Update SpatialDataWrapper. Bump js version

Author: keller-mark

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.6.6"
+version = "3.6.7"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/file_def_utils.py

@@ -127,29 +127,25 @@ def gen_path_schema(key: str, path: Optional[str], options: dict):
 gen_feature_labels_schema = partial(gen_path_schema, "featureLabels")
 
 
-def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
         options["image"] = {
             "path": path
         }
-        if affine_transformation is not None:
-            options["image"]['coordinateTransformations'] = affine_transformation
         if coordinate_system is not None:
             options["image"]['coordinateSystem'] = coordinate_system
     return options
 
 
-def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict:
+def gen_sdata_obs_segmentations_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None) -> dict:
     if path is not None:
-        options["labels"] = {
+        options["obsSegmentations"] = {
             "path": path
         }
         if table_path is not None:
-            options["labels"]['tablePath'] = table_path
-        if affine_transformation is not None:
-            options["labels"]['coordinateTransformations'] = affine_transformation
+            options["obsSegmentations"]['tablePath'] = table_path
         if coordinate_system is not None:
-            options["labels"]['coordinateSystem'] = coordinate_system
+            options["obsSegmentations"]['coordinateSystem'] = coordinate_system
     return options
 
 

src/vitessce/widget.py

@@ -131,6 +131,11 @@ def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_nam
         port, DEFAULT_PORT, proxy=proxy, base_url=base_url, host_name=host_name)
     config_dict = config.to_dict(base_url=base_url)
     routes = config.get_routes()
+
+    stores = config.get_stores(base_url=base_url)
+    if len(stores) > 0:
+        raise ValueError('One or more files in this configuration have been provided via Zarr store, which can only be loaded via the widget. Either use VitessceConfig.widget or VitessceConfig.display (instead of .web_app), or provide the files via _path or _url (rather than _store) parameters.')
+
     serve_routes(config, routes, use_port)
     vitessce_url = f"http://vitessce.io/#?theme={theme}&url=data:," + quote_plus(
         json.dumps(config_dict))
@@ -626,7 +631,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.7').tag(sync=True)
+    js_package_version = Unicode('3.6.8').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)
@@ -639,7 +644,7 @@ 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='3.6.7', 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):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.8', 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):
         """
         Construct a new Vitessce widget.
 
@@ -775,7 +780,7 @@ 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='3.6.7', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.8', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

src/vitessce/wrappers.py

@@ -29,7 +29,7 @@
     gen_obs_labels_schema,
     gen_obs_sets_schema,
     gen_sdata_image_schema,
-    gen_sdata_labels_schema,
+    gen_sdata_obs_segmentations_schema,
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
@@ -1401,7 +1401,7 @@ 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, affine_transformation: Optional[np.ndarray] = None, obs_spots_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", 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, table_path: str = "tables/table", coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1421,8 +1421,8 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         :type affine_transformation: Optional[np.ndarray]
         :param obs_spots_path: Location of shapes that should be interpreted as spot observations, by default None
         :type obs_spots_path: Optional[str]
-        :param labels_path: Location of the labels (segmentation bitmask image), by default None
-        :type labels_path: Optional[str]
+        :param obs_segmentations_path: Path to a labels or shapes element (segmentation bitmask label image or segmentation polygon shapes), by default None
+        :type obs_segmentations_path: Optional[str]
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1437,14 +1437,21 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
             kwargs.get('adata_artifact', None)
         ])
         super().__init__(adata_path=sdata_path, adata_url=sdata_url, adata_store=sdata_store, adata_artifact=sdata_artifact, **kwargs)
+        if "labels_path" in kwargs:
+            warnings.warn("`labels_path` is deprecated. Use `obs_segmentations_path` instead.", DeprecationWarning)
+            self._obs_segmentations_path = kwargs["labels_path"]
+        if "shapes_path" in kwargs:
+            warnings.warn("`shapes_path` is deprecated. Use `obs_segmentations_path` instead.", DeprecationWarning)
+        if "affine_transformation" in kwargs:
+            warnings.warn("`affine_transformation` is deprecated. Store transformations in the SpatialData object, then specify `coordinate_system`.", DeprecationWarning)
+
         self.local_dir_uid = make_unique_filename(".sdata.zarr")
         self._image_path = image_path
         self._region = region
         self._coordinate_system = coordinate_system
-        self._affine_transformation = affine_transformation
         self._kwargs = kwargs
         self._obs_spots_path = obs_spots_path
-        self._labels_path = labels_path
+        self._obs_segmentations_path = obs_segmentations_path
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
@@ -1530,8 +1537,8 @@ def generator(base_url):
             options = gen_sdata_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter, self._region)
             options = gen_sdata_obs_sets_schema(options, self._obs_set_elems, self._obs_set_names, self._table_path, self._region)
             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, self._affine_transformation)
-            options = gen_sdata_labels_schema(options, self._labels_path, self._table_path, self._coordinate_system, self._affine_transformation)
+            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_feature_labels_schema(self._feature_labels, options)
             if len(options.keys()) > 0:
                 obj_file_def = {