Don't use alt functions to read and save the base SE class. (#3)

* Don't use alt functions to read and save objects.

This is simpler and avoids repeated calls to the override when traversing down
the SCE class hierarchy via save_object() and read_object().

This reverts commit 3960958.

setup.cfg

@@ -49,8 +49,8 @@ python_requires = >=3.8
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite-base>=0.2.4
-    dolomite-se>=0.1.3
+    dolomite-base>=0.3.0
+    dolomite-se>=0.2.0
     singlecellexperiment>=0.4.5
 
 

src/dolomite_sce/read_single_cell_experiment.py

@@ -2,6 +2,7 @@
 import os
 
 import dolomite_base as dl
+import dolomite_se as dlse
 from dolomite_base.read_object import read_object_registry
 from singlecellexperiment import SingleCellExperiment
 
@@ -36,8 +37,8 @@ def read_single_cell_experiment(
         with file-backed arrays in the assays.
     """
 
-    metadata["type"] = "range_summarized_experiment"
-    rse = dl.alt_read_object(path, metadata=metadata, **kwargs)
+    # see comments in read_ranged_summarized_experiment in dolomite_se.
+    rse = dlse.read_ranged_summarized_experiment(path, metadata=metadata, **kwargs)
 
     _main_expt_name = None
     if "main_experiment_name" in metadata["single_cell_experiment"]:

src/dolomite_sce/save_single_cell_experiment.py

@@ -2,6 +2,7 @@
 import os
 
 import dolomite_base as dl
+import dolomite_se as dlse
 from singlecellexperiment import SingleCellExperiment
 from summarizedexperiment import RangedSummarizedExperiment
 
@@ -63,18 +64,9 @@ def save_single_cell_experiment(
     if alt_expts_args is None:
         alt_expts_args = {}
 
-    ## Convert to RSE
-    _rse = RangedSummarizedExperiment(
-        assays=x.get_assays(),
-        row_data=x.get_row_data(),
-        column_data=x.get_column_data(),
-        row_ranges=x.get_row_ranges(),
-        row_names=x.get_row_names(),
-        column_names=x.get_column_names(),
-        metadata=x.get_metadata(),
-    )
-    dl.alt_save_object(
-        _rse, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs
+    # see comments in save_ranged_summarized_experiment in dolomite_se.
+    dlse.save_ranged_summarized_experiment(
+        x, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs
     )
 
     # Modify OBJECT