hit my first cursor usage limit

Author: cudmore

src/kymflow/core/image_loaders/kym_analysis.py

@@ -25,7 +25,8 @@
 from kymflow.core.analysis.utils import _medianFilter, _removeOutliers
 from kymflow.core.utils.logging import get_logger
 
-from kymflow.core.analysis.stall_analysis import StallAnalysis, StallAnalysisParams
+# DEPRECATED: Stall analysis is deprecated
+# from kymflow.core.analysis.stall_analysis import StallAnalysis, StallAnalysisParams
 from kymflow.core.analysis.velocity_events.velocity_events import (
     UserType,
     VelocityEvent,
@@ -145,7 +146,8 @@ def __init__(
         self._analysis_metadata: Dict[int, RoiAnalysisMetadata] = {}
         self._df: Optional[pd.DataFrame] = None
         self._dirty: bool = False
-        self._stall_analysis: Dict[int, StallAnalysis] = {}
+        # DEPRECATED: Stall analysis is deprecated
+        # self._stall_analysis: Dict[int, StallAnalysis] = {}
         # Stall analysis is computed on-demand from stored analysis values (e.g., velocity).
         self._velocity_events: Dict[int, List[VelocityEvent]] = {}
         # Velocity events are computed on-demand from stored analysis values (e.g., velocity).
@@ -449,9 +451,10 @@ def save_analysis(self) -> bool:
                     }
                     for rid, meta in self._analysis_metadata.items()
                 },
-                "stall_analysis": {
-                    str(rid): sa.to_dict() for rid, sa in self._stall_analysis.items()
-                },
+                # DEPRECATED: Stall analysis is deprecated
+                # "stall_analysis": {
+                #     str(rid): sa.to_dict() for rid, sa in self._stall_analysis.items()
+                # },
                 "velocity_events": {
                     str(rid): [ev.to_dict() for ev in evs]
                     for rid, evs in self._velocity_events.items()
@@ -534,15 +537,15 @@ def load_analysis(self) -> bool:
             except Exception as e:
                 logger.warning(f"Skipping invalid analysis metadata entry {key}: {e}")
 
-
-        # Load stall analysis (optional; may be absent in older analysis JSON).
-        self._stall_analysis.clear()
-        for roi_id_str, payload in json_data.get("stall_analysis", {}).items():
-            try:
-                roi_id = int(roi_id_str)
-                self._stall_analysis[roi_id] = StallAnalysis.from_dict(payload)
-            except Exception as e:
-                logger.warning(f"Skipping invalid stall_analysis entry {roi_id_str}: {e}")
+        # DEPRECATED: Stall analysis is deprecated
+        # # Load stall analysis (optional; may be absent in older analysis JSON).
+        # self._stall_analysis.clear()
+        # for roi_id_str, payload in json_data.get("stall_analysis", {}).items():
+        #     try:
+        #         roi_id = int(roi_id_str)
+        #         self._stall_analysis[roi_id] = StallAnalysis.from_dict(payload)
+        #     except Exception as e:
+        #         logger.warning(f"Skipping invalid stall_analysis entry {roi_id_str}: {e}")
 
         # Load velocity events (optional; may be absent in older analysis JSON).
         self._velocity_events.clear()
@@ -568,9 +571,10 @@ def load_analysis(self) -> bool:
         self._analysis_metadata = {
             rid: meta for rid, meta in self._analysis_metadata.items() if rid in current_roi_ids
         }
-        self._stall_analysis = {
-            rid: sa for rid, sa in self._stall_analysis.items() if rid in current_roi_ids
-        }
+        # DEPRECATED: Stall analysis is deprecated
+        # self._stall_analysis = {
+        #     rid: sa for rid, sa in self._stall_analysis.items() if rid in current_roi_ids
+        # }
         # Remove events for deleted ROIs and clean up UUID mappings
         removed_roi_ids = set(self._velocity_events.keys()) - current_roi_ids
         for removed_roi_id in removed_roi_ids:
@@ -655,53 +659,54 @@ def get_analysis_value(
         return values
 
