>Max iterations</label>
+        <input type="number" id="restart-max-iter" value="3" min="1" max="3" style="width:80px" />
+      </div>
+    </div>
+    <input type="hidden" id="restart-venue-format" />
+    <input type="hidden" id="restart-venue-pages" />
+    <div class="form-group">
+      <label>Model</label>
+      <div style="display:flex;gap:8px;flex-wrap:wrap" id="restart-model-options">
+        <label class="model-option"><input type="radio" name="restart-model" value="claude-sonnet-4-6" checked /><span class="model-chip">Sonnet 4.6</span></label>
+        <label class="model-option restart-model-admin" style="display:none"><input type="radio" name="restart-model" value="claude-opus-4-6" /><span class="model-chip">Opus 4.6</span></label>
+        <label class="model-option restart-model-admin" style="display:none"><input type="radio" name="restart-model" value="claude-haiku-4-5" /><span class="model-chip">Haiku 4.5</span></label>
+        <label class="model-option restart-model-admin" style="display:none"><input type="radio" name="restart-model" value="gemini" /><span class="model-chip">Gemini</span></label>
+      </div>
+    </div>
+    <div class="tg-section" style="margin-top:12px">
+      <div class="tg-section-title">
+        <svg width="18" height="18" viewBox="0 0 24 24" fill="none" style="flex-shrink:0">
+          <circle cx="12" cy="12" r="12" fill="#29B6F6"/>
+          <path d="M5.5 11.5l10-4.5-1.5 9-3-2.5-2 2v-3l5-4.5-6.5 3.5-2-1z" fill="white"/>
+        </svg>
+        <span>Telegram Notifications</span>
+      </div>
+      <div class="form-row" style="margin-top:8px">
+        <div class="form-group" style="margin-bottom:0">
+          <label>Bot Token</label>
+          <input type="text" id="restart-tg-token" placeholder="123456789:ABCdef..." autocomplete="off" />
+        </div>
+        <div class="form-group" style="margin-bottom:0">
+          <label>Chat ID</label>
+          <input type="text" id="restart-tg-chatid" placeholder="1234567890" />
+        </div>
+      </div>
+    </div>
+    <div id="restart-deep-research-section" style="margin-top:16px;display:none">
+      <label style="display:flex;align-items:center;gap:8px;cursor:pointer">
+        <input type="checkbox" id="restart-keep-dr" checked />
+        <span>Keep existing Deep Research report <span style="color:var(--text-muted);font-weight:400">(uncheck to redo)</span></span>
+      </label>
+    </div>
+    <div class="modal-footer">
+      <button type="button" class="btn-secondary" onclick="closeModal('modal-restart')">Cancel</button>
+      <button class="btn-primary" id="restart-btn" onclick="submitRestart()">Restart</button>
+    </div>
+  </div>
+</div>
+
 <!-- ADMIN EDIT MODAL -->
 <div class="modal-backdrop" id="modal-admin-edit">
   <div class="modal" style="max-width:620px">
@@ -1903,7 +1969,7 @@ <h3 data-i18n="edit_project">Edit Project</h3>
     html += `<button class="btn-secondary" onclick="stopProject('${p.id}')">${t('stop')}</button>`;
   }
   if (p.status === 'stopped' || p.status === 'failed') {
-    html += `<button class="btn-primary" onclick="startProject('${p.id}')">${t('start')}</button>`;
+    html += `<button class="btn-primary" onclick="openRestartModal('${p.id}')">Restart</button>`;
   }
   if (p.status === 'done') {
     html += `<button class="btn-primary" onclick="openContinueModal('${p.id}')">${t('continue_action')}</button>`;
@@ -2259,6 +2325,107 @@ <h3 data-i18n="edit_project">Edit Project</h3>
   }
 }
 
+// ══════════════════════════════════════════════════════
+//  Restart Modal
+// ══════════════════════════════════════════════════════
+let restartProjectId = null;
+
+async function openRestartModal(id) {
+  restartProjectId = id;
+  // Fetch project detail to pre-fill fields
+  const res = await fetch(`/api/projects/${id}`);
+  if (!res.ok) { alert('Failed to load project details'); return; }
+  const p = await res.json();
+
