vitessce 3.5.10__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/wrappers.py

@@ -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-3.5.10.dist-info → vitessce-3.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.5.10
+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>

{vitessce-3.5.10.dist-info → vitessce-3.6.0.dist-info}/RECORD

@@ -1,7 +1,7 @@
 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
@@ -9,7 +9,7 @@ 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=TJjpOBCSS9EBd-klEStvd_NCWejHG0QUROmI3b_7lrQ,33146
-vitessce/wrappers.py,sha256=gmHDRc_8u0A0XtDZr64sMsRi2ZStLFadKu0aMwmk9Jo,74649
+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
@@ -18,7 +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-3.5.10.dist-info/METADATA,sha256=HdUfZXntYA19rVpU547wUkw8cjKwDcME5Hx5feP0E7k,9757
-vitessce-3.5.10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.5.10.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.5.10.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,,