 
-    def run_stall_analysis(self, roi_id: int, params: StallAnalysisParams) -> StallAnalysis:
-        """Run stall analysis for a single ROI and store results.
-
-        This method is intentionally **on-demand**: it does not run automatically
-        when flow analysis is computed. A caller (GUI/script) supplies parameters and
-        explicitly requests stall detection once the underlying analysis values exist.
-
-        The source signal is selected via `params.velocity_key` (e.g. 'velocity',
-        'cleanVelocity', 'signedVelocity').
-
-        Args:
-            roi_id: Identifier of the ROI to analyze.
-            params: Stall analysis parameters.
-
-        Returns:
-            The computed `StallAnalysis` instance.
-
-        Raises:
-            ValueError: If the requested analysis values are missing for this ROI.
-        """
-        values = self.get_analysis_value(
-            roi_id=roi_id,
-            key=params.velocity_key,
-            remove_outliers=False,
-        )
-        if values is None:
-            raise ValueError(
-                f"Cannot run stall analysis: ROI {roi_id} has no analysis values for key '{params.velocity_key}'."
-            )
-
-        analysis = StallAnalysis.run(velocity=values, params=params)
-        self._stall_analysis[roi_id] = analysis
-        # Mark dirty so callers know there are unsaved results.
-        self._dirty = True
-        return analysis
-
-    def get_stall_analysis(self, roi_id: int) -> Optional[StallAnalysis]:
-        """Return stall analysis results for roi_id, or None if not present.
-
-        Args:
-            roi_id: Identifier of the ROI.
-
-        Returns:
-            Stored `StallAnalysis` results, or None if stall analysis has not been run
-            for this ROI (or results were not loaded).
-        """
-        return self._stall_analysis.get(roi_id)
+    # DEPRECATED: Stall analysis is deprecated
+    # def run_stall_analysis(self, roi_id: int, params: StallAnalysisParams) -> StallAnalysis:
+    #     """Run stall analysis for a single ROI and store results.
+    #
+    #     This method is intentionally **on-demand**: it does not run automatically
+    #     when flow analysis is computed. A caller (GUI/script) supplies parameters and
+    #     explicitly requests stall detection once the underlying analysis values exist.
+    #
+    #     The source signal is selected via `params.velocity_key` (e.g. 'velocity',
+    #     'cleanVelocity', 'signedVelocity').
+    #
+    #     Args:
+    #         roi_id: Identifier of the ROI to analyze.
+    #         params: Stall analysis parameters.
+    #
+    #     Returns:
+    #         The computed `StallAnalysis` instance.
+    #
+    #     Raises:
+    #         ValueError: If the requested analysis values are missing for this ROI.
+    #     """
+    #     values = self.get_analysis_value(
+    #         roi_id=roi_id,
+    #         key=params.velocity_key,
+    #         remove_outliers=False,
+    #     )
+    #     if values is None:
+    #         raise ValueError(
+    #             f"Cannot run stall analysis: ROI {roi_id} has no analysis values for key '{params.velocity_key}'."
+    #         )
+    #
+    #     analysis = StallAnalysis.run(velocity=values, params=params)
+    #     self._stall_analysis[roi_id] = analysis
+    #     # Mark dirty so callers know there are unsaved results.
+    #     self._dirty = True
+    #     return analysis
+    #
+    # def get_stall_analysis(self, roi_id: int) -> Optional[StallAnalysis]:
+    #     """Return stall analysis results for roi_id, or None if not present.
+    #
+    #     Args:
+    #         roi_id: Identifier of the ROI.
+    #
+    #     Returns:
+    #         Stored `StallAnalysis` results, or None if stall analysis has not been run
+    #         for this ROI (or results were not loaded).
+    #     """
+    #     return self._stall_analysis.get(roi_id)
 
     def run_velocity_event_analysis(
         self,

src/kymflow/core/plotting/line_plots.py

@@ -372,49 +372,50 @@ def plot_image_line_plotly(
         )
 
