Merge branch 'rewrite' of https://github.com/BiocPy/rds2py into rewrite

src/rds2py/generics.py

@@ -37,7 +37,6 @@
     "RangedSummarizedExperiment": "rds2py.parse_ranged_summarized_experiment",
     # single-cell experiment
     "SingleCellExperiment": "rds2py.parse_single_cell_experiment",
-
 }
 
 

src/rds2py/read_sce.py

@@ -7,8 +7,7 @@
 
 
 def parse_single_cell_experiment(robject: dict):
-    """Parse an R object as
-    :py:class:`~singlecellexperiment.SingleCellExperiment.SingleCellExperiment`.
+    """Parse an R object as :py:class:`~singlecellexperiment.SingleCellExperiment.SingleCellExperiment`.
 
     Args:
         robject:
@@ -24,7 +23,9 @@ def parse_single_cell_experiment(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["SingleCellExperiment"]:
-        raise RuntimeError(f"`robject` does not contain a 'SingleCellExperiment' object, contains `{_cls}`.")
+        raise RuntimeError(
+            f"`robject` does not contain a 'SingleCellExperiment' object, contains `{_cls}`."
+        )
 
     robject["class_name"] = "RangedSummarizedExperiment"
     _rse = _dispatcher(robject)
@@ -36,21 +37,31 @@ def parse_single_cell_experiment(robject: dict):
 
     for idx in range(len(col_attrs)):
         idx_col = col_attrs[idx]
-        idx_value = robject["attributes"]["int_colData"]["attributes"]["listData"]["data"][idx]
+        idx_value = robject["attributes"]["int_colData"]["attributes"]["listData"][
+            "data"
+        ][idx]
 
         if idx_col == "reducedDims" and idx_value["data"] is not None:
             robj_reduced_dims = _dispatcher(idx_value)
 
         if idx_col == "altExps":
-            alt_names = idx_value["attributes"]["listData"]["attributes"]["names"]["data"]
+            alt_names = idx_value["attributes"]["listData"]["attributes"]["names"][
+                "data"
+            ]
             robj_altExps = {}
             for idx_alt_names in range(len(alt_names)):
                 altn = alt_names[idx_alt_names]
 
-                alt_key = list(idx_value["attributes"]["listData"]["data"][idx_alt_names]["attributes"].keys())[0]
+                alt_key = list(
+                    idx_value["attributes"]["listData"]["data"][idx_alt_names][
+                        "attributes"
+                    ].keys()
+                )[0]
 
                 robj_altExps[altn] = _dispatcher(
-                    idx_value["attributes"]["listData"]["data"][idx_alt_names]["attributes"][alt_key]
+                    idx_value["attributes"]["listData"]["data"][idx_alt_names][
+                        "attributes"
+                    ][alt_key]
                 )
 
         # ignore colpairs for now, does anyone even use this ?

test.json

@@ -1,2 +1,2 @@
 {'type': 'S4', 'package_name': 'SummarizedExperiment', 'class_name': 'SummarizedExperiment', 'attributes': {'colData': {'type': 'S4', 'package_name': 'S4Vectors', 'class_name': 'DFrame', 'attributes': {'rownames': {'type': 'string', 'data': ['A', 'B', 'C', 'D', 'E', 'F'], 'class_name': 'string_vector'}, 'nrows': {'type': 'integer', 'data': array([6], dtype=int32), 'attributes': {}, 'class_name': 'integer_vector'}, 'listData': {'type': 'vector', 'data': [{'type': 'string', 'data': ['ChIP', 'Input', 'ChIP', 'Input', 'ChIP', 'Input'], 'class_name': 'string_vector'}], 'attributes': {'names': {'type': 'string', 'data': ['Treatment'], 'class_name': 'string_vector'}}, 'class_name': 'vector'}, 'elementType': {'type': 'string', 'data': ['ANY'], 'class_name': 'string_vector'}, 'elementMetadata': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}, 'elