From a7ed25d734edab5dd8e9fa2a425c47ad108700b4 Mon Sep 17 00:00:00 2001
From: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: Wed, 23 Oct 2024 09:35:29 -0700
Subject: [PATCH] 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 3960958b1338cbfe2501c889df43c1a25132e2a0.
---
 setup.cfg                                       |  4 ++--
 src/dolomite_sce/read_single_cell_experiment.py |  5 +++--
 src/dolomite_sce/save_single_cell_experiment.py | 16 ++++------------
 3 files changed, 9 insertions(+), 16 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index bda99a7..9c9c331 100644
--- a/setup.cfg
+++ b/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
 
 
diff --git a/src/dolomite_sce/read_single_cell_experiment.py b/src/dolomite_sce/read_single_cell_experiment.py
index 87cdda1..4e5857d 100644
--- a/src/dolomite_sce/read_single_cell_experiment.py
+++ b/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"]:
diff --git a/src/dolomite_sce/save_single_cell_experiment.py b/src/dolomite_sce/save_single_cell_experiment.py
index 746d337..4e8981c 100644
--- a/src/dolomite_sce/save_single_cell_experiment.py
+++ b/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