vitessce 3.5.3__py3-none-any.whl → 3.5.5__py3-none-any.whl

vitessce/config.py

@@ -478,7 +478,7 @@ class VitessceConfigView:
     A class to represent a view (i.e. visualization component) in the Vitessce view config layout.
     """
 
-    def __init__(self, component, coordination_scopes, x, y, w, h):
+    def __init__(self, component, coordination_scopes, x, y, w, h, uid=None):
         """
         Not meant to be instantiated directly, but instead created and returned by the ``VitessceConfig.add_view()`` method.
 
@@ -498,6 +498,8 @@ class VitessceConfigView:
             "w": w,
             "h": h
         }
+        if uid is not None:
+            self.view["uid"] = uid
 
     def _to_py_params(self):
         params_dict = {
@@ -505,7 +507,7 @@ class VitessceConfigView:
             "x": self.view["x"],
             "y": self.view["y"],
             "w": self.view["w"],
-            "h": self.view["h"]
+            "h": self.view["h"],
         }
         # Only include coordination_scopes if there are coordination scopes other than
         # the coorindation scope for the 'dataset' coordination type.
@@ -516,6 +518,8 @@ class VitessceConfigView:
         }
         if len(non_dataset_coordination_scopes) > 0:
             params_dict["coordination_scopes"] = non_dataset_coordination_scopes
+        if "uid" in self.view:
+            params_dict["uid"] = self.view["uid"]
         return params_dict
 
     def get_coordination_scope(self, c_type):
@@ -1018,7 +1022,7 @@ class VitessceConfig:
         """
         return self.config["datasets"]
 
-    def add_view(self, view_type, dataset=None, dataset_uid=None, x=0, y=0, w=1, h=1, mapping=None, coordination_scopes=None, props=None):
+    def add_view(self, view_type, dataset=None, dataset_uid=None, x=0, y=0, w=1, h=1, mapping=None, coordination_scopes=None, props=None, uid=None):
         """
         Add a view to the config.
 
@@ -1086,7 +1090,7 @@ class VitessceConfig:
         if coordination_scopes is not None:
             internal_coordination_scopes.update(coordination_scopes)
         vcv = VitessceConfigView(
-            component_str, internal_coordination_scopes, x, y, w, h)
+            component_str, internal_coordination_scopes, x, y, w, h, uid=uid)
 
         # Use the mapping parameter if component is scatterplot and the mapping is not None
         if mapping is not None:
@@ -1743,7 +1747,9 @@ class VitessceConfig:
                 raise ValueError(
                     "Multiple datasets are present, so every view must have an explicit dataset coordination scope.")
             new_view = VitessceConfigView(
-                c['component'], c_coord_scopes, c['x'], c['y'], c['w'], c['h'])
+                c['component'], c_coord_scopes, c['x'], c['y'], c['w'], c['h'],
+                uid=(c["uid"] if "uid" in c else None)
+            )
             if 'props' in c.keys():
                 new_view.set_props(**c['props'])
             vc.config['layout'].append(new_view)

vitessce/widget.py

@@ -1,6 +1,7 @@
 import importlib.util
 from urllib.parse import quote_plus
 import json
+import sys
 
 # Widget dependencies
 import anywidget
@@ -104,7 +105,8 @@ def get_base_url_and_port(port, next_port, proxy=False, base_url=None, host_name
 
     if base_url is None:
         if proxy:
-            if importlib.util.find_spec('jupyter_server_proxy') is None:
+            is_in_workspaces = sys.executable.startswith('/hive')
+            if importlib.util.find_spec('jupyter_server_proxy') is None and not is_in_workspaces:
                 raise ValueError(
                     "To use the widget through a proxy, jupyter-server-proxy must be installed.")
             if host_name is None:
@@ -161,37 +163,52 @@ const React = await importWithMap("react", importMap);
 const { createRoot } = await importWithMap("react-dom/client", importMap);
 
