vitessce 3.6.1__py3-none-any.whl → 3.6.3__py3-none-any.whl

vitessce/__init__.py

@@ -27,11 +27,6 @@ from .constants import (
     BASE_URL_PLACEHOLDER,
 )
 
-from .config_converter import (
-    CellBrowserToAnndataZarrConverter,  # only exported for testing.
-    convert_cell_browser_project_to_anndata,
-)
-
 from .wrappers import AbstractWrapper
 
 # We allow installation without all of the dependencies that the widget requires.

vitessce/config.py

@@ -602,7 +602,7 @@ class VitessceConfigView:
             })
             spatial_view.use_coordination_by_dict(scopes)
         """
-        if "coordinationScopes" not in self.view["coordinationScopes"] or self.view["coordinationScopes"] is None:
+        if "coordinationScopes" not in self.view or self.view["coordinationScopes"] is None:
             self.view["coordinationScopes"] = {}
 
         if "coordinationScopesBy" not in self.view or self.view["coordinationScopesBy"] is None:

vitessce/data_utils/ome.py

@@ -99,7 +99,9 @@ def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256,
     z_root.attrs["omero"] = {
         "name": img_name,
         "version": "0.3",
-        "rdefs": {},
+        "rdefs": {
+            "model": "color",
+        },
         "channels": [
             {
                 "label": "R",
@@ -156,7 +158,9 @@ def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Ima
     z_root.attrs["omero"] = {
         "name": img_name,
         "version": "0.3",
-        "rdefs": {},
+        "rdefs": {
+            "model": "greyscale",
+        },
         "channels": [
             {
                 "label": channel_name,

vitessce/file_def_utils.py

@@ -101,6 +101,17 @@ def gen_obs_labels_schema(options: dict, paths: Optional[list[str]] = None, name
     return options
 
 
+def gen_obs_feature_columns_schema(options: dict, obs_feature_column_paths: Optional[list[str]] = None):
+    if obs_feature_column_paths is not None:
+        options["obsFeatureColumns"] = [
+            {
+                "path": col_path
+            }
+            for col_path in obs_feature_column_paths
+        ]
+    return options
+
+
 def gen_path_schema(key: str, path: Optional[str], options: dict):
     if path is not None:
         options[key] = {

vitessce/widget.py

@@ -2,21 +2,11 @@ import importlib.util
 from urllib.parse import quote_plus
 import json
 import sys
-
-# Widget dependencies
-import anywidget
-from traitlets import Unicode, Dict, List, Int, Bool
 import time
 import uuid
+import anywidget
+from traitlets import Unicode, Dict, List, Int, Bool
 
-# Server dependencies
-from uvicorn import Config, Server
-
-from starlette.applications import Starlette
-from starlette.middleware import Middleware
-from starlette.middleware.cors import CORSMiddleware
-from threading import Thread
-import socket
 
 MAX_PORT_TRIES = 1000
 DEFAULT_PORT = 8000
@@ -25,6 +15,10 @@ DEFAULT_PORT = 8000
 class BackgroundServer:
     # Reference: https://github.com/gosling-lang/gos/blob/main/gosling/data/_background_server.py#L10
     def __init__(self, routes):
+        from starlette.applications import Starlette
+        from starlette.middleware import Middleware
+        from starlette.middleware.cors import CORSMiddleware
+
         middleware = [
             Middleware(CORSMiddleware, allow_origins=[
                        '*'], allow_methods=["OPTIONS", "GET"], allow_headers=['Range'])
@@ -47,6 +41,9 @@ class BackgroundServer:
         return self
 
     def start(self, port=None, timeout=1, daemon=True, log_level="warning"):
+        from uvicorn import Config, Server
+        from threading import Thread
+
         if self.thread is not None:
             return self
 
@@ -87,6 +84,7 @@ data_server = VitessceDataServer()
 
 
 def is_port_in_use(port):
+    import socket
     with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
         return s.connect_ex(('localhost', port)) == 0
 
