Use alt functions for readers and writers (#2)

ArtifactDB · May 21, 2024 · c9c2c39 · c9c2c39
1 parent 87af353
commit c9c2c39
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/setup.cfg b/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_sce>=0.1.0
-    dolomite_se>=0.1.0
-    multiassayexperiment>=0.4.2,<0.5.0
+    dolomite_base>=0.2.4
+    dolomite_sce>=0.1.2
+    dolomite_se>=0.1.3
+    multiassayexperiment>=0.4.2
     biocutils
     pandas
     numpy

diff --git a/src/dolomite_mae/read_multi_assay_experiment.py b/src/dolomite_mae/read_multi_assay_experiment.py
@@ -7,9 +7,9 @@
 from dolomite_base.read_object import read_object_registry
 from multiassayexperiment import MultiAssayExperiment
 
-read_object_registry[
-    "multi_sample_dataset"
-] = "dolomite_mae.read_multi_assay_experiment"
+read_object_registry["multi_sample_dataset"] = (
+    "dolomite_mae.read_multi_assay_experiment"
+)
 
 
 def read_multi_assay_experiment(
@@ -30,7 +30,7 @@ def read_multi_assay_experiment(
             Metadata for the object.
 
         kwargs:
-            Further arguments, ignored.
+            Further arguments.
 
     Returns:
         A
@@ -41,7 +41,7 @@ def read_multi_assay_experiment(
     _sample_path = os.path.join(path, "sample_data")
     _sample_data = None
     if os.path.exists(_sample_path):
-        _sample_data = dl.read_object(_sample_path)
+        _sample_data = dl.alt_read_object(_sample_path, **kwargs)
 
     if _sample_data is None:
         raise RuntimeError("Cannot read 'sample_data'.")
@@ -70,7 +70,7 @@ def read_multi_assay_experiment(
                 _expt_read_path = os.path.join(_expts_path, str(_aidx))
 
                 try:
-                    _expts[_aname] = dl.read_object(_expt_read_path)
+                    _expts[_aname] = dl.alt_read_object(_expt_read_path, **kwargs)
                 except Exception as ex:
                     raise RuntimeError(
                         f"failed to load experiment '{_aname}' from '{path}'; "
@@ -95,7 +95,7 @@ def read_multi_assay_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)
         mae = mae.set_metadata(_meta.as_dict())
 
     return mae
diff --git a/src/dolomite_mae/save_multi_assay_experiment.py b/src/dolomite_mae/save_multi_assay_experiment.py
@@ -36,7 +36,8 @@ def save_multi_assay_experiment(
             Further arguments to pass to the ``save_object`` method for the
             assays.
 
-        kwargs: Further arguments, ignored.
+        kwargs: 
+            Further arguments.
 
     Returns:
         ``x`` is saved to path.
@@ -49,14 +50,12 @@ def save_multi_assay_experiment(
     if assay_args is None:
         assay_args = {}
 
-    with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
-        handle.write(
-            '{ "type": "multi_sample_dataset", "multi_sample_dataset": { "version": "1.0" } }'
-        )
+    _info = {"multi_sample_dataset": {"version": "1.0"}}
+    dl.save_object_file(path, "multi_sample_dataset", _info)
 
     # sample/column data
     _sample_path = os.path.join(path, "sample_data")
-    dl.save_object(x.get_column_data(), _sample_path, **data_frame_args)
+    dl.alt_save_object(x.get_column_data(), _sample_path, **data_frame_args, **kwargs)
 
     # save alt expts.
     _expt_names = x.get_experiment_names()
@@ -70,11 +69,12 @@ def save_multi_assay_experiment(
         for _aidx, _aname in enumerate(_expt_names):
             _expt_save_path = os.path.join(_expt_path, str(_aidx))
             try:
-                dl.save_object(
+                dl.alt_save_object(
                     x.experiment(_aname),
                     path=_expt_save_path,
                     data_frame_args=data_frame_args,
                     assay_args=assay_args,
+                    **kwargs,
                 )
             except Exception as ex:
                 raise RuntimeError(
@@ -125,6 +125,6 @@ def save_multi_assay_experiment(
 
     _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)
 
     return