vitessce 3.5.9__py3-none-any.whl → 3.6.0__py3-none-any.whl

vitessce/constants.py

@@ -164,6 +164,7 @@ class FileType(DocEnum):
     ANNDATA_ZARR = "anndata.zarr", "Joint file type for AnnData objects"
     SPATIALDATA_ZARR = "spatialdata.zarr", "Joint file type for SpatialData objects"
     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"
     OBS_LOCATIONS_CSV = 'obsLocations.csv', "File type for obsLocations values stored in a CSV file"
     OBS_LABELS_CSV = 'obsLabels.csv', "File type for obsLabels values stored in a CSV file"

vitessce/responses.py

@@ -0,0 +1,11 @@
+import ujson
+from starlette.responses import JSONResponse
+
+# References:
+# - https://www.starlette.io/responses/#custom-json-serialization
+# - https://github.com/encode/starlette/releases/tag/0.14.1
+
+
+class UJSONResponse(JSONResponse):
+    def render(self, content):
+        return ujson.dumps(content, ensure_ascii=False).encode("utf-8")

vitessce/widget.py

@@ -233,6 +233,7 @@ async function render(view) {
     const remountOnUidChange = view.model.get('remount_on_uid_change');
     const storeUrls = view.model.get('store_urls');
     const invokeTimeout = view.model.get('invoke_timeout');
+    const invokeBatched = view.model.get('invoke_batched');
 
     const pageMode = view.model.get('page_mode');
     const pageEsm = view.model.get('page_esm');
@@ -319,23 +320,25 @@ async function render(view) {
             storeUrl,
             {
                 async get(key) {
-                    return enqueue([storeUrl, key]);
-                    /*
-                    const [data, buffers] = await view.experimental.invoke("_zarr_get", [storeUrl, key], {
-                        signal: AbortSignal.timeout(invokeTimeout),
-                    });
-                    if (!data.success) return undefined;
-
-                    if (key.includes("spatialdata_attrs") && key.endsWith("0") && !ArrayBuffer.isView(buffers[0].buffer)) {
-                        // For some reason, the Zarrita.js UnicodeStringArray does not seem to work with
-                        // ArrayBuffers (throws a TypeError), so here we convert to Uint8Array if needed.
-                        // This error is occurring specifically for the arr.getChunk call within the AnnDataSource._loadString function.
-                        // TODO: figure out a more long-term solution.
-                        return new Uint8Array(buffers[0].buffer);
-                    }
+                    if (invokeBatched) {
+                        return enqueue([storeUrl, key]);
+                    } else {
+                        // Do not submit zarr gets in batches. Instead, submit individually.
+                        const [data, buffers] = await view.experimental.invoke("_zarr_get", [storeUrl, key], {
+                            signal: AbortSignal.timeout(invokeTimeout),
+                        });
+                        if (!data.success) return undefined;
+
+                        if (key.includes("spatialdata_attrs") && key.endsWith("0") && !ArrayBuffer.isView(buffers[0].buffer)) {
+                            // For some reason, the Zarrita.js UnicodeStringArray does not seem to work with
+                            // ArrayBuffers (throws a TypeError), so here we convert to Uint8Array if needed.
+                            // This error is occurring specifically for the arr.getChunk call within the AnnDataSource._loadString function.
+                            // TODO: figure out a more long-term solution.
+                            return new Uint8Array(buffers[0].buffer);
+                        }
 
-                    return buffers[0].buffer;
-                    */
+                        return buffers[0].buffer;
+                    }
                 },
             }
         ])),
@@ -413,7 +416,7 @@ async function render(view) {
     }
 
     function VitessceWidget(props) {
-        const { model } = props;
+        const { model, styleContainer } = props;
 
         const [config, setConfig] = React.useState(prependBaseUrl(model.get('config'), model.get('proxy'), model.get('has_host_name')));
         const [validateConfig, setValidateConfig] = React.useState(true);
@@ -477,7 +480,7 @@ async function render(view) {
             height, theme, config, onConfigChange, validateConfig,
             pluginViewTypes, pluginCoordinationTypes,
             pluginFileTypes,pluginJointFileTypes, pluginAsyncFunctions,
-            remountOnUidChange, stores, pageMode,
+            remountOnUidChange, stores, pageMode, styleContainer,
         };
 
         return e('div', { ref: divRef, style: { height: height + 'px' } },
@@ -492,7 +495,10 @@ async function render(view) {
     }
 