@@ -234,6 +232,7 @@ async function render(view) {
     const storeUrls = view.model.get('store_urls');
     const invokeTimeout = view.model.get('invoke_timeout');
     const invokeBatched = view.model.get('invoke_batched');
+    const preventScroll = view.model.get('prevent_scroll');
 
     const pageMode = view.model.get('page_mode');
     const pageEsm = view.model.get('page_esm');
@@ -426,7 +425,7 @@ async function render(view) {
         const divRef = React.useRef();
 
         React.useEffect(() => {
-            if(!divRef.current) {
+            if(!divRef.current || !preventScroll) {
                 return () => {};
             }
 
@@ -452,7 +451,7 @@ async function render(view) {
                     divRef.current.removeEventListener("mouseleave", handleMouseLeave);
                 }
             };
-        }, [divRef]);
+        }, [divRef, preventScroll]);
 
         // Config changed on JS side (from within <Vitessce/>),
         // send updated config to Python side.
@@ -602,7 +601,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.2').tag(sync=True)
+    js_package_version = Unicode('3.6.4').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)
@@ -611,10 +610,11 @@ class VitessceWidget(anywidget.AnyWidget):
     page_esm = Unicode('').tag(sync=True)
     invoke_timeout = Int(300000).tag(sync=True)
     invoke_batched = Bool(True).tag(sync=True)
+    prevent_scroll = Bool(True).tag(sync=True)
 
     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='3.6.2', 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):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.4', 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.
 
@@ -634,6 +634,7 @@ class VitessceWidget(anywidget.AnyWidget):
         :param bool invoke_batched: Should invocations (Zarr gets) be submitted in batch, or individually? By default, True.
         :param bool page_mode: Whether to render the <Vitessce/> component in grid-mode or page-mode. By default, False.
         :param str page_esm: The ES module string for the page component creation function. Optional.
+        :param bool prevent_scroll: Should mouseover in the Vitessce widget prevent disable the scrolling of the notebook? By default, True.
 
         .. code-block:: python
             :emphasize-lines: 4
@@ -667,7 +668,7 @@ class VitessceWidget(anywidget.AnyWidget):
             js_package_version=js_package_version, js_dev_mode=js_dev_mode, custom_js_url=custom_js_url,
             plugin_esm=plugin_esm, remount_on_uid_change=remount_on_uid_change,
             page_mode=page_mode, page_esm=('' if page_esm is None else page_esm),
-            invoke_timeout=invoke_timeout, invoke_batched=invoke_batched,
+            invoke_timeout=invoke_timeout, invoke_batched=invoke_batched, prevent_scroll=prevent_scroll,
             uid=uid_str, store_urls=list(self._stores.keys())
         )
 
@@ -749,7 +750,7 @@ 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='3.6.2', 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='3.6.4', 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

@@ -33,6 +33,7 @@ from vitessce.file_def_utils import (
     gen_sdata_obs_spots_schema,
     gen_sdata_obs_sets_schema,
     gen_sdata_obs_feature_matrix_schema,
+    gen_obs_feature_columns_schema,
 )
 
 from .constants import (
@@ -1192,7 +1193,7 @@ def raise_error_if_more_than_one(inputs):
 
 
 class AnnDataWrapper(AbstractWrapper):
-    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, is_zip=None, **kwargs):
+    def __init__(self, adata_path=None, adata_url=None, adata_store=None, adata_artifact=None, ref_path=None, ref_url=None, ref_artifact=None, obs_feature_matrix_path=None, obs_feature_column_paths=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, obs_spots_path=None, obs_points_path=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, is_zip=None, **kwargs):
         """
         Wrap an AnnData object by creating an instance of the ``AnnDataWrapper`` class.
 
