fix: write saves and plots into one murano_outputs/ tree; add Save ru…

docs/src/content/docs/docs/guides/pipeline.md

@@ -114,6 +114,8 @@ results = pipeline.run()
 results.save(output_dir="my_experiment", model_id=model.model_id)
 ```
 
+Both default `output_dir` to `murano_outputs/` in the current directory, and the `Plot` step writes there too, so a run's artifacts and plots share one tree. Results go directly into `output_dir`, so re-running overwrites the previous run; pass `run_name="..."` to keep runs side by side under `murano_outputs/<run_name>/`.
+
 The output structure:
 
 ```

src/murano/io.py

@@ -1083,7 +1083,7 @@ def _find_serializer(
 
 def save_results(
     results: Any,
-    output_dir: str = "murano_outputs",
+    output_dir: str = keys.DEFAULT_OUTPUT_DIR,
     model_id: str = "",
     run_name: str | None = None,
 ) -> Path:

src/murano/keys.py

@@ -27,6 +27,11 @@
 WEIGHT_ABLATION: Final = "weight_ablation"
 OUTPUT_DIR: Final = "output_dir"
 
+# Default base directory (relative to the current working directory) for saved
+# artifacts, shared by the Save step, Results.save, and the Plot step so they
+# all write into one predictable tree.
+DEFAULT_OUTPUT_DIR: Final = "murano_outputs"
+
 # Default keys for the configurable metric steps (callers may override these).
 FINAL_LOGITS: Final = "final_logits"
 TARGET_IDS: Final = "target_ids"

src/murano/results.py

@@ -4,6 +4,8 @@
 
 from typing import Any
 
+from murano.keys import DEFAULT_OUTPUT_DIR
+
 
 class Results:
     """Dict-like container for pipeline step outputs.
@@ -60,7 +62,7 @@ def copy(self) -> Results:
 
     def save(
         self,
-        output_dir: str = "murano_outputs",
+        output_dir: str = DEFAULT_OUTPUT_DIR,
         run_name: str | None = None,
         model_id: str = "",
     ):

src/murano/steps/plot.py

@@ -53,7 +53,8 @@ class Plot(Step):
     ``plot_sae_token_activations``, ...) directly instead.
 
     Args:
-        output_dir: Root output directory. If None, uses results['output_dir'].
+        output_dir: Root output directory. If None, uses results['output_dir']
+            when a preceding Save set it, otherwise ``murano_outputs``.
         show: Display each figure inline when run in a notebook. Defaults to True.
         save_format: File format for saved figures. ``"png"`` (default) writes a
             static image via kaleido and falls back to a self-contained
@@ -94,7 +95,7 @@ def __call__(self, results: Results) -> Results:
         root = (
             Path(self.output_dir)
             if self.output_dir
-            else Path(results.get(keys.OUTPUT_DIR, "."))
+            else Path(results.get(keys.OUTPUT_DIR, keys.DEFAULT_OUTPUT_DIR))
         )
         plots_dir = root / "plots"
         plots_dir.mkdir(parents=True, exist_ok=True)

src/murano/steps/save.py

@@ -26,23 +26,34 @@ class Save(Step):
         results['output_dir']: Path to the output directory.
 
     Args:
-        output_dir: Base directory for outputs.
+        output_dir: Base directory for outputs. Defaults to ``murano_outputs``
+            in the current working directory.
         model_id: Model identifier for metadata.
+        run_name: Optional subdirectory inside ``output_dir`` for this run. By
+            default results are written directly into ``output_dir`` and a
+            re-run overwrites them; set ``run_name`` to keep runs separate.
     """
 
     reads = []
     writes = [keys.OUTPUT_DIR]
     write_types = {keys.OUTPUT_DIR: Path}
 
-    def __init__(self, output_dir: str = "murano_outputs", model_id: str = ""):
+    def __init__(
+        self,
+        output_dir: str = keys.DEFAULT_OUTPUT_DIR,
+        model_id: str = "",
+        run_name: str | None = None,
+    ):
         self.output_dir = output_dir
         self.model_id = model_id
+        self.run_name = run_name
 
     def __call__(self, results: Results) -> Results:
         out_dir = save_results(
             results,
             output_dir=self.output_dir,
             model_id=self.model_id,
+            run_name=self.run_name,
         )
         results[keys.OUTPUT_DIR] = out_dir
         return results

tests/test_coverage.py

@@ -191,3 +191,28 @@ def test_plot_step_html_format_writes_html(tmp_path):
     )
     Plot(output_dir=str(tmp_path), save_format="html")(results)
     assert (tmp_path / "plots" / "separation_scores.html").exists()
+
+
+def test_plot_step_defaults_to_shared_output_root(tmp_path, monkeypatch):
+    pytest.importorskip("plotly")
+    from murano import keys
+    from murano.results import Results
+    from murano.steps.plot import Plot
+    from murano.steps.train import SteeringResult
+
+    monkeypatch.chdir(tmp_path)
+    results = Results()
+    results[keys.STEERING] = SteeringResult(
+        direction_per_layer={
+            (0, "residual"): torch.ones(4),
+            (1, "residual"): torch.ones(4),
+        },
+        separation_scores={(0, "residual"): 1.0, (1, "residual"): 0.5},
+        best_layer=(0, "residual"),
+    )
+    # No output_dir and no results['output_dir']: writes under the shared
+    # murano_outputs/ root, not a bare ./plots/ in the CWD.
+    Plot(save_format="html")(results)
+    plots = tmp_path / keys.DEFAULT_OUTPUT_DIR / "plots"
+    assert (plots / "separation_scores.html").exists()
+    assert not (tmp_path / "plots").exists()

tests/test_steps.py

@@ -581,6 +581,14 @@ def test_save_serializes_prompt_and_metric_artifacts(self, tmp_path):
         assert (out_dir / "evaluation" / "generations.json").exists()
         assert (out_dir / "metrics" / "metric.json").exists()
 
+    def test_save_step_passes_run_name(self, tmp_path):
+        from murano.steps.save import Save
+
+        r = Results()
+        Save(output_dir=str(tmp_path), run_name="run1")(r)
+        assert (tmp_path / "run1" / "metadata.json").exists()
+        assert r["output_dir"] == tmp_path / "run1"
+
 
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