         # ------------------------------------------------------------------
-        # Stall analysis overlays (row=2: velocity vs time)
+        # DEPRECATED: Stall analysis is deprecated
+        # # Stall analysis overlays (row=2: velocity vs time)
+        # #
+        # # Stalls are stored on the KymAnalysis object (computed on-demand).
+        # # We map stall bin indices to time using analysis_time_values and draw
+        # # vertical rectangles spanning the full subplot height.
+        # # ------------------------------------------------------------------
+        # if selected_roi_id is not None:
+        #     stall_analysis = kym_analysis.get_stall_analysis(selected_roi_id)
+        # else:
+        #     stall_analysis = None
         #
-        # Stalls are stored on the KymAnalysis object (computed on-demand).
-        # We map stall bin indices to time using analysis_time_values and draw
-        # vertical rectangles spanning the full subplot height.
-        # ------------------------------------------------------------------
-        if selected_roi_id is not None:
-            stall_analysis = kym_analysis.get_stall_analysis(selected_roi_id)
-        else:
-            stall_analysis = None
-
-        if stall_analysis is not None and stall_analysis.stalls:
-            n_time = len(analysis_time_values)
-            for stall in stall_analysis.stalls:
-                if not (0 <= stall.bin_start < n_time and 0 <= stall.bin_stop < n_time):
-                    logger.warning(
-                        "Skipping out-of-range stall for ROI %s: [%s, %s] (time_len=%s)",
-                        selected_roi_id,
-                        stall.bin_start,
-                        stall.bin_stop,
-                        n_time,
-                    )
-                    continue
-
-                x0 = float(analysis_time_values[stall.bin_start])
-                x1 = float(analysis_time_values[stall.bin_stop])
-                if x1 < x0:
-                    x0, x1 = x1, x0
-
-                # Use yref='y2 domain' so rectangles span the full height of row=2.
-                fig.add_shape(
-                    type="rect",
-                    xref="x2",
-                    yref="y2 domain",
-                    x0=x0,
-                    x1=x1,
-                    y0=0,
-                    y1=1,
-                    fillcolor="cyan",
-                    opacity=0.25,
-                    line_width=0,
-                    layer="below",
-                )
+        # if stall_analysis is not None and stall_analysis.stalls:
+        #     n_time = len(analysis_time_values)
+        #     for stall in stall_analysis.stalls:
+        #         if not (0 <= stall.bin_start < n_time and 0 <= stall.bin_stop < n_time):
+        #             logger.warning(
+        #                 "Skipping out-of-range stall for ROI %s: [%s, %s] (time_len=%s)",
+        #                 selected_roi_id,
+        #                 stall.bin_start,
+        #                 stall.bin_stop,
+        #                 n_time,
+        #             )
+        #             continue
+        #
+        #         x0 = float(analysis_time_values[stall.bin_start])
+        #         x1 = float(analysis_time_values[stall.bin_stop])
+        #         if x1 < x0:
+        #             x0, x1 = x1, x0
+        #
+        #         # Use yref='y2 domain' so rectangles span the full height of row=2.
+        #         fig.add_shape(
+        #             type="rect",
+        #             xref="x2",
+        #             yref="y2 domain",
+        #             x0=x0,
+        #             x1=x1,
+        #             y0=0,
+        #             y1=1,
+        #             fillcolor="cyan",
+        #             opacity=0.25,
+        #             line_width=0,
+        #             layer="below",
+        #         )
     else:
         # No analysis data - show message
         fig.add_annotation(
@@ -539,9 +540,10 @@ def _add_single_roi_line_plot(
             col=1,
         )
 
-        # Add stall analysis overlays
-        logger.warning('turned of stall analysis plot')
-        if 0:
+        # DEPRECATED: Stall analysis is deprecated
+        # # Add stall analysis overlays
+        # logger.warning('turned of stall analysis plot')
+        if 0:  # DEPRECATED: Stall analysis is deprecated
             stall_analysis = kym_analysis.get_stall_analysis(roi_id)
             if stall_analysis is not None and stall_analysis.stalls:
                 n_time = len(analysis_time_values)

src/kymflow/core/user_config.py

@@ -310,6 +310,9 @@ def save(self) -> None:
         payload = self.data.to_json_dict()
         logger.info('saving user_config to disk')
         # logger.info(f'payload: {payload}')
+        from pprint import pprint
+        pprint(payload, sort_dicts=False, indent=4)
+        
         self.path.write_text(json.dumps(payload, indent=2), encoding="utf-8")
 
     def ensure_exists(self) -> None:

src/kymflow/gui_v2/app.py

@@ -98,7 +98,7 @@ def _warm_mpl_font_cache_once() -> None:
 # _DEFAULT_DEV_FOLDER = Path("/Users/cudmore/Dropbox/data/declan/2026/data/20251204")
 
 DEV_FOLDER = Path(os.getenv("KYMFLOW_DEV_FOLDER", str(_DEFAULT_DEV_FOLDER))).expanduser()
-USE_DEV_FOLDER = os.getenv("KYMFLOW_USE_DEV_FOLDER", "1") == "1"
+USE_DEV_FOLDER = os.getenv("KYMFLOW_USE_DEV_FOLDER", "0") == "1"  # Default to "0" (disabled)
 
 # USE_DEV_FOLDER = False  # abb turn of before impleenting ~/ kymflow config json
 
@@ -265,7 +265,8 @@ def main(*, reload: bool | None = None, native: bool | None = None) -> None:
 
     reload = False
     native = True
-    install_shutdown_handlers(context)
+
+    install_shutdown_handlers(context, native=native)
 
     ui.run(
         port=DEFAULT_PORT,

src/kymflow/gui_v2/app_context.py

@@ -8,6 +8,7 @@
 from __future__ import annotations
 
 import multiprocessing as mp
+import os
 from pathlib import Path
 from typing import Optional
 
@@ -78,7 +79,11 @@ def __init__(self) -> None:
 
         # Shared state instances
         self.app_state = AppState()
-        self.user_config = UserConfig.load()
+        user_config_path = os.getenv("KYMFLOW_USER_CONFIG_PATH")
+        if user_config_path:
+            self.user_config = UserConfig.load(config_path=Path(user_config_path))
+        else:
+            self.user_config = UserConfig.load()
         logger.info(f"User config loaded from: {self.user_config.path}")
         self.home_task = TaskState()
         self.batch_task = TaskState()