Fix GPU detection and bokeh plasmid map rendering

- Remove --extra-index-url for CPU torch — was forcing CPU-only install on
T4 GPU machine, causing device=cpu
- Fix bokeh map: wrap file_html output in iframe with srcdoc so the full
HTML document renders inside Gradio's gr.HTML component

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app.py

@@ -654,7 +654,15 @@ def _annotate(dna: str) -> tuple[str | None, pd.DataFrame | None, str]:
     html_map = None
     try:
         fig = _plannotate_bokeh(hits, linear=False)
-        html_map = file_html(fig, BOKEH_CDN, "Plasmid Map")
+        raw_html = file_html(fig, BOKEH_CDN, "Plasmid Map")
+        # Wrap in iframe so the full HTML doc renders inside Gradio
+        import html as _html_mod
+        escaped = _html_mod.escape(raw_html)
+        html_map = (
+            f'<iframe srcdoc="{escaped}" '
+            f'style="width:100%;height:600px;border:none;" '
+            f'sandbox="allow-scripts allow-same-origin"></iframe>'
+        )
     except Exception as exc:
         print(f"[annotate] bokeh error: {exc}")
 

requirements.txt

@@ -1,4 +1,3 @@
---extra-index-url https://download.pytorch.org/whl/cpu
 torch
 transformers>=4.38,<5
 accelerate>=0.26