Use alt functions to save and read objects. (#2)

Update documentation and bump versions for dependencies

setup.cfg

@@ -49,9 +49,9 @@ python_requires = >=3.8
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite-base>=0.2.0
-    dolomite-se>=0.1.1
-    singlecellexperiment>=0.4.3,<0.5.0
+    dolomite-base>=0.2.4
+    dolomite-se>=0.1.3
+    singlecellexperiment>=0.4.5
 
 
 [options.packages.find]

src/dolomite_sce/read_single_cell_experiment.py

@@ -3,12 +3,11 @@
 
 import dolomite_base as dl
 from dolomite_base.read_object import read_object_registry
-from dolomite_se import read_common_se_props
 from singlecellexperiment import SingleCellExperiment
 
-read_object_registry[
-    "single_cell_experiment"
-] = "dolomite_sce.read_single_cell_experiment"
+read_object_registry["single_cell_experiment"] = (
+    "dolomite_sce.read_single_cell_experiment"
+)
 
 
 def read_single_cell_experiment(
@@ -29,37 +28,30 @@ def read_single_cell_experiment(
             Metadata for the object.
 
         kwargs:
-            Further arguments, ignored.
+            Further arguments.
 
     Returns:
         A
         :py:class:`~singlecellexperiment.SingleCellExperiment.SingleCellExperiment`
         with file-backed arrays in the assays.
     """
 
-    _row_data, _column_data, _assays = read_common_se_props(path)
+    metadata["type"] = "range_summarized_experiment"
+    rse = dl.alt_read_object(path, metadata=metadata, **kwargs)
 
     _main_expt_name = None
     if "main_experiment_name" in metadata["single_cell_experiment"]:
         _main_expt_name = metadata["single_cell_experiment"]["main_experiment_name"]
 
     sce = SingleCellExperiment(
-        assays=_assays,
-        row_data=_row_data,
-        column_data=_column_data,
+        assays=rse.get_assays(),
+        row_data=rse.get_row_data(),
+        column_data=rse.get_column_data(),
+        row_ranges=rse.get_row_ranges(),
+        metadata=rse.get_metadata(),
         main_experiment_name=_main_expt_name,
     )
 
-    _meta_path = os.path.join(path, "other_data")
-    if os.path.exists(_meta_path):
-        _meta = dl.read_object(_meta_path)
-        sce = sce.set_metadata(_meta.as_dict())
-
-    _ranges_path = os.path.join(path, "row_ranges")
-    if os.path.exists(_ranges_path):
-        _ranges = dl.read_object(_ranges_path)
-        sce = sce.set_row_ranges(_ranges)
-
     _rdim_path = os.path.join(path, "reduced_dimensions")
     if os.path.exists(_rdim_path):
         _rdims = {}
@@ -71,7 +63,7 @@ def read_single_cell_experiment(
             _rdim_read_path = os.path.join(_rdim_path, str(_aidx))
 
             try:
-                _rdims[_aname] = dl.read_object(_rdim_read_path)
+                _rdims[_aname] = dl.alt_read_object(_rdim_read_path, **kwargs)
             except Exception as ex:
                 raise RuntimeError(
                     f"failed to load reduced dimension '{_aname}' from '{path}'; "
@@ -91,7 +83,7 @@ def read_single_cell_experiment(
             _alt_read_path = os.path.join(_alt_path, str(_aidx))
 
             try:
-                _alts[_aname] = dl.read_object(_alt_read_path)
+                _alts[_aname] = dl.alt_read_object(_alt_read_path, **kwargs)
             except Exception as ex:
                 raise RuntimeError(
                     f"failed to load alternative experiment '{_aname}' from '{path}'; "

src/dolomite_sce/save_single_cell_experiment.py

@@ -2,8 +2,8 @@
 import os
 
 import dolomite_base as dl
-from dolomite_se import save_common_se_props
 from singlecellexperiment import SingleCellExperiment
+from summarizedexperiment import RangedSummarizedExperiment
 
 
 @dl.save_object.register
@@ -46,13 +46,11 @@ def save_single_cell_experiment(
             alternative experiments.
 
         kwargs:
-            Further arguments, ignored.
+            Further arguments.
 
     Returns:
         ``x`` is saved to path.
     """
-    os.mkdir(path)
-
     if data_frame_args is None:
         data_frame_args = {}
 
@@ -65,34 +63,28 @@ def save_single_cell_experiment(
     if alt_expts_args is None:
         alt_expts_args = {}
 
-    _se_meta = f"{list(x.shape)}"
+    ## 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
+    )
 
-    _sce_meta = '"single_cell_experiment": { "version": "1.0" }'
+    # Modify OBJECT
+    _info = dl.read_object_file(path)
+    _info["single_cell_experiment"] = {"version": "1.0"}
     if x.get_main_experiment_name() is not None:
-        _sce_meta = (
-            '"single_cell_experiment": { "version": "1.0", "main_experiment_name": "'
-            + str(x.get_main_experiment_name())
-            + '" }'
-        )
-
-    with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
-        handle.write(
-            '{ "type": "single_cell_experiment", '
-            + _sce_meta
-            + ", "
-            + '"ranged_summarized_experiment": { "version": "1.0" },'
-            + '"summarized_experiment": {"version": "1.0", "dimensions": '
-            + _se_meta
-            + " } }"
+        _info["single_cell_experiment"]["main_experiment_name"] = str(
+            x.get_main_experiment_name()
         )
-
-    save_common_se_props(
-        x, path, data_frame_args=data_frame_args, assay_args=assay_args
-    )
-
-    _ranges = x.get_row_ranges()
-    if _ranges is not None:
-        dl.save_object(_ranges, path=os.path.join(path, "row_ranges"))
+    dl.save_object_file(path, "single_cell_experiment", _info)
 
     # save rdims
     _rdim_names = x.get_reduced_dim_names()
@@ -106,7 +98,9 @@ def save_single_cell_experiment(
         for _aidx, _aname in enumerate(_rdim_names):
             _rdim_save_path = os.path.join(_rdim_path, str(_aidx))
             try:
-                dl.save_object(x.reduced_dim(_aname), path=_rdim_save_path, **rdim_args)
+                dl.alt_save_object(
+                    x.reduced_dim(_aname), path=_rdim_save_path, **rdim_args, **kwargs
+                )
             except Exception as ex:
                 raise RuntimeError(
                     "failed to stage reduced dimension '"
@@ -129,10 +123,11 @@ def save_single_cell_experiment(
         for _aidx, _aname in enumerate(_alt_names):
             _alt_save_path = os.path.join(_alt_path, str(_aidx))
             try:
-                dl.save_object(
+                dl.alt_save_object(
                     x.alternative_experiment(_aname),
                     path=_alt_save_path,
                     **alt_expts_args,
+                    **kwargs,
                 )
             except Exception as ex:
                 raise RuntimeError(