     const root = createRoot(view.el);
-    root.render(e(VitessceWidget, { model: view.model }));
+    // Marimo puts AnyWidgets in a Shadow Root, so we need to tell Emotion to
+    // insert styles within the Shadow DOM.
+    const styleContainer = view.el.getRootNode();
+    root.render(e(VitessceWidget, { model: view.model, styleContainer }));
 
     return () => {
         // Re-enable scrolling.
@@ -603,10 +609,11 @@ class VitessceWidget(anywidget.AnyWidget):
     page_mode = Bool(False).tag(sync=True)
     page_esm = Unicode('').tag(sync=True)
     invoke_timeout = Int(300000).tag(sync=True)
+    invoke_batched = 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='3.5.12', 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):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.5.12', 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):
         """
         Construct a new Vitessce widget.
 
@@ -623,6 +630,7 @@ class VitessceWidget(anywidget.AnyWidget):
         :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.
 
@@ -658,7 +666,7 @@ 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_timeout=invoke_timeout, invoke_batched=invoke_batched,
             uid=uid_str, store_urls=list(self._stores.keys())
         )
 
@@ -763,6 +771,7 @@ def ipython_display(config, height=600, theme='auto', base_url=None, host_name=N
         "page_esm": ('' if page_esm is None else page_esm),
         "remount_on_uid_change": remount_on_uid_change,
         "invoke_timeout": 30000,
+        "invoke_batched": False,
         "proxy": proxy,
         "has_host_name": host_name is not None,
         "height": height,

vitessce/wrappers.py

@@ -390,8 +390,8 @@ class OmeTiffWrapper(AbstractWrapper):
         else:
             # TODO: Move imports back to top when this is factored out.
             from .routes import range_repsonse, JsonRoute, FileRoute
+            from .responses import UJSONResponse
             from generate_tiff_offsets import get_offsets
-            from starlette.responses import UJSONResponse
 
             offsets = get_offsets(self._img_path)
 
@@ -533,8 +533,8 @@ class ImageOmeTiffWrapper(AbstractWrapper):
         else:
             # TODO: Move imports back to top when this is factored out.
             from .routes import range_repsonse, JsonRoute, FileRoute
+            from .responses import UJSONResponse
             from generate_tiff_offsets import get_offsets
-            from starlette.responses import UJSONResponse
 
             offsets = get_offsets(self._img_path)
 
@@ -666,8 +666,8 @@ class ObsSegmentationsOmeTiffWrapper(AbstractWrapper):
         else:
             # TODO: Move imports back to top when this is factored out.
             from .routes import range_repsonse, JsonRoute, FileRoute
+            from .responses import UJSONResponse
             from generate_tiff_offsets import get_offsets
-            from starlette.responses import UJSONResponse
 
             offsets = get_offsets(self._img_path)
 
@@ -1192,7 +1192,7 @@ 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, **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, 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.
 
@@ -1220,6 +1220,7 @@ class AnnDataWrapper(AbstractWrapper):
         :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 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.
         :type coordination_values: dict or None
         :param \\*\\*kwargs: Keyword arguments inherited from :class:`~vitessce.wrappers.AbstractWrapper`
         """
@@ -1229,6 +1230,7 @@ class AnnDataWrapper(AbstractWrapper):
         self._adata_url = adata_url
         self._adata_store = adata_store
         self._adata_artifact = adata_artifact
+        self.is_zip = is_zip
 
         # For reference spec JSON with .h5ad files
         self._ref_path = ref_path
@@ -1250,11 +1252,14 @@ class AnnDataWrapper(AbstractWrapper):
             self.is_remote = False
             self.is_store = False
             self.zarr_folder = 'anndata.zarr'
+            if is_zip is None and '.zip' in str(adata_path):
+                self.is_zip = True
         elif adata_url is not None or adata_artifact is not None:
             self.is_remote = True
             self.is_store = False
             self.zarr_folder = None
-
+            if is_zip is None and '.zip' in str(adata_url):
+                self.is_zip = True
             # Store artifacts on AbstractWrapper.artifacts for downstream access,
             # e.g. in lamindb.save_vitessce_config
             if adata_artifact is not None:
@@ -1356,9 +1361,8 @@ class AnnDataWrapper(AbstractWrapper):
             if len(options.keys()) > 0:
                 if self.is_h5ad:
                     options["refSpecUrl"] = self.get_ref_url(base_url, dataset_uid, obj_i)
-
                 obj_file_def = {
-                    "fileType": ft.ANNDATA_ZARR.value if not self.is_h5ad else ft.ANNDATA_H5AD.value,
+                    "fileType": ft.ANNDATA_ZARR_ZIP.value if self.is_zip else ft.ANNDATA_H5AD.value if self.is_h5ad else ft.ANNDATA_ZARR.value,
                     "url": self.get_zarr_url(base_url, dataset_uid, obj_i) if not self.is_h5ad else self.get_h5ad_url(base_url, dataset_uid, obj_i),
                     "options": options
                 }

