vitessce 3.7.4__py3-none-any.whl → 3.7.6__py3-none-any.whl

vitessce/file_def_utils.py

@@ -147,6 +147,18 @@ 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:
+    if path is not None:
+        options["obsPoints"] = {
+            "path": path
+        }
+        if table_path is not None:
+            options["obsPoints"]['tablePath'] = table_path
+        if coordinate_system is not None:
+            options["obsPoints"]['coordinateSystem'] = coordinate_system
+    return options
+
+
 def gen_sdata_obs_spots_schema(options: dict, shapes_path: str, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict:
     if shapes_path is not None:
         options['obsSpots'] = {

vitessce/widget.py

@@ -651,7 +651,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.18').tag(sync=True)
+    js_package_version = Unicode('3.8.3').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)
@@ -664,7 +664,7 @@ 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='3.6.18', 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='3.8.3', 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``.
 
@@ -798,7 +798,7 @@ 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='3.6.18', 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='3.8.3', 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)
 

vitessce/wrappers.py

@@ -28,6 +28,7 @@ from vitessce.file_def_utils import (
     gen_obs_sets_schema,
     gen_sdata_image_schema,
     gen_sdata_obs_segmentations_schema,
+    gen_sdata_obs_points_schema,
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
@@ -73,6 +74,7 @@ class AbstractWrapper:
         self.routes = []
         self.is_remote = False  # TODO: change to needs_localhost_serving for clarity
         self.is_store = False  # TODO: change to needs_store_registration for clarity
+        self.is_zip = False
         self.file_def_creators = []
         self.base_dir = None
         self.stores = {}
@@ -1325,6 +1327,12 @@ class AnnDataWrapper(AbstractWrapper):
                     *self.get_local_file_route(dataset_uid, obj_i, self._adata_path, self.local_file_uid),
                     *self.get_local_file_route(dataset_uid, obj_i, self._ref_path, self.local_ref_uid)
                 ]
+            elif self.is_zip:
+                return [
+                    # TODO: modify so that the .zip file extension is used
+                    # (not necessary, but could help with debugging or with base_dir mode)
+                    *self.get_local_file_route(dataset_uid, obj_i, self._adata_path, self.local_dir_uid)
+                ]
             else:
                 return self.get_local_dir_route(dataset_uid, obj_i, self._adata_path, self.local_dir_uid)
 
@@ -1399,7 +1407,7 @@ 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", 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, table_path: str = "tables/table", is_zip=None, coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1422,6 +1430,8 @@ class SpatialDataWrapper(AnnDataWrapper):
         :type obs_spots_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]
+        :param obs_points_path: Path to a points element, by default None
+        :type obs_points_path: Optional[str]
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1451,6 +1461,7 @@ class SpatialDataWrapper(AnnDataWrapper):
         self._kwargs = kwargs
         self._obs_spots_path = obs_spots_path
         self._obs_segmentations_path = obs_segmentations_path
+        self._obs_points_path = obs_points_path
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
@@ -1538,6 +1549,7 @@ class SpatialDataWrapper(AnnDataWrapper):
             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_feature_labels_schema(self._feature_labels, options)
             if len(options.keys()) > 0:
                 obj_file_def = {

{vitessce-3.7.4.dist-info → vitessce-3.7.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.7.4
+Version: 3.7.6
 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-3.7.4.dist-info → vitessce-3.7.6.dist-info}/RECORD

@@ -3,13 +3,13 @@ vitessce/config.py,sha256=vZyxrvzsrDpbp3QMcfOZghSO-kSb4myUbRNTGl6Ur6o,83101
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
 vitessce/constants.py,sha256=7w71Z5TLJIWy7ieNxTmNaC-KB3G5mok_U0tTrcUG6g4,15500
 vitessce/export.py,sha256=L7j5sVC0nBSqGocFWQyyHImSiAF4IjXhmqV1QtpuNc4,3874
-vitessce/file_def_utils.py,sha256=heFDrJMO4fYoondtVALjUiIxe4swOiR24KVGEu8ZTM0,6688
+vitessce/file_def_utils.py,sha256=uAYRSePwhtow0l1izxzxRLqAuLYEKoWvx2cZ3F24CsI,7147
 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=waiBX2RS-5Y4nXIzg3Q5u4v-oA2RBAmHVJ-enxUE6PM,36231
-vitessce/wrappers.py,sha256=eGsR6fd24zT9OfasmOg1oyR9GpiVPyKh-PqZwPnXXz4,76257
+vitessce/widget.py,sha256=QJKneYYvBl_WdLiWo1jDaSYlqsc8UXnXtlJRBqj3yjw,36228
+vitessce/wrappers.py,sha256=WdOQ9w4ElGZH_nKrZAfyrtHxW3iVDzIQ1eqBPlrucj0,76993
 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=te1X933QTRfCm8N5uVXZREShtxDdAEggZZKKEoJdlhU,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-3.7.4.dist-info/METADATA,sha256=J_Y3jJ7pajuAeQo_Wp4r9aF9ePIHU5Vbg8Zj7kk_-RY,9826
-vitessce-3.7.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.7.4.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.7.4.dist-info/RECORD,,
+vitessce-3.7.6.dist-info/METADATA,sha256=zZa9zK1kYG2XO3xLOMRnQcqLiP8CytyoSRwMGw6TyEk,9826
+vitessce-3.7.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.7.6.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.7.6.dist-info/RECORD,,