Use alt funcs for reading and writing objects (#3)

setup.cfg

@@ -49,10 +49,10 @@ 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-matrix>=0.1.0
-    dolomite-ranges>=0.1.0
-    summarizedexperiment>=0.4.2,<0.5.0
+    dolomite-base>=0.2.3
+    dolomite-matrix>=0.2.1
+    dolomite-ranges>=0.1.3
+    summarizedexperiment>=0.4.4
 
 
 [options.packages.find]

src/dolomite_se/read_ranged_summarized_experiment.py

@@ -4,11 +4,9 @@
 from dolomite_base.read_object import read_object_registry
 from summarizedexperiment import RangedSummarizedExperiment
 
-from .utils import read_common_se_props
-
-read_object_registry[
-    "ranged_summarized_experiment"
-] = "dolomite_se.read_ranged_summarized_experiment"
+read_object_registry["ranged_summarized_experiment"] = (
+    "dolomite_se.read_ranged_summarized_experiment"
+)
 
 
 def read_ranged_summarized_experiment(
@@ -36,23 +34,19 @@ def read_ranged_summarized_experiment(
         :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`
         with file-backed arrays in the assays.
     """
-
-    _row_data, _column_data, _assays = read_common_se_props(path)
+    metadata["type"] = "summarized_experiment"
+    se = dl.alt_read_object(path, metadata=metadata, **kwargs)
 
     rse = RangedSummarizedExperiment(
-        assays=_assays,
-        row_data=_row_data,
-        column_data=_column_data,
+        assays=se.get_assays(),
+        row_data=se.get_row_data(),
+        column_data=se.get_column_data(),
+        metadata=se.get_metadata(),
     )
 
-    _meta_path = os.path.join(path, "other_data")
-    if os.path.exists(_meta_path):
-        _meta = dl.read_object(_meta_path)
-        rse = rse.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)
+        _ranges = dl.alt_read_object(_ranges_path, **kwargs)
         rse = rse.set_row_ranges(_ranges)
 
     return rse

src/dolomite_se/read_summarized_experiment.py

@@ -43,7 +43,7 @@ def read_summarized_experiment(
 
     _meta_path = os.path.join(path, "other_data")
     if os.path.exists(_meta_path):
-        _meta = dl.read_object(_meta_path)
+        _meta = dl.alt_read_object(_meta_path, **kwargs)
         se = se.set_metadata(_meta.as_dict())
 
     return se

src/dolomite_se/save_ranged_summarized_experiment.py

@@ -1,9 +1,9 @@
 import os
 
 import dolomite_base as dl
-from summarizedexperiment import RangedSummarizedExperiment
+from summarizedexperiment import RangedSummarizedExperiment, SummarizedExperiment
 
-from .utils import save_common_se_props
+# from .utils import save_common_se_props
 
 
 @dl.save_object.register
@@ -40,30 +40,32 @@ def save_ranged_summarized_experiment(
     Returns:
         ``x`` is saved to path.
     """
-    os.mkdir(path)
 
     if data_frame_args is None:
         data_frame_args = {}
 
     if assay_args is None:
         assay_args = {}
 
-    _se_meta = f"{list(x.shape)}"
-
-    with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
-        handle.write(
-            '{ "type": "ranged_summarized_experiment", "ranged_summarized_experiment": { "version": "1.0" },'
-            + '"summarized_experiment": {"version": "1.0", "dimensions": '
-            + _se_meta
-            + " } }"
-        )
-
-    save_common_se_props(
-        x, path, data_frame_args=data_frame_args, assay_args=assay_args
+    # convert to SE
+    _se = SummarizedExperiment(
+        assays=x.get_assays(),
+        row_data=x.get_row_data(),
+        column_data=x.get_column_data(),
+        metadata=x.get_metadata(),
+    )
+    dl.alt_save_object(
+        _se, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs
     )
 
+    # save row_ranges
     _ranges = x.get_row_ranges()
     if _ranges is not None:
-        dl.save_object(_ranges, path=os.path.join(path, "row_ranges"))
+        dl.alt_save_object(_ranges, path=os.path.join(path, "row_ranges"), **kwargs)
+
+    # Modify OBJECT
+    _info = dl.read_object_file(path)
+    _info["ranged_summarized_experiment"] = {"version": "1.0"}
+    dl.save_object_file(path, "ranged_summarized_experiment", _info)
 
     return

src/dolomite_se/save_summarized_experiment.py

@@ -48,16 +48,8 @@ def save_summarized_experiment(
     if assay_args is None:
         assay_args = {}
 