{vitessce-3.5.9.dist-info → vitessce-3.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.5.9
+Version: 3.6.0
 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>
@@ -37,7 +37,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Multimedia :: Graphics
 Requires-Python: >=3.10
-Requires-Dist: anndata<0.11.0,>=0.7.8
+Requires-Dist: anndata>=0.7.8
 Requires-Dist: black>=21.11b1
 Requires-Dist: jsonschema>=3.2
 Requires-Dist: negspy>=0.2.24
@@ -58,7 +58,7 @@ 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: oxc-py>=0.1.1; extra == 'all'
-Requires-Dist: starlette==0.14.0; extra == 'all'
+Requires-Dist: starlette>=0.14.0; extra == 'all'
 Requires-Dist: ujson>=4.0.1; extra == 'all'
 Requires-Dist: uvicorn>=0.17.0; extra == 'all'
 Provides-Extra: building
@@ -68,9 +68,9 @@ Requires-Dist: pyyaml; extra == 'demos'
 Requires-Dist: snakemake; extra == 'demos'
 Provides-Extra: dev
 Provides-Extra: docs
-Requires-Dist: jinja2==3.0.3; extra == 'docs'
+Requires-Dist: jinja2; extra == 'docs'
 Requires-Dist: nbclean==0.3.2; extra == 'docs'
-Requires-Dist: nbconvert==5.6.1; extra == 'docs'
+Requires-Dist: nbconvert>=6.2; extra == 'docs'
 Requires-Dist: nbsphinx==0.8.8; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme==1.0.0; extra == 'docs'
 Requires-Dist: sphinx==4.2.0; extra == 'docs'
@@ -83,6 +83,10 @@ Requires-Dist: sphinxcontrib-serializinghtml==1.1.5; extra == 'docs'
 Requires-Dist: sqlalchemy==1.3.24; extra == 'docs'
 Provides-Extra: linting
 Provides-Extra: notebook
+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'
 Provides-Extra: testing
 Description-Content-Type: text/markdown
 

{vitessce-3.5.9.dist-info → vitessce-3.6.0.dist-info}/RECORD

@@ -1,14 +1,15 @@
 vitessce/__init__.py,sha256=03pAJROyDfo6EErBx8Oqb9Emqol1QKQ_9zKhkwuQ36Q,1781
 vitessce/config.py,sha256=vZX4k-kS3zspYVT08PRuLSBeB-tU4GJgbN93z1Ed1iY,81228
 vitessce/config_converter.py,sha256=IRPnGPGaETvJbYZNUv2pe54SHHHsDY9VWo3JRjSI5FM,14681
-vitessce/constants.py,sha256=NTir8PzJAGX6a5Q3Ike0qy2n75WyFAezMP05PZ4mgWA,15233
+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/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=-8zK7h3AeFU8VWncuPWR2vAA8StHWYNjbrwVm5ld03w,32418
-vitessce/wrappers.py,sha256=kVqXFcpbuIb8MtZQSB4F7k32JM8bwCgMBrOkcAAhmvc,74676
+vitessce/widget.py,sha256=TJjpOBCSS9EBd-klEStvd_NCWejHG0QUROmI3b_7lrQ,33146
+vitessce/wrappers.py,sha256=3ZNldH2uDhOzUl8ahil7GxnPcr0nKwqfrjjbgS2IL0Y,75010
 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 +18,7 @@ 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-3.5.9.dist-info/METADATA,sha256=g_LIqo1wtjJamdEcoUuyv7di45t_X0MhleRnSianTTQ,9558
-vitessce-3.5.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.5.9.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.5.9.dist-info/RECORD,,
+vitessce-3.6.0.dist-info/METADATA,sha256=LHEQzRra80wKjvCJnln_yQMvmULNcZsbsohcmaUlKL0,9756
+vitessce-3.6.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.6.0.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.6.0.dist-info/RECORD,,