 const e = React.createElement;
-
+const WORKSPACES_URL_KEYWORD = 'https://workspaces-pt'
 const prefersDark = window.matchMedia && window.matchMedia('(prefers-color-scheme: dark)').matches;
-
 // The jupyter server may be running through a proxy,
 // which means that the client needs to prepend the part of the URL before /proxy/8000 such as
 // https://hub.gke2.mybinder.org/user/vitessce-vitessce-python-swi31vcv/proxy/8000/A/0/cells
+// For workspaces: https://workspaces-pt.hubmapconsortium.org/passthrough/HOSTNAME/PORT/ADDITIONAL_PATH_INFO?QUERY_PARAMS=HELLO_WORLD
 function prependBaseUrl(config, proxy, hasHostName) {
-  if(!proxy || hasHostName) {
-    return config;
-  }
-  const { origin } = new URL(window.location.href);
-  let baseUrl;
-  const jupyterLabConfigEl = document.getElementById('jupyter-config-data');
-
-  if (jupyterLabConfigEl) {
-    // This is jupyter lab
-    baseUrl = JSON.parse(jupyterLabConfigEl.textContent || '').baseUrl;
-  } else {
-    // This is jupyter notebook
-    baseUrl = document.getElementsByTagName('body')[0].getAttribute('data-base-url');
-  }
-  return {
-    ...config,
-    datasets: config.datasets.map(d => ({
-      ...d,
-      files: d.files.map(f => ({
-        ...f,
-        url: `${origin}${baseUrl}${f.url}`,
-      })),
-    })),
-  };
+    if (!proxy || hasHostName) {
+        return config;
+    }
+    const { origin, pathname } = new URL(window.location.href);
+    const isInWorkspaces = origin.startsWith(WORKSPACES_URL_KEYWORD);
+
+    const jupyterLabConfigEl = document.getElementById('jupyter-config-data');
+
+    let baseUrl;
+    if (isInWorkspaces) {
+        const pathSegments = pathname.split('/');
+        const passthroughIndex = pathSegments.indexOf('passthrough');
+        if (passthroughIndex !== -1) {
+            baseUrl = pathSegments.slice(0, passthroughIndex + 2).join('/');
+        }
+    } else if (jupyterLabConfigEl) {
+        // This is jupyter lab
+        baseUrl = JSON.parse(jupyterLabConfigEl.textContent || '').baseUrl;
+    } else {
+        // This is jupyter notebook
+        baseUrl = document.getElementsByTagName('body')[0].getAttribute('data-base-url');
+    }
+    return {
+        ...config,
+        datasets: config.datasets.map(d => ({
+            ...d,
+            files: d.files.map(f => {
+                if (isInWorkspaces && f.url.startsWith('proxy')) {
+                    // When the user is in workspaces, we do not use jupyter_server_proxy.
+                    // Instead, the workspaces infrastructure has its own "passthrough" functionality.
+                    f.url = f.url.replace('proxy', '');
+                }
+                return {
+                    ...f,
+                    url: `${origin}${baseUrl}${f.url}`,
+                };
+            }),
+        })),
+    };
 }
 
 async function render(view) {
@@ -204,6 +221,9 @@ async function render(view) {
     const storeUrls = view.model.get('store_urls');
     const invokeTimeout = view.model.get('invoke_timeout');
 
+    const pageMode = view.model.get('page_mode');
+    const pageEsm = view.model.get('page_esm');
+
     const pkgName = (jsDevMode ? "@vitessce/dev" : "vitessce");
 
     importMap.imports["vitessce"] = (customJsUrl.length > 0
@@ -217,8 +237,10 @@ async function render(view) {
         PluginViewType,
         PluginCoordinationType,
         PluginJointFileType,
+        PluginAsyncFunction,
         z,
         useCoordination,
+        usePageModeView,
         useGridItemSize,
         // TODO: names and function signatures are subject to change for the following functions
         // Reference: https://github.com/keller-mark/use-coordination/issues/37#issuecomment-1946226827
@@ -234,6 +256,7 @@ async function render(view) {
     let pluginCoordinationTypes = [];
     let pluginFileTypes = [];
     let pluginJointFileTypes = [];
+    let pluginAsyncFunctions = [];
 
     let pending = [];
     let batchId = 0;
@@ -318,12 +341,13 @@ async function render(view) {
             const pluginModule = (await import(pluginEsmUrl)).default;
             URL.revokeObjectURL(pluginEsmUrl);
 
-            const pluginsObj = await pluginModule.createPlugins({
+            const pluginDeps = {
                 React,
                 PluginFileType,
                 PluginViewType,
                 PluginCoordinationType,
                 PluginJointFileType,
+                PluginAsyncFunction,
                 z,
                 invokeCommand: invokePluginCommand,
                 useCoordination,
@@ -334,7 +358,8 @@ async function render(view) {
                 useComplexCoordinationSecondary,
                 useCoordinationScopes,
                 useCoordinationScopesBy,
-            });
+            };
+            const pluginsObj = await pluginModule.createPlugins(pluginDeps);
             if(Array.isArray(pluginsObj.pluginViewTypes)) {
                 pluginViewTypes = [...pluginViewTypes, ...pluginsObj.pluginViewTypes];
             }
@@ -347,7 +372,29 @@ async function render(view) {
             if(Array.isArray(pluginsObj.pluginJointFileTypes)) {
                 pluginJointFileTypes = [...pluginJointFileTypes, ...pluginsObj.pluginJointFileTypes];
             }
+            if(Array.isArray(pluginsObj.pluginAsyncFunctions)) {
+                pluginAsyncFunctions = [...pluginAsyncFunctions, ...pluginsObj.pluginAsyncFunctions];
+            }
         } catch(e) {
+            console.error("Error loading plugin ESM or executing createPlugins function.");
+            console.error(e);
+        }
+    }
+
+    let PageComponent;
+    if(pageMode && pageEsm.length > 0) {
+        try {
+            const pageEsmUrl = URL.createObjectURL(new Blob([pageEsm], { type: "text/javascript" }));
+            const pageModule = (await import(pageEsmUrl)).default;
+            URL.revokeObjectURL(pageEsmUrl);
+
+            const pageDeps = {
+                React,
+                usePageModeView,
+            };
+            PageComponent = await pageModule.createPage(pageDeps);
+        } catch(e) {
+            console.error("Error loading page ESM or executing createPage function.")
             console.error(e);
         }
     }
@@ -415,14 +462,17 @@ async function render(view) {
 
