Dega 514 scalebar bug fix

js/utils/scale_bar.js

@@ -26,6 +26,7 @@ export const create_scale_bar = (micronsPerPixel, tech) => {
   const rev_labelColor = labelColor === 'white' ? 'black' : 'white';
 
   const container = document.createElement('div');
+  container.className = 'celldega-scale-bar';
   container.style.position = 'absolute';
   container.style.bottom = '10px';
   container.style.left = '10px';

js/viz/landscape_ist.js

@@ -473,7 +473,11 @@ export const landscape_ist = async (
   const defaultMicronsPerPixel = PIXEL_SIZE_MICRONS[tech];
   const micronsPerPixel = defaultMicronsPerPixel ?? userMicronsPerPixel;
 
-  if (micronsPerPixel) {
+  // Only show the scale bar when explicitly enabled. Defaults to the value the
+  // Python widget resolves from whether a real transformation matrix was passed
+  // (identity fallback => hidden, since the pixel->micron scale is unknown).
+  const display_scalebar = ini_model.get('display_scalebar');
+  if (micronsPerPixel && display_scalebar !== false) {
     viz_state.scale_bar = create_scale_bar(micronsPerPixel, tech);
     root.appendChild(viz_state.scale_bar.container);
   }

js/viz/yearbook.js

@@ -379,7 +379,8 @@
   const micronsPerPixel = defaultMicronsPerPixel ?? userMicronsPerPixel;
   viz_state.yearbook.micronsPerPixel = micronsPerPixel;
 
-  if (micronsPerPixel) {
+  const display_scalebar = ini_model.get('display_scalebar');
+  if (micronsPerPixel && display_scalebar !== false) {
     viz_state.scale_bar = create_scale_bar(micronsPerPixel, tech);
     root.appendChild(viz_state.scale_bar.container);
   }
@@ -575,11 +576,11 @@
     }
 
     const geneCounts = viz_state.yearbook.geneCountScratch;
     const activeGeneIds = viz_state.yearbook.activeGeneIds;
     activeGeneIds.length = 0;
 
     for (let i = 0; i < trxCompact.geneIds.length; i++) {
       const positions = trxCompact.positions;
       const x = positions[i * trxCompact.size];
       const y = positions[i * trxCompact.size + 1];
       const inPortrait = centers.some((center) => {
@@ -636,11 +637,11 @@
     }
 
     const cellCounts = viz_state.yearbook.cellCountScratch;
     const activeCellIds = viz_state.yearbook.activeCellIds;
     activeCellIds.length = 0;
 
     for (let i = 0; i < cellCompact.categoryIds.length; i++) {
       const positions = cellCompact.positions;
       const x = positions[i * cellCompact.size];
       const y = positions[i * cellCompact.size + 1];
       const inPortrait = centers.some((center) => {

pyproject.toml

@@ -29,7 +29,9 @@ dependencies = [
     "requests",
     "scanpy~=1.10.0",
     "shapely~=2.0.0",
-    "setuptools",
+    # Pin <81: setuptools 81+ removed pkg_resources, which xarray_schema
+    # (a spatialdata/squidpy transitive dep) still imports at import time.
+    "setuptools<81",
     "spatialdata",
     "spatialdata_io~=0.1.0",
     "squidpy~=1.6.0",
@@ -48,7 +50,7 @@ dev = [
     "pytest-html",       # HTML coverage reports
     "pytest-mock",       # Mocking utilities
     "pre-commit",        # Git hooks automation
-    "setuptools",
+    "setuptools<81",     # <81: keeps pkg_resources for xarray_schema
     "build",             # Package building
     "twine",             # PyPI publishing
     # Documentation dependencies

src/celldega/viz/widget.py

@@ -231,6 +231,11 @@ class Landscape(anywidget.AnyWidget):
         cell_name_prefix (bool, optional): If True, cell names in adata.obs.index
             are assumed to have a dataset prefix (e.g., "dataset-name_cell-name")
             that should be trimmed when mapping to LandscapeFiles. Default: False.
+        display_scalebar (bool, optional): Whether to show the scale bar. If omitted,
+            it is shown only when a real transformation matrix is passed (via
+            ``transform``) or loaded from ``micron_to_image_transform.csv`` — when the
+            identity fallback is used the pixel-to-micron scale is unknown, so the bar
+            is hidden. Pass True/False to force it on or off.
 
     The AnnData input automatically extracts cell attributes (e.g., ``leiden``
     clusters), the corresponding colors (or derives them when missing), and any
@@ -261,6 +266,10 @@ class Landscape(anywidget.AnyWidget):
     scale_bar_microns_per_pixel = traitlets.Float(default_value=None, allow_none=True).tag(
         sync=True
     )
+    # Whether to show the scale bar. Resolved in __init__: defaults to True only
+    # when a real transformation matrix is passed/loaded (identity fallback => False),
+    # and can be overridden explicitly via the ``display_scalebar`` kwarg.
+    display_scalebar = traitlets.Bool(True).tag(sync=True)
 
     nbhd = traitlets.Instance(gpd.GeoDataFrame, allow_none=True)
     nbhd_geojson = traitlets.Dict({}).tag(sync=True)
@@ -301,6 +310,8 @@ def __init__(self, **kwargs):
         nbhd_gdf = kwargs.pop("nbhd", None)
         meta_nbhd_df = kwargs.pop("meta_nbhd", None)
         transform = kwargs.pop("transform", None)
+        # None => auto (show only when a real transform is resolved); True/False => force.
+        display_scalebar = kwargs.pop("display_scalebar", None)
         image_scale = kwargs.pop("image_scale", None)
         nbhd_edit = kwargs.pop("nbhd_edit", False)
         meta_cluster_df = None
@@ -368,16 +379,22 @@ def __init__(self, **kwargs):
         base_path = (kwargs.get("base_url") or "") + "/"
         path_transformation_matrix = base_path + "micron_to_image_transform.csv"
 
+        # Explicit signal for whether a real transform was resolved (vs. the identity
+        # fallback). Drives the scale bar default so it isn't shown against an unknown
+        # pixel->micron scale.
         if transform is not None:
             transformation_matrix = _coerce_transform_matrix(transform)
+            has_transform = True
         else:
             try:
                 transformation_matrix = pd.read_csv(
                     path_transformation_matrix, header=None, sep=r"\s+"
                 ).values
                 transformation_matrix = _coerce_transform_matrix(transformation_matrix)
+                has_transform = True
             except (FileNotFoundError, urllib.error.HTTPError, urllib.error.URLError):
                 transformation_matrix = np.eye(3)  # Fallback for testing
+                has_transform = False
                 warnings.warn(
                     f"Transformation matrix not found at {path_transformation_matrix}. "
                     "Using identity.",
@@ -512,6 +529,11 @@ def _reset_index_for_parquet(df):
 
         super().__init__(**kwargs)
 
+        # Auto (None) => show only when a real transform was resolved; else honor the override.
+        self.display_scalebar = (
+            has_transform if display_scalebar is None else bool(display_scalebar)
+        )
+
         self.cell_attr = cell_attr
 
         # store DataFrames locally without syncing to the frontend
@@ -769,6 +791,9 @@ class Yearbook(anywidget.AnyWidget):
     scale_bar_microns_per_pixel = traitlets.Float(default_value=None, allow_none=True).tag(
         sync=True
     )
+    # Show the scale bar (Yearbook portraits use a fixed micron size, so this defaults
+    # to True). Set ``display_scalebar=False`` to hide it.
+    display_scalebar = traitlets.Bool(True).tag(sync=True)
 
     # Pagination
     current_page = traitlets.Int(0).tag(sync=True)