@@ -1218,6 +1219,7 @@ class AnnDataWrapper(AbstractWrapper):
         :param str obs_labels_path: (DEPRECATED) The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. Use `obs_labels_paths` and `obs_labels_names` instead. This arg will be removed in a future release.
         :param list[str] obs_labels_paths: The names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
         :param list[str] obs_labels_names: The optional display names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
+        :param list[str] obs_feature_column_paths: The paths to columns (typically in `obs`) that contain numerical values per observation (e.g., cell size, quality control metrics, etc.) which are not part of the main expression matrix.
         :param bool convert_to_dense: Whether or not to convert `X` to dense the zarr store (dense is faster but takes more disk space).
         :param coordination_values: Coordination values for the file definition.
         :param is_zip: Boolean indicating whether the Zarr store is in a zipped format.
@@ -1289,6 +1291,7 @@ class AnnDataWrapper(AbstractWrapper):
         self._spatial_spots_obsm = obs_spots_path
         self._spatial_points_obsm = obs_points_path
         self._feature_labels = feature_labels_path
+        self._obs_feature_column_paths = obs_feature_column_paths
         # Support legacy provision of single obs labels path
         if (obs_labels_path is not None):
             warnings.warn("`obs_labels_path` will be deprecated in a future release.", DeprecationWarning)
@@ -1357,6 +1360,7 @@ class AnnDataWrapper(AbstractWrapper):
             options = gen_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter)
             options = gen_feature_labels_schema(self._feature_labels, options)
             options = gen_obs_labels_schema(options, self._obs_labels_elems, self._obs_labels_names)
+            options = gen_obs_feature_columns_schema(options, self._obs_feature_column_paths)
 
             if len(options.keys()) > 0:
                 if self.is_h5ad:
@@ -1397,7 +1401,7 @@ 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, affine_transformation: Optional[np.ndarray] = None, obs_spots_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", **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, affine_transformation: Optional[np.ndarray] = None, obs_spots_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", coordination_values=None, **kwargs):
         """
         Wrap a SpatialData object.
 
@@ -1444,6 +1448,7 @@ class SpatialDataWrapper(AnnDataWrapper):
         if self._adata_path is not None:
             self.zarr_folder = 'spatialdata.zarr'
         self.obs_type_label = None
+        self._coordination_values = coordination_values
         if self._coordination_values is not None and "obsType" in self._coordination_values:
             self.obs_type_label = self._coordination_values["obsType"]
         self._table_path = table_path

{vitessce-3.6.1.dist-info → vitessce-3.6.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.6.1
+Version: 3.6.3
 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>
@@ -37,28 +37,26 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Multimedia :: Graphics
 Requires-Python: >=3.10
-Requires-Dist: anndata>=0.7.8
 Requires-Dist: black>=21.11b1
-Requires-Dist: jsonschema>=3.2
-Requires-Dist: negspy>=0.2.24
 Requires-Dist: numcodecs<0.16.0,>=0.5.7
 Requires-Dist: numpy>=1.21.2
-Requires-Dist: ome-zarr<0.10.3
 Requires-Dist: pandas>=1.1.2
-Requires-Dist: scanpy>=1.10.2
 Requires-Dist: scipy>=1.2.1
-Requires-Dist: tifffile>=2020.10.1
-Requires-Dist: tqdm>=4.1.0
 Requires-Dist: zarr<3,>=2.5.0
 Provides-Extra: all
 Requires-Dist: aiofiles>=0.6.0; extra == 'all'
+Requires-Dist: anndata>=0.7.8; extra == 'all'
 Requires-Dist: anywidget>=0.9.10; extra == 'all'
 Requires-Dist: fsspec; extra == 'all'
 Requires-Dist: generate-tiff-offsets>=0.1.9; extra == 'all'
 Requires-Dist: jupyter-server-proxy>=1.5.2; extra == 'all'
 Requires-Dist: kerchunk>=0.2.6; extra == 'all'
+Requires-Dist: negspy>=0.2.24; extra == 'all'
+Requires-Dist: ome-zarr<0.10.3; extra == 'all'
 Requires-Dist: oxc-py>=0.1.1; extra == 'all'
+Requires-Dist: scanpy>=1.10.2; extra == 'all'
 Requires-Dist: starlette>=0.14.0; extra == 'all'
+Requires-Dist: tifffile>=2020.10.1; extra == 'all'
 Requires-Dist: ujson>=4.0.1; extra == 'all'
 Requires-Dist: uvicorn>=0.17.0; extra == 'all'
 Provides-Extra: building
@@ -87,6 +85,7 @@ Requires-Dist: dask[dataframe]==2024.11.1; extra == 'notebook'
 Requires-Dist: marimo; extra == 'notebook'
 Requires-Dist: spatialdata>=0.3.0; extra == 'notebook'
 Requires-Dist: starlette>=0.42.0; extra == 'notebook'
+Requires-Dist: tqdm>=4.1.0; extra == 'notebook'
 Provides-Extra: testing
 Description-Content-Type: text/markdown
 

{vitessce-3.6.1.dist-info → vitessce-3.6.3.dist-info}/RECORD

@@ -1,24 +1,24 @@
-vitessce/__init__.py,sha256=03pAJROyDfo6EErBx8Oqb9Emqol1QKQ_9zKhkwuQ36Q,1781
-vitessce/config.py,sha256=vZX4k-kS3zspYVT08PRuLSBeB-tU4GJgbN93z1Ed1iY,81228
+vitessce/__init__.py,sha256=GWGahpQMOGFotQXilRccGT0Bnn3OyoCQUCUphW_DtTI,1632
+vitessce/config.py,sha256=GLiFSYh-ACJvQhrEVu3-nqFj1HtlCF86V_mMDljvwFo,81206
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
 vitessce/constants.py,sha256=nBMH55TcnSavcpvYE-epyx3cJ0iDS31eHsL_1e9qb9M,15360
 vitessce/export.py,sha256=L7j5sVC0nBSqGocFWQyyHImSiAF4IjXhmqV1QtpuNc4,3874
-vitessce/file_def_utils.py,sha256=RM9Hj1uwPY-Y37JLOHiKA_acGY40p8C9WsDk8iVjDz8,6692
+vitessce/file_def_utils.py,sha256=0Q1jxTOBDtvbRJEDX3s80oPr1EYrwkqixjkA5-rzAFM,7028
 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=2ConheUZqGuA2zAPsqKeliDCxegnderWgTxXkStYVNU,33210
-vitessce/wrappers.py,sha256=3ZNldH2uDhOzUl8ahil7GxnPcr0nKwqfrjjbgS2IL0Y,75010
+vitessce/widget.py,sha256=OX9L6mnliYh2j5jQo_BcDYRCgccdYpgJqEOQzybZQ9I,33543
+vitessce/wrappers.py,sha256=garL6KfL5hEqGBQpf3NV_ZsZhaV_-RN1GrCmA1Fc_1I,75557
 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
 vitessce/data_utils/multivec.py,sha256=YVc68uKNdS-ga89GapQjY9lDjmje0dm-MExq1yT_6ZE,11571
-vitessce/data_utils/ome.py,sha256=aK-iGNgjUmUMsWgdZhW78VrtMBKMW_jIQDYnsupq6BE,5436
+vitessce/data_utils/ome.py,sha256=tJHlSHbZTxpjRgYfTxbYMS9zSnSHQwJVWPZpREAvHtU,5518
 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-3.6.1.dist-info/METADATA,sha256=2MqadRVK49A5pj1SgGfpLxJX479mA2FRyxMaj_bp9dQ,9756
-vitessce-3.6.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.6.1.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.6.1.dist-info/RECORD,,
+vitessce-3.6.3.dist-info/METADATA,sha256=P0ImyRQlP8PlT9aJJfVJRMyJG3AvDF7FyYmoR-orMko,9826
+vitessce-3.6.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.6.3.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.6.3.dist-info/RECORD,,