vitessce 3.7.3__tar.gz → 3.7.5__tar.gz

{vitessce-3.7.3 → vitessce-3.7.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.7.3
+Version: 3.7.5
 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-3.7.3 → vitessce-3.7.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.7.3"
+version = "3.7.5"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

{vitessce-3.7.3 → vitessce-3.7.5}/src/vitessce/config.py

@@ -1815,6 +1815,7 @@ class VitessceConfig:
         :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.
+        :param str server_host: The host to which the Uvicorn server should bind. Specify "0.0.0.0" to bind to all interfaces. By default, "127.0.0.1".
 
         :returns: The Jupyter widget.
         :rtype: VitessceWidget

{vitessce-3.7.3 → vitessce-3.7.5}/src/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-3.7.3 → vitessce-3.7.5}/src/vitessce/widget.py

@@ -40,7 +40,7 @@ class BackgroundServer:
             self.thread = None
         return self
 
-    def start(self, port=None, timeout=1, daemon=True, log_level="warning"):
+    def start(self, port=None, host=None, timeout=1, daemon=True, log_level="warning"):
         from uvicorn import Config, Server
         from threading import Thread
 
@@ -50,6 +50,7 @@ class BackgroundServer:
         config = Config(
             app=self.app,
             port=port,
+            host=(host if host is not None else "127.0.0.1"),
             timeout_keep_alive=timeout,
             log_level=log_level
         )
@@ -117,15 +118,15 @@ def get_base_url_and_port(port, next_port, proxy=False, base_url=None, host_name
     return base_url, use_port, next_port
 
 
-def serve_routes(config, routes, use_port):
+def serve_routes(config, routes, use_port, server_host):
     if not config.has_server(use_port) and len(routes) > 0:
         server = BackgroundServer(routes)
         config.register_server(use_port, server)
         data_server.register(config)
-        server.start(port=use_port)
+        server.start(port=use_port, host=server_host)
 
 
-def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_name=None, proxy=False, open=True):
+def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_name=None, proxy=False, open=True, server_host=None):
     import webbrowser
     base_url, use_port, _ = get_base_url_and_port(
         port, DEFAULT_PORT, proxy=proxy, base_url=base_url, host_name=host_name)
@@ -136,7 +137,7 @@ def launch_vitessce_io(config, theme='light', port=None, base_url=None, host_nam
     if len(stores) > 0:
         raise ValueError('One or more files in this configuration have been provided via Zarr store, which can only be loaded via the widget. Either use VitessceConfig.widget or VitessceConfig.display (instead of .web_app), or provide the files via _path or _url (rather than _store) parameters.')
 
-    serve_routes(config, routes, use_port)
+    serve_routes(config, routes, use_port, server_host)
     vitessce_url = f"http://vitessce.io/#?theme={theme}&url=data:," + quote_plus(
         json.dumps(config_dict))
     if open:
@@ -650,7 +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)
@@ -663,7 +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):
+    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``.
 
@@ -684,6 +685,7 @@ class VitessceWidget(anywidget.AnyWidget):
         :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.
+        :param str server_host: The host to which the Uvicorn server should bind. Specify "0.0.0.0" to bind to all interfaces. By default, "127.0.0.1".
 
         Note: these parameter docstrings need to be manually kept in sync with the VitessceConfig.widget docstring.
         """
@@ -732,7 +734,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
         self.observe(handle_config_change, names=['_config'])
 
-        serve_routes(config, routes, use_port)
+        serve_routes(config, routes, use_port, server_host)
 
     def _get_coordination_value(self, coordination_type, coordination_scope):
         obj = self._config['coordinationSpace'][coordination_type]
@@ -796,7 +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):
+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)
 
@@ -804,7 +806,7 @@ def ipython_display(config, height=600, theme='auto', base_url=None, host_name=N
         port, DEFAULT_PORT, proxy=proxy, base_url=base_url, host_name=host_name)
     config_dict = config.to_dict(base_url=base_url)
     routes = config.get_routes()
-    serve_routes(config, routes, use_port)
+    serve_routes(config, routes, use_port, server_host)
 
     plugins = plugins or []
     plugin_esm = [p.plugin_esm for p in plugins]

{vitessce-3.7.3 → vitessce-3.7.5}/src/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,
@@ -1399,7 +1400,7 @@ 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 +1423,8 @@ 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 +1454,7 @@ 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 +1542,7 @@ 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-3.7.3 → vitessce-3.7.5}/uv.lock

@@ -4496,7 +4496,7 @@ wheels = [
 
 [[package]]
 name = "vitessce"
-version = "3.7.3"
+version = "3.7.5"
 source = { editable = "." }
 dependencies = [
     { name = "black" },