remove experimental reembedding support (#2301)

* remove experimental reembedding support

* lint

* lint

* add prepare requirements to requirements-dev

* oops, revert accidental deletion of import

* more test modifications

* remove obsolete unit tests

backend/server/data_anndata/anndata_adaptor.py

@@ -1,20 +1,17 @@
 import warnings
-from datetime import datetime
 
 import anndata
 import numpy as np
 from packaging import version
 from pandas.core.dtypes.dtypes import CategoricalDtype
 from scipy import sparse
-from server_timing import Timing as ServerTiming
 
 import backend.common.compute.diffexp_generic as diffexp_generic
 from backend.common.colors import convert_anndata_category_colors_to_cxg_category_colors
 from backend.common.constants import Axis, MAX_LAYOUTS
 from backend.server.common.corpora import corpora_get_props_from_anndata
-from backend.common.errors import PrepareError, DatasetAccessError, FilterError
+from backend.common.errors import PrepareError, DatasetAccessError
 from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
-from backend.server.compute.scanpy import scanpy_umap
 from backend.server.data_common.data_adaptor import DataAdaptor
 from backend.common.fbs.matrix import encode_matrix_fbs
 
@@ -301,28 +298,6 @@ class AnndataAdaptor(DataAdaptor):
         full_embedding = self.data.obsm[f"X_{ename}"]
         return full_embedding[:, 0:dims]
 
-    def compute_embedding(self, method, obsFilter):
-        if Axis.VAR in obsFilter:
-            raise FilterError("Observation filters may not contain variable conditions")
-        if method != "umap":
-            raise NotImplementedError(f"re-embedding method {method} is not available.")
-        try:
-            shape = self.get_shape()
-            obs_mask = self._axis_filter_to_mask(Axis.OBS, obsFilter["obs"], shape[0])
-        except (KeyError, IndexError):
-            raise FilterError("Error parsing filter")
-        with ServerTiming.time("layout.compute"):
-            X_umap = scanpy_umap(self.data, obs_mask)
-
-        # Server picks reemedding name, which must not collide with any other
-        # embedding name generated by this backend.
-        name = f"reembed:{method}_{datetime.now().isoformat(timespec='milliseconds')}"
-        dims = [f"{name}_0", f"{name}_1"]
-        layout_schema = {"name": name, "type": "float32", "dims": dims}
-        self.schema["layout"]["obs"].append(layout_schema)
-        self.data.obsm[f"X_{name}"] = X_umap
-        return layout_schema
-
     def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
         if top_n is None:
             top_n = self.dataset_config.diffexp__top_n