Version bump

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.8.0"
+version = "3.8.1"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

src/vitessce/file_def_utils.py

@@ -147,7 +147,7 @@ def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "ta
     return options
 
 
-def gen_sdata_obs_points_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None) -> dict:
+def gen_sdata_obs_points_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None, feature_index_column: Optional[str] = None, morton_code_column: Optional[str] = None) -> dict:
     if path is not None:
         options["obsPoints"] = {
             "path": path
@@ -156,6 +156,10 @@ def gen_sdata_obs_points_schema(options, path: str, table_path: str = "tables/ta
             options["obsPoints"]['tablePath'] = table_path
         if coordinate_system is not None:
             options["obsPoints"]['coordinateSystem'] = coordinate_system
+        if feature_index_column is not None:
+            options["obsPoints"]['featureIndexColumn'] = feature_index_column
+        if morton_code_column is not None:
+            options["obsPoints"]['mortonCodeColumn'] = morton_code_column
     return options
 
 

src/vitessce/widget.py

@@ -729,7 +729,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.9.0').tag(sync=True)
+    js_package_version = Unicode('3.9.1').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -742,7 +742,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.9.0', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.9.1', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
         """
         Construct a new Vitessce widget. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
@@ -876,7 +876,7 @@ def _plugin_command(self, params, buffers):
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.9.0', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.9.1', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

src/vitessce/wrappers.py

@@ -1407,7 +1407,7 @@ def auto_view_config(self, vc):
 
 class SpatialDataWrapper(AnnDataWrapper):
 
-    def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, obs_spots_path: Optional[str] = None, obs_segmentations_path: Optional[str] = None, obs_points_path: Optional[str] = None, table_path: str = "tables/table", is_zip=None, coordination_values=None, **kwargs):
+    def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, obs_spots_path: Optional[str] = None, obs_segmentations_path: Optional[str] = None, obs_points_path: Optional[str] = None, obs_points_feature_index_column: Optional[str] = None, obs_points_morton_code_column: Optional[str] = None, table_path: str = "tables/table", is_zip=None, coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1432,6 +1432,10 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         :type obs_segmentations_path: Optional[str]
         :param obs_points_path: Path to a points element, by default None
         :type obs_points_path: Optional[str]
+        :param obs_points_feature_index_column: Column in the points dataframe that contains a feature index value (i.e., index into table.var.index to specify a gene) for each point, by default None
+        :type obs_points_feature_index_column: Optional[str]
+        :param obs_points_morton_code_column: Column in the points dataframe that contains a morton code for each point, by default None
+        :type obs_points_morton_code_column: Optional[str]
         :param str feature_labels_path: Path to a table var column containing feature labels (e.g., alternate gene symbols), instead of the default index column of the `var` dataframe.
         :param list[str] obs_embedding_paths: Column names like `['obsm/X_umap', 'obsm/X_pca']` for showing scatterplots
         :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA']` for displaying above scatterplots
@@ -1466,6 +1470,8 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         self._obs_spots_path = obs_spots_path
         self._obs_segmentations_path = obs_segmentations_path
         self._obs_points_path = obs_points_path
+        self._obs_points_feature_index_column = obs_points_feature_index_column
+        self._obs_points_morton_code_column = obs_points_morton_code_column
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
@@ -1553,7 +1559,10 @@ def generator(base_url):
             options = gen_sdata_obs_spots_schema(options, self._obs_spots_path, self._table_path, self._region, self._coordinate_system)
             options = gen_sdata_image_schema(options, self._image_path, self._coordinate_system)
             options = gen_sdata_obs_segmentations_schema(options, self._obs_segmentations_path, self._table_path, self._coordinate_system)
-            options = gen_sdata_obs_points_schema(options, self._obs_points_path, self._table_path, self._coordinate_system)
+            options = gen_sdata_obs_points_schema(
+                options, self._obs_points_path, self._table_path, self._coordinate_system,
+                self._obs_points_feature_index_column, self._obs_points_morton_code_column
+            )
             options = gen_feature_labels_schema(self._feature_labels, options)
             options = gen_obs_embedding_schema(options, self._mappings_obsm, self._mappings_obsm_names, self._mappings_obsm_dims)
             if len(options.keys()) > 0: