vitessce 3.7.0__py3-none-any.whl → 3.7.2__py3-none-any.whl

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"

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('3.6.15').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='3.6.15', 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 @@ class VitessceWidget(anywidget.AnyWidget):
 # 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='3.6.15', 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)
 

vitessce/wrappers.py

@@ -1399,7 +1399,7 @@ SpatialDataWrapperType = TypeVar('SpatialDataWrapperType', bound='SpatialDataWra
 
 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 @@ class SpatialDataWrapper(AnnDataWrapper):
         :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 @@ class SpatialDataWrapper(AnnDataWrapper):
             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 @@ class SpatialDataWrapper(AnnDataWrapper):
             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
                 }

{vitessce-3.7.0.dist-info → vitessce-3.7.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.7.0
+Version: 3.7.2
 Summary: Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce
 Project-URL: repository, https://github.com/vitessce/vitessce-python
 Author-email: Mark Keller <mark_keller@hms.harvard.edu>

{vitessce-3.7.0.dist-info → vitessce-3.7.2.dist-info}/RECORD

@@ -1,15 +1,15 @@
 vitessce/__init__.py,sha256=GWGahpQMOGFotQXilRccGT0Bnn3OyoCQUCUphW_DtTI,1632
 vitessce/config.py,sha256=0U10mtZZx_DBKM8AipD1Xw-L1hRgQcfOFASKHSGJ5BE,82949
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
-vitessce/constants.py,sha256=nBMH55TcnSavcpvYE-epyx3cJ0iDS31eHsL_1e9qb9M,15360
+vitessce/constants.py,sha256=7w71Z5TLJIWy7ieNxTmNaC-KB3G5mok_U0tTrcUG6g4,15500
 vitessce/export.py,sha256=L7j5sVC0nBSqGocFWQyyHImSiAF4IjXhmqV1QtpuNc4,3874
 vitessce/file_def_utils.py,sha256=heFDrJMO4fYoondtVALjUiIxe4swOiR24KVGEu8ZTM0,6688
 vitessce/repr.py,sha256=qMmefmZ3E-3sRVxeI5q1DTZnfuwbXKiA85eyqk5MCT4,2287
 vitessce/responses.py,sha256=Z6Wo4AXN-RyzmxMPhSuhpIsHTItHM4GyIgMLGoVEYcU,339
 vitessce/routes.py,sha256=U8T-L-3QCD_tAbPF8LsUlSMhPWNbyzbLNUnxP9Z9s9o,2140
 vitessce/utils.py,sha256=obzjj65qsagu60_yuhGc-0jmHO-BW0Y-bDs0FgrBqLY,981
-vitessce/widget.py,sha256=D4xrcIZWp_nZwaWe9X5rH2EThRBbECt1uYlRGYQpyXk,35898
-vitessce/wrappers.py,sha256=gbJggLGoFTRa1odnBvBDE5EspQ8vc_CpNq_eTbZBGSM,76091
+vitessce/widget.py,sha256=flUVMhD2y1Tg5KlyVrGld8yH2tXVR-PD9jS4pY81Y7U,35882
+vitessce/wrappers.py,sha256=eGsR6fd24zT9OfasmOg1oyR9GpiVPyKh-PqZwPnXXz4,76257
 vitessce/data_utils/__init__.py,sha256=3mWi1lMjoj4_dNbhMOvyE-HEJu0qpMzcmkhfz_5T6n8,361
 vitessce/data_utils/anndata.py,sha256=iLa5-bRezHgBzL_XCHO7w0pc0RQ4urzZbDsqJbBYeCk,10668
 vitessce/data_utils/entities.py,sha256=X8enC_TQbgwBzjgD1x53IPS6aVr9wyP0s-NLuYBeMeU,11705
@@ -18,7 +18,7 @@ vitessce/data_utils/ome.py,sha256=tJHlSHbZTxpjRgYfTxbYMS9zSnSHQwJVWPZpREAvHtU,55
 vitessce/widget_plugins/__init__.py,sha256=lto2GXnc7KwjIoT-jvzyRYLj0XTJG3uxoX45Hc9EcWA,82
 vitessce/widget_plugins/demo_plugin.py,sha256=14S7nOxdlKSxIHw9DUcNCN83NE_U1EMPy2D4k0FDues,1797
 vitessce/widget_plugins/spatial_query.py,sha256=CYxvmMT1Je_jguikPROQxlegkPgIIzemKGbZSJfZMyI,12314
-vitessce-3.7.0.dist-info/METADATA,sha256=C_3I3Pgll9lUncQxm-jUKm3NA11AQWgcVzYE4yBoWJM,9826
-vitessce-3.7.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.7.0.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.7.0.dist-info/RECORD,,
+vitessce-3.7.2.dist-info/METADATA,sha256=7dzskMRsAqgRcLQ9vJwcQ5k5Svkph4VFSIJVjj_yDtc,9826
+vitessce-3.7.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.7.2.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.7.2.dist-info/RECORD,,