Bump js version

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.7.8"
+version = "3.7.9"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/widget.py

@@ -181,7 +181,7 @@ def get_uid_str(uid):
         "react-dom": "https://cdn.vitessce.io/[email protected]/index.js",
         "react-dom/client": "https://cdn.vitessce.io/[email protected]/es2022/client.mjs",
         // Replaced with version-specific URL below.
-        "vitessce": "https://cdn.vitessce.io/vitessce@3.8.5/dist/index.min.js",
+        "vitessce": "https://cdn.vitessce.io/vitessce@VERSION/dist/index.min.js",
     },
 };
 /*
@@ -191,7 +191,7 @@ def get_uid_str(uid):
         "react-dom": "https://cdn.vitessce.io/[email protected]/index_dev.js",
         "react-dom/client": "https://cdn.vitessce.io/[email protected]/es2022/client.development.mjs",
         // Replaced with version-specific URL below.
-        "vitessce": "https://cdn.vitessce.io/@vitessce/dev@3.8.5/dist/index.js",
+        "vitessce": "https://cdn.vitessce.io/@vitessce/dev@VERSION/dist/index.js",
     },
 };
 */
@@ -729,7 +729,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.8.5').tag(sync=True)
+    js_package_version = Unicode('3.8.8').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)
@@ -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='3.8.5', 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='3.8.8', 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, 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='3.8.5', 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='3.8.8', 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

@@ -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 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
+        :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like `[[0, 1], [4, 5]]` where `[0, 1]` is just the normal x and y but `[4, 5]` could be comparing the third and fourth principal components, for example.
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1551,6 +1555,7 @@ def generator(base_url):
             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_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:
                 obj_file_def = {
                     "fileType": ft.SPATIALDATA_ZARR_ZIP.value if self.is_zip else ft.SPATIALDATA_ZARR.value,

tests/test_wrappers.py

@@ -481,7 +481,10 @@ def test_spatial_data_with_base_dir(self):
                     'obsSets': [{'name': 'Cell Type', 'path': 'obs/CellType'}],
                     'tablePath': 'tables/table'
                 },
-                'image': {'path': 'images/picture'}
+                'image': {'path': 'images/picture'},
+                'obsEmbedding': [
+                    {'dims': [0, 1], 'embeddingType': 'UMAP', 'path': 'obsm/X_umap'},
+                ],
             }})
 
     def test_spatial_data_with_base_dir_2(self):