         const vitessceProps = {
             height, theme, config, onConfigChange, validateConfig,
-            pluginViewTypes, pluginCoordinationTypes, pluginFileTypes, pluginJointFileTypes,
-            remountOnUidChange, stores,
+            pluginViewTypes, pluginCoordinationTypes,
+            pluginFileTypes,pluginJointFileTypes, pluginAsyncFunctions,
+            remountOnUidChange, stores, pageMode,
         };
 
         return e('div', { ref: divRef, style: { height: height + 'px' } },
             e(React.Suspense, { fallback: e('div', {}, 'Loading...') },
                 e(React.StrictMode, {},
-                    e(Vitessce, vitessceProps)
+                    e(Vitessce, vitessceProps,
+                        (pageMode ? e(PageComponent, {}) : null)
+                    ),
                 ),
             ),
         );
@@ -456,6 +506,7 @@ function createPlugins(utilsForPlugins) {
         PluginViewType,
         PluginCoordinationType,
         PluginJointFileType,
+        PluginAsyncFunction,
         z,
         useCoordination,
         invokeCommand,
@@ -465,11 +516,33 @@ function createPlugins(utilsForPlugins) {
         pluginFileTypes: undefined,
         pluginCoordinationTypes: undefined,
         pluginJointFileTypes: undefined,
+        pluginAsyncFunctions: undefined,
     };
 }
 export default { createPlugins };
 """
 
+DEFAULT_PAGE_ESM = """
+function createPage(utilsForPage) {
+    const {
+        React,
+        usePageModeView,
+    } = utilsForPage;
+
+    function PageComponent(props) {
+        const BiomarkerSelect = usePageModeView('biomarker-select');
+
+        return (
+            <div>
+                <BiomarkerSelect />
+            </div>
+        );
+    }
+    return PageComponent;
+}
+export default { createPage };
+"""
+
 
 class VitesscePlugin:
     """
@@ -514,11 +587,13 @@ class VitessceWidget(anywidget.AnyWidget):
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
     remount_on_uid_change = Bool(True).tag(sync=True)
+    page_mode = Bool(False).tag(sync=True)
+    page_esm = Unicode('').tag(sync=True)
     invoke_timeout = Int(300000).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='3.5.11', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.5.11', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, page_mode=False, page_esm=None):
         """
         Construct a new Vitessce widget.
 
@@ -531,10 +606,12 @@ class VitessceWidget(anywidget.AnyWidget):
         :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[WidgetPlugin] plugins: A list of subclasses of VitesscePlugin. Optional.
+        :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, 30000.
+        :param int invoke_timeout: The timeout in milliseconds for invoking Python functions from JavaScript. By default, 300000.
+        :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.
 
         .. code-block:: python
             :emphasize-lines: 4
@@ -566,7 +643,9 @@ class VitessceWidget(anywidget.AnyWidget):
         super(VitessceWidget, self).__init__(
             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, invoke_timeout=invoke_timeout,
+            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,
             uid=uid_str, store_urls=list(self._stores.keys())
         )
 
@@ -648,7 +727,7 @@ 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='3.5.11', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.5.11', 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)
 
@@ -658,12 +737,17 @@ def ipython_display(config, height=600, theme='auto', base_url=None, host_name=N
     routes = config.get_routes()
     serve_routes(config, routes, use_port)
 