-    _se_meta = f"{list(x.shape)}"
-    with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
-        handle.write(
-            '{ "type": "summarized_experiment", "summarized_experiment": { "version": "1.0", "dimensions": '
-            + _se_meta
-            + " } }"
-        )
-
     save_common_se_props(
-        x, path, data_frame_args=data_frame_args, assay_args=assay_args
+        x, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs
     )
 
     return

src/dolomite_se/utils.py

@@ -4,7 +4,7 @@
 import dolomite_base as dl
 
 
-def save_common_se_props(x, path, data_frame_args, assay_args):
+def save_common_se_props(x, path, data_frame_args, assay_args, **kwargs):
     """Save common :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`
     properties to the specified path.
 
@@ -25,6 +25,10 @@ def save_common_se_props(x, path, data_frame_args, assay_args):
             Further arguments to pass to the ``save_object`` method for the
             assays.
     """
+    # save OBJECT
+    _info = {"summarized_experiment": {"version": "1.0", "dimensions": list(x.shape)}}
+    dl.save_object_file(path, "summarized_experiment", _info)
+
     # save assays
     _assay_names = x.get_assay_names()
     if len(_assay_names) > 0:
@@ -37,7 +41,9 @@ def save_common_se_props(x, path, data_frame_args, assay_args):
         for _aidx, _aname in enumerate(_assay_names):
             _assay_save_path = os.path.join(_assays_path, str(_aidx))
             try:
-                dl.save_object(x.assays[_aname], path=_assay_save_path, **assay_args)
+                dl.alt_save_object(
+                    x.assays[_aname], path=_assay_save_path, **assay_args
+                )
             except Exception as ex:
                 raise RuntimeError(
                     "failed to stage assay '"
@@ -51,21 +57,23 @@ def save_common_se_props(x, path, data_frame_args, assay_args):
     # save row data
     _rdata = x.get_row_data()
     if _rdata is not None and (_rdata.row_names is not None or _rdata.shape[1] > 0):
-        dl.save_object(_rdata, path=os.path.join(path, "row_data"), **data_frame_args)
+        dl.alt_save_object(
+            _rdata, path=os.path.join(path, "row_data"), **data_frame_args
+        )
 
     # save column data
     _cdata = x.get_column_data()
     if _cdata is not None and (_cdata.row_names is not None or _cdata.shape[1] > 0):
-        dl.save_object(
+        dl.alt_save_object(
             _cdata, path=os.path.join(path, "column_data"), **data_frame_args
         )
 
     _meta = x.get_metadata()
     if _meta is not None and len(_meta) > 0:
-        dl.save_object(_meta, path=os.path.join(path, "other_data"))
+        dl.alt_save_object(_meta, path=os.path.join(path, "other_data"), **kwargs)
 
 
-def read_common_se_props(path):
+def read_common_se_props(path, **kwargs):
     """Read shared properties from a directory containing
     :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` or
     its derivatives.
@@ -80,12 +88,12 @@ def read_common_se_props(path):
     _row_data = None
     _rdata_path = os.path.join(path, "row_data")
     if os.path.exists(_rdata_path):
-        _row_data = dl.read_object(_rdata_path)
+        _row_data = dl.alt_read_object(_rdata_path, **kwargs)
 
     _column_data = None
     _cdata_path = os.path.join(path, "column_data")
     if os.path.exists(_cdata_path):
-        _column_data = dl.read_object(_cdata_path)
+        _column_data = dl.alt_read_object(_cdata_path, **kwargs)
 
     _assays = {}
     _assays_path = os.path.join(path, "assays")
@@ -97,7 +105,7 @@ def read_common_se_props(path):
             _assay_read_path = os.path.join(_assays_path, str(_aidx))
 
             try:
-                _assays[_aname] = dl.read_object(_assay_read_path)
+                _assays[_aname] = dl.alt_read_object(_assay_read_path, **kwargs)
             except Exception as ex:
                 raise RuntimeError(
                     f"failed to load assay '{_aname}' from '{path}'; " + str(ex)