vitessce 3.6.9__tar.gz → 3.7.1__tar.gz

{vitessce-3.6.9 → vitessce-3.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.6.9
+Version: 3.7.1
 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-3.6.9 → vitessce-3.7.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.6.9"
+version = "3.7.1"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]

{vitessce-3.6.9 → vitessce-3.7.1}/src/vitessce/config.py

@@ -925,6 +925,19 @@ class VitessceConfig:
             del self.background_servers[port]
 
     def stop_all_servers(self):
+        """
+        Stop all background servers associated with this config instance.
+
+        .. code-block:: python
+            :emphasize-lines: 5
+
+            from vitessce import VitessceConfig
+
+            vc = VitessceConfig(schema_version="1.0.18", name='My Config')
+            vw = vc.widget()
+            # ... do something with the widget ...
+            vc.stop_all_servers()
+        """
         for server in self.background_servers.values():
             server.stop()
         self.background_servers = {}
@@ -1791,6 +1804,17 @@ class VitessceConfig:
         :param int height: The height of the widget, in pixels. By default, 600.
         :param int port: The port to use when serving data objects on localhost. By default, 8000.
         :param bool proxy: Is this widget being served through a proxy, for example with a cloud notebook (e.g. Binder)?
+        :param str js_package_version: The version of the NPM package ('vitessce' if not js_dev_mode else '@vitessce/dev').
+        :param bool js_dev_mode: Should @vitessce/dev be used (typically for debugging purposes)? By default, False.
+        :param str custom_js_url: A URL to a JavaScript file to use (instead of 'vitessce' or '@vitessce/dev' NPM package).
+        :param list[VitesscePlugin] plugins: A list of subclasses of VitesscePlugin. Optional.
+        :param bool remount_on_uid_change: Passed to the remountOnUidChange prop of the <Vitessce/> React component. By default, True.
+        :param bool prefer_local: Should local data be preferred (only applies to `*_artifact` data objects)? By default, True.
+        :param int invoke_timeout: The timeout in milliseconds for invoking Python functions from JavaScript. By default, 300000.
+        :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.
 
         :returns: The Jupyter widget.
         :rtype: VitessceWidget

{vitessce-3.6.9 → vitessce-3.7.1}/src/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-3.6.9 → vitessce-3.7.1}/src/vitessce/widget.py

@@ -445,7 +445,7 @@ async function render(view) {
     function VitessceWidget(props) {
         const { model, styleContainer } = props;
 
-        const [config, setConfig] = React.useState(prependBaseUrl(model.get('config'), model.get('proxy'), model.get('has_host_name')));
+        const [config, setConfig] = React.useState(prependBaseUrl(model.get('_config'), model.get('proxy'), model.get('has_host_name')));
         const [validateConfig, setValidateConfig] = React.useState(true);
         const height = model.get('height');
         const theme = model.get('theme') === 'auto' ? (prefersDark ? 'dark' : 'light') : model.get('theme');
@@ -484,7 +484,7 @@ async function render(view) {
         // Config changed on JS side (from within <Vitessce/>),
         // send updated config to Python side.
         const onConfigChange = React.useCallback((config) => {
-            model.set('config', config);
+            model.set('_config', config);
             setValidateConfig(false);
             model.save_changes();
         }, [model]);
@@ -492,8 +492,8 @@ async function render(view) {
         // Config changed on Python side,
         // pass to <Vitessce/> component to it is updated on JS side.
         React.useEffect(() => {
-            model.on('change:config', () => {
-                const newConfig = prependBaseUrl(model.get('config'), model.get('proxy'), model.get('has_host_name'));
+            model.on('change:_config', () => {
+                const newConfig = prependBaseUrl(model.get('_config'), model.get('proxy'), model.get('has_host_name'));
 
                 // Force a re-render and re-validation by setting a new config.uid value.
                 // TODO: make this conditional on a parameter from Python.
@@ -597,8 +597,12 @@ class VitesscePlugin:
     """
     A class that represents a Vitessce widget plugin. Custom plugins can be created by subclassing this class.
     """
-    plugin_esm = DEFAULT_PLUGIN_ESM
-    commands = {}
+
+    #: The ES module string for the plugin.
+    plugin_esm = DEFAULT_PLUGIN_ESM  # type: str
+
+    #: A dictionary mapping command name strings to functions. Functions should take two arguments (message, buffers) and return a tuple (response, buffers).
+    commands = {}  # type: dict
 
     def on_config_change(self, new_config):
         """
@@ -614,7 +618,16 @@ class VitesscePlugin:
 
 class VitessceWidget(anywidget.AnyWidget):
     """
-    A class to represent a Jupyter widget for Vitessce.
+    A class to represent a Jupyter widget for Vitessce. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
+
+    .. code-block:: python
+        :emphasize-lines: 4
+
+        from vitessce import VitessceConfig
+
+        vc = VitessceConfig.from_object(my_scanpy_object)
+        vw = vc.widget()
+        vw
     """
     _esm = ESM
 
