fix: pipeline

ntv3_tracks_pipeline.py

@@ -331,7 +331,7 @@ class NTv3TracksPipeline(Pipeline):
                     "If passing a model module, pass tokenizer explicitly."
                 )
             self.tokenizer = AutoTokenizer.from_pretrained(
-                self.model_id, trust_remote_code=trust_remote_code, token=token
+                self.model_id, trust_remote_code=trust_remote_code, token=token,
             )
         elif isinstance(tokenizer, str):
             self.tokenizer = AutoTokenizer.from_pretrained(
@@ -488,14 +488,22 @@ class NTv3TracksPipeline(Pipeline):
     def postprocess(
         self, model_outputs: dict[str, Any], **kwargs: Any
     ) -> NTv3TracksOutput:
-        meta = model_outputs.pop("meta", {})
+        # Extract model_output and meta from the dict returned by _forward
+        if isinstance(model_outputs, dict) and "model_output" in model_outputs:
+            model_out = model_outputs["model_output"]
+            meta = model_outputs.get("meta", {})
+        else:
+            # Fallback for direct ModelOutput (shouldn't happen with current code)
+            model_out = model_outputs
+            meta = {}
 
         def to_np(x):
             return x.detach().float().cpu().numpy()
 
-        bigwig_np = to_np(model_outputs["bigwig_tracks_logits"])
-        bed_np = to_np(model_outputs["bed_tracks_logits"])
-        mlm_np = to_np(model_outputs["logits"])
+        # Access model output - ModelOutput objects support both dict and attribute access
+        bigwig_np = to_np(model_out["bigwig_tracks_logits"])
+        bed_np = to_np(model_out["bed_tracks_logits"])
+        mlm_np = to_np(model_out["logits"])
 
         # Normalize shapes to remove batch/(optional assembly) dims
         if bigwig_np.ndim == 3:
@@ -540,8 +548,9 @@ class NTv3TracksPipeline(Pipeline):
                 input_ids=model_inputs["input_ids"],
                 species_ids=model_inputs["species_ids"],
             )
-        out["meta"] = meta
-        return out
+        # Return a dict containing the model output and meta separately
+        # since ModelOutput objects are immutable
+        return {"model_output": out, "meta": meta}
 
     def __call__(
         self,

style.css

@@ -2,8 +2,8 @@
 :root {
   --bg: #0b1020;
   --card: rgba(255, 255, 255, 0.06);
-  --text: rgba(255, 255, 255, 0.92);
-  --muted: rgba(255, 255, 255, 0.65);
+  --text: rgba(255, 255, 255, 0.75);
+  --muted: rgba(255, 255, 255, 0.55);
   --link: #7dd3fc;
   --border: rgba(255, 255, 255, 0.12);
   --shadow: 0 10px 30px rgba(0,0,0,0.35);
@@ -12,7 +12,7 @@
   --input-border: rgba(125, 211, 252, 0.2);
   --input-focus-bg: rgba(125, 211, 252, 0.12);
   --input-focus-border: rgba(125, 211, 252, 0.35);
-  --placeholder: rgba(255, 255, 255, 0.5);
+  --placeholder: rgba(255, 255, 255, 0.4);
   --modebar-bg: rgba(255, 255, 255, 0.9);
 }
 
@@ -21,8 +21,8 @@
   :root {
     --bg: #ffffff;
     --card: rgba(0, 0, 0, 0.04);
-    --text: rgba(0, 0, 0, 0.92);
-    --muted: rgba(0, 0, 0, 0.65);
+    --text: rgba(0, 0, 0, 0.75);
+    --muted: rgba(0, 0, 0, 0.55);
     --link: #0369a1;
     --border: rgba(0, 0, 0, 0.12);
     --shadow: 0 10px 30px rgba(0,0,0,0.1);
@@ -30,7 +30,7 @@
     --input-border: rgba(3, 105, 161, 0.2);
     --input-focus-bg: rgba(3, 105, 161, 0.12);
     --input-focus-border: rgba(3, 105, 161, 0.35);
-    --placeholder: rgba(0, 0, 0, 0.5);
+    --placeholder: rgba(0, 0, 0, 0.4);
     --modebar-bg: rgba(255, 255, 255, 0.95);
   }
 }
@@ -39,6 +39,7 @@
 body, .gradio-container {
   background: var(--bg) !important;
   min-height: 100vh;
+  color: var(--text) !important;
 }
 
 /* Add subtle gradient only in dark mode */
@@ -51,6 +52,61 @@ body, .gradio-container {
   }
 }
 
+/* Ensure all text elements use the correct color - default to white for dark mode */
+body, .gradio-container {
+  color: var(--text) !important;
+}
+
+/* All text elements in gradio container */
+.gradio-container *,
+.gradio-container p,
+.gradio-container span,
+.gradio-container div:not([class*="plotly"]):not([class*="modebar"]),
+.gradio-container label,
+.gradio-container h1,
+.gradio-container h2,
+.gradio-container h3,
+.gradio-container h4,
+.gradio-container h5,
+.gradio-container h6,
+.gradio-container li,
+.gradio-container td,
+.gradio-container th {
+  color: var(--text) !important;
+}
+
+/* Input values and selected text */
+.gradio-container input,
+.gradio-container textarea,
+.gradio-container select,
+.gradio-container input::placeholder,
+.gradio-container textarea::placeholder {
+  color: var(--text) !important;
+}
+
+/* Links */
+.gradio-container a {
+  color: var(--link) !important;
+}
+
+.gradio-container a:hover {
+  color: var(--link) !important;
+  opacity: 0.8;
+}
+
+/* Markdown content */
+.gradio-container .markdown,
+.gradio-container .markdown *,
+.gradio-container [class*="markdown"] * {
+  color: var(--text) !important;
+}
+
+/* Ensure dropdown options are visible */
+.gradio-container select option {
+  color: var(--text) !important;
+  background: var(--input-bg) !important;
+}
+
 /* Plot container */
 #tracks_plot { 
   position: relative;