vitessce 3.7.8__py3-none-any.whl → 3.8.0__py3-none-any.whl

vitessce/widget.py

@@ -181,7 +181,7 @@ const fallbackImportMap = {
         "react-dom": "https://cdn.vitessce.io/react-dom@18.2.0/index.js",
         "react-dom/client": "https://cdn.vitessce.io/react-dom@18.2.0/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 @@ const fallbackDevImportMap = {
         "react-dom": "https://cdn.vitessce.io/react-dom@18.2.0/index_dev.js",
         "react-dom/client": "https://cdn.vitessce.io/react-dom@18.2.0/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('3.9.0').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='3.9.0', 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 @@ 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='3.8.5', 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='3.9.0', 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

@@ -1432,6 +1432,10 @@ class SpatialDataWrapper(AnnDataWrapper):
         :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 @@ class SpatialDataWrapper(AnnDataWrapper):
             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,

{vitessce-3.7.8.dist-info → vitessce-3.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.7.8
+Version: 3.8.0
 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-3.7.8.dist-info → vitessce-3.8.0.dist-info}/RECORD

@@ -8,8 +8,8 @@ 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=ndgKqwNLrgYnXnA5pGCu2mgQe0_vF1ZMedWuHDYqPpo,39260
-vitessce/wrappers.py,sha256=WdOQ9w4ElGZH_nKrZAfyrtHxW3iVDzIQ1eqBPlrucj0,76993
+vitessce/widget.py,sha256=rR7JipphZy1R8NhzwXVrLoz6DfJBcAe76BlqWv6ox3Q,39264
+vitessce/wrappers.py,sha256=UBUc2lbN3b0G31ZyE3XAxMlaFI3PKKAvv9KuuExxaEA,77804
 vitessce/data_utils/__init__.py,sha256=lZZ58HlbMiWYIBw3JckGorjmySR_8N4RCZS3U00jUsQ,716
 vitessce/data_utils/anndata.py,sha256=iLa5-bRezHgBzL_XCHO7w0pc0RQ4urzZbDsqJbBYeCk,10668
 vitessce/data_utils/entities.py,sha256=X8enC_TQbgwBzjgD1x53IPS6aVr9wyP0s-NLuYBeMeU,11705
@@ -19,7 +19,7 @@ vitessce/data_utils/spatialdata_points_zorder.py,sha256=pAga1GGyiFgvJCxiqjpsqDpV
 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-3.7.8.dist-info/METADATA,sha256=GhjWJVZ8ENw7o44GSQIAM9KiTzPq3dKV_ec_fxCHQYo,9826
-vitessce-3.7.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.7.8.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.7.8.dist-info/RECORD,,
+vitessce-3.8.0.dist-info/METADATA,sha256=xtVyDhn3LWuQp5M2ww2ybyoyX_hcrQ-aeg2MA3pWyKM,9826
+vitessce-3.8.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+vitessce-3.8.0.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.8.0.dist-info/RECORD,,

{vitessce-3.7.8.dist-info → vitessce-3.8.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any