@@ -622,7 +635,13 @@ class VitessceWidget(anywidget.AnyWidget):
     # Widget properties are defined as traitlets. Any property tagged with `sync=True`
     # is automatically synced to the frontend *any* time it changes in Python.
     # It is synced back to Python from the frontend *any* time the model is touched.
-    config = Dict({}).tag(sync=True)
+
+    #: Dictionary representation of the Vitessce JSON configuration. Synced via traitlets upon interactions.
+    _config = Dict({}).tag(sync=True)  # type: dict
+
+    #: The VitessceConfig instance used to create this widget. Not synced upon interactions.
+    config = None  # type: vitessce.config.VitessceConfig
+
     height = Int(600).tag(sync=True)
     theme = Unicode('auto').tag(sync=True)
     proxy = Bool(False).tag(sync=True)
@@ -631,7 +650,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.11').tag(sync=True)
+    js_package_version = Unicode('3.6.13').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)
@@ -644,9 +663,9 @@ 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='3.6.11', 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='3.6.13', 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.
+        Construct a new Vitessce widget. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
         :param config: A view config instance.
         :type config: VitessceConfig
@@ -666,19 +685,16 @@ class VitessceWidget(anywidget.AnyWidget):
         :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
-
-            from vitessce import VitessceConfig, VitessceWidget
-
-            vc = VitessceConfig.from_object(my_scanpy_object)
-            vw = vc.widget()
-            vw
+        Note: these parameter docstrings need to be manually kept in sync with the VitessceConfig.widget docstring.
         """
 
         base_url, use_port, VitessceWidget.next_port = get_base_url_and_port(
             port, VitessceWidget.next_port, proxy=proxy)
-        self.config_obj = config
+        # Note:
+        # - self.config is the VitessceConfig instance.
+        # - self._config is the JSON configuration, synced via traitlets
+
+        self.config = config
         self.port = use_port
         config_dict = config.to_dict(base_url=base_url)
         routes = config.get_routes()
@@ -694,7 +710,7 @@ class VitessceWidget(anywidget.AnyWidget):
         uid_str = get_uid_str(uid)
 
         super(VitessceWidget, self).__init__(
-            config=config_dict, height=height, theme=theme, proxy=proxy,
+            _config=config_dict, height=height, theme=theme, proxy=proxy,
             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),
@@ -712,14 +728,14 @@ class VitessceWidget(anywidget.AnyWidget):
                     # It is optional for plugins to implement on_config_change.
                     pass
             if new_config is not None:
-                self.config = new_config
+                self._config = new_config
 
-        self.observe(handle_config_change, names=['config'])
+        self.observe(handle_config_change, names=['_config'])
 
         serve_routes(config, routes, use_port)
 
     def _get_coordination_value(self, coordination_type, coordination_scope):
-        obj = self.config['coordinationSpace'][coordination_type]
+        obj = self._config['coordinationSpace'][coordination_type]
         obj_scopes = list(obj.keys())
         if coordination_scope is not None:
             if coordination_scope in obj_scopes:
@@ -742,7 +758,7 @@ class VitessceWidget(anywidget.AnyWidget):
         return self._get_coordination_value('cellSelection', scope)
 
     def close(self):
-        self.config_obj.stop_server(self.port)
+        self.config.stop_server(self.port)
         super().close()
 
     @anywidget.experimental.command
@@ -780,7 +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='3.6.11', 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='3.6.13', 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)
 
@@ -808,7 +824,7 @@ def ipython_display(config, height=600, theme='auto', base_url=None, host_name=N
         "has_host_name": host_name is not None,
         "height": height,
         "theme": theme,
-        "config": config_dict,
+        "_config": config_dict,
         "store_urls": [],
     }
 

{vitessce-3.6.9 → vitessce-3.7.1}/src/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-3.6.9 → vitessce-3.7.1}/uv.lock

@@ -1,5 +1,5 @@
 version = 1
-revision = 2
+revision = 3
 requires-python = ">=3.10"
 resolution-markers = [
     "python_full_version < '3.11'",
@@ -4496,7 +4496,7 @@ wheels = [
 
 [[package]]
 name = "vitessce"
-version = "3.6.9"
+version = "3.7.1"
 source = { editable = "." }
 dependencies = [
     { name = "black" },