Updated version and added zip support (#464)

* Updated version and added zip support

* Wrapper changes added

* Version update in Widget

Author: tkakar

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.7.0"
+version = "3.7.1"
 authors = [
   { name="Mark Keller", email="[email protected]" },
 ]

src/vitessce/constants.py

@@ -163,6 +163,7 @@ class FileType(DocEnum):
     """
     ANNDATA_ZARR = "anndata.zarr", "Joint file type for AnnData objects"
     SPATIALDATA_ZARR = "spatialdata.zarr", "Joint file type for SpatialData objects"
+    SPATIALDATA_ZARR_ZIP = "spatialdata.zarr.zip", "Joint file type for SpatialData objects in a Zarr directory store that has been zipped"
     ANNDATA_H5AD = "anndata.h5ad", "Joint file type for AnnData objects"
     ANNDATA_ZARR_ZIP = "anndata.zarr.zip", "Joint file type for AnnData object in a Zarr directory store that has been zipped"
     OBS_EMBEDDING_CSV = 'obsEmbedding.csv', "File type for obsEmbedding values stored in a CSV file"

src/vitessce/widget.py

@@ -650,7 +650,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.12').tag(sync=True)
+    js_package_version = Unicode('3.6.13').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)
@@ -663,8 +663,7 @@ 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='3.6.12', 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='3.6.13', 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. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
@@ -797,7 +796,7 @@ 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='3.6.12', 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='3.6.13', 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

@@ -1399,7 +1399,7 @@ 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, 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", is_zip=None, coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1415,6 +1415,7 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
         :type image_path: Optional[str]
         :param coordinate_system: Name of a target coordinate system.
         :type coordinate_system: Optional[str]
+        :param is_zip: Boolean indicating whether the Zarr store is in a zipped format.
         :param affine_transformation: Transformation to be applied to the image. By default, None. Prefer coordinate_system.
         :type affine_transformation: Optional[np.ndarray]
         :param obs_spots_path: Location of shapes that should be interpreted as spot observations, by default None
@@ -1434,7 +1435,7 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
             kwargs.get('adata_store', None),
             kwargs.get('adata_artifact', None)
         ])
-        super().__init__(adata_path=sdata_path, adata_url=sdata_url, adata_store=sdata_store, adata_artifact=sdata_artifact, **kwargs)
+        super().__init__(adata_path=sdata_path, adata_url=sdata_url, adata_store=sdata_store, adata_artifact=sdata_artifact, is_zip=is_zip, **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"]
@@ -1540,7 +1541,7 @@ def generator(base_url):
             options = gen_feature_labels_schema(self._feature_labels, options)
             if len(options.keys()) > 0:
                 obj_file_def = {
-                    "fileType": ft.SPATIALDATA_ZARR.value,
+                    "fileType": ft.SPATIALDATA_ZARR_ZIP.value if self.is_zip else ft.SPATIALDATA_ZARR.value,
                     "url": self.get_zarr_url(base_url, dataset_uid, obj_i),
                     "options": options
                 }