+    plugins = plugins or []
+    plugin_esm = [p.plugin_esm for p in plugins]
+
     model_vals = {
         "uid": uid_str,
         "js_package_version": js_package_version,
         "js_dev_mode": js_dev_mode,
         "custom_js_url": custom_js_url,
         "plugin_esm": plugin_esm,
+        "page_mode": page_mode,
+        "page_esm": ('' if page_esm is None else page_esm),
         "remount_on_uid_change": remount_on_uid_change,
         "invoke_timeout": 30000,
         "proxy": proxy,

vitessce/wrappers.py

@@ -130,10 +130,13 @@ class AbstractWrapper:
     def try_getting_artifact_stores(self):
         artifact_stores = dict()
         for artifact_url, artifact in self.artifacts.items():
-            local_path = artifact._local_filepath
-            if local_path is not None and os.path.isdir(local_path):
-                store = zarr.DirectoryStore(local_path)
-                artifact_stores[artifact_url] = store
+            if hasattr(artifact, "_local_filepath"):
+                # The attribute ._local_filepath is deleted upon running .save()
+                # Reference: https://github.com/laminlabs/lamindb/blob/58ee954c9f363524e2c47b358727f0b921467078/lamindb/models/save.py#L167
+                local_path = artifact._local_filepath
+                if local_path is not None and os.path.isdir(local_path):
+                    store = zarr.DirectoryStore(local_path)
+                    artifact_stores[artifact_url] = store
         return artifact_stores
 
     def get_stores(self, base_url, prefer_local=False):

{vitessce-3.5.3.dist-info → vitessce-3.5.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.5.3
+Version: 3.5.5
 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>
@@ -37,13 +37,13 @@ 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: anndata<0.11.0,>=0.7.8
 Requires-Dist: black>=21.11b1
 Requires-Dist: jsonschema>=3.2
 Requires-Dist: negspy>=0.2.24
-Requires-Dist: numcodecs>=0.5.7
+Requires-Dist: numcodecs<0.16.0,>=0.5.7
 Requires-Dist: numpy>=1.21.2
-Requires-Dist: ome-zarr<9
+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
@@ -200,6 +200,8 @@ or
 vc.display(proxy=True, host_name="http://localhost:8888")
 ```
 
+For more information see the [data location options documentation](https://python-docs.vitessce.io/data_options.html).
+
 ### Ensure that Vitessce and Jupyter are installed in the same environment
 
 With the environment activated, run `pip list` on the command line:

{vitessce-3.5.3.dist-info → vitessce-3.5.5.dist-info}/RECORD

@@ -1,5 +1,5 @@
 vitessce/__init__.py,sha256=03pAJROyDfo6EErBx8Oqb9Emqol1QKQ_9zKhkwuQ36Q,1781
-vitessce/config.py,sha256=OhFbbyx3bSLysZwx2DI_O9fPPck4nPyErxMVTrFeHTs,80985
+vitessce/config.py,sha256=vZX4k-kS3zspYVT08PRuLSBeB-tU4GJgbN93z1Ed1iY,81228
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
 vitessce/constants.py,sha256=NTir8PzJAGX6a5Q3Ike0qy2n75WyFAezMP05PZ4mgWA,15233
 vitessce/export.py,sha256=L7j5sVC0nBSqGocFWQyyHImSiAF4IjXhmqV1QtpuNc4,3874
@@ -7,8 +7,8 @@ vitessce/file_def_utils.py,sha256=RM9Hj1uwPY-Y37JLOHiKA_acGY40p8C9WsDk8iVjDz8,66
 vitessce/repr.py,sha256=qMmefmZ3E-3sRVxeI5q1DTZnfuwbXKiA85eyqk5MCT4,2287
 vitessce/routes.py,sha256=U8T-L-3QCD_tAbPF8LsUlSMhPWNbyzbLNUnxP9Z9s9o,2140
 vitessce/utils.py,sha256=obzjj65qsagu60_yuhGc-0jmHO-BW0Y-bDs0FgrBqLY,981
-vitessce/widget.py,sha256=pLG0IuAnGdbqIVj_JkSY2TCPJH0qQlnvKG7YRmOLrr8,28336
-vitessce/wrappers.py,sha256=6IS8D1zbfi6GM9n_0wgcksTvHCWObKb8wHTQgoeyknU,74386
+vitessce/widget.py,sha256=1NEtcdWNi7zvxaaVApPdcmVWLFdnSAepkP9mhM-MNdg,31848
+vitessce/wrappers.py,sha256=kVqXFcpbuIb8MtZQSB4F7k32JM8bwCgMBrOkcAAhmvc,74676
 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
@@ -17,7 +17,7 @@ vitessce/data_utils/ome.py,sha256=aK-iGNgjUmUMsWgdZhW78VrtMBKMW_jIQDYnsupq6BE,54
 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-3.5.3.dist-info/METADATA,sha256=lgxBkcU4raG3MRzoxm5tjoEE5-WsitmEyPiZVG4jNwM,9415
-vitessce-3.5.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.5.3.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.5.3.dist-info/RECORD,,
+vitessce-3.5.5.dist-info/METADATA,sha256=TxKrmFE7fIgpxR_ipuLnjB3oiw52VsXPqk_oLJnmRu8,9556
+vitessce-3.5.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.5.5.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.5.5.dist-info/RECORD,,