+  document.getElementById('restart-idea').value = p.idea || '';
+  document.getElementById('restart-comment').value = '';
+  document.getElementById('restart-max-iter').value = p.max_iterations || 3;
+  document.getElementById('restart-tg-token').value = p.telegram_token || '';
+  document.getElementById('restart-tg-chatid').value = p.telegram_chat_id || '';
+
+  // Populate venue select (reuse venues from hero form)
+  const venueSelect = document.getElementById('restart-venue');
+  const heroSelect = document.getElementById('hero-venue-select');
+  venueSelect.innerHTML = heroSelect.innerHTML;
+  // Set current venue
+  if (p.venue) {
+    for (const opt of venueSelect.options) {
+      if (opt.value === p.venue || opt.textContent === p.venue) {
+        opt.selected = true;
+        break;
+      }
+    }
+  }
+  // Set hidden venue_format and venue_pages from current project
+  document.getElementById('restart-venue-format').value = p.venue_format || 'neurips';
+  document.getElementById('restart-venue-pages').value = p.venue_pages || 9;
+
+  // Set model radio
+  const modelMap = { 'claude-sonnet-4-6': 'claude-sonnet-4-6', 'claude-opus-4-6': 'claude-opus-4-6',
+                     'claude-haiku-4-5': 'claude-haiku-4-5', 'gemini': 'gemini', 'sonnet': 'claude-sonnet-4-6',
+                     'opus': 'claude-opus-4-6', 'haiku': 'claude-haiku-4-5' };
+  const modelVal = modelMap[p.model] || 'claude-sonnet-4-6';
+  document.querySelectorAll('input[name="restart-model"]').forEach(r => {
+    r.checked = (r.value === modelVal);
+  });
+  // Show admin model options if user is admin
+  if (currentUser && currentUser.is_admin) {
+    document.querySelectorAll('.restart-model-admin').forEach(el => el.style.display = '');
+  }
+
+  // Deep research checkbox
+  const drSection = document.getElementById('restart-deep-research-section');
+  if (p.has_deep_research) {
+    drSection.style.display = '';
+    document.getElementById('restart-keep-dr').checked = true;
+  } else {
+    drSection.style.display = 'none';
+  }
+
+  document.getElementById('modal-restart').classList.add('open');
+}
+
+function restartVenueChanged(sel) {
+  const opt = sel.options[sel.selectedIndex];
+  if (opt && opt.dataset.format) {
+    document.getElementById('restart-venue-format').value = opt.dataset.format;
+    document.getElementById('restart-venue-pages').value = opt.dataset.pages || 9;
+  }
+}
+
+async function submitRestart() {
+  const btn = document.getElementById('restart-btn');
+  btn.disabled = true;
+  try {
+    const body = {
+      idea: document.getElementById('restart-idea').value.trim(),
+      venue: document.getElementById('restart-venue').value,
+      venue_format: document.getElementById('restart-venue-format').value,
+      venue_pages: parseInt(document.getElementById('restart-venue-pages').value) || 9,
+      max_iterations: Math.max(1, Math.min(3, parseInt(document.getElementById('restart-max-iter').value) || 3)),
+      model: ([...document.querySelectorAll('input[name="restart-model"]')].find(r => r.checked) || {}).value || 'claude-sonnet-4-6',
+      telegram_token: document.getElementById('restart-tg-token').value.trim(),
+      telegram_chat_id: document.getElementById('restart-tg-chatid').value.trim(),
+      comment: document.getElementById('restart-comment').value.trim(),
+      redo_deep_research: !document.getElementById('restart-keep-dr').checked,
+    };
+    const res = await fetch(`/api/projects/${restartProjectId}/restart`, {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify(body),
+    });
+    if (!res.ok) {
+      const e = await res.json().catch(() => ({}));
+      alert(e.detail || 'Failed to restart project.');
+      return;
+    }
+    closeModal('modal-restart');
+    loadDetail(restartProjectId);
+  } finally {
+    btn.disabled = false;
+  }
+}
+
 // ══════════════════════════════════════════════════════
 //  Utils
 // ══════════════════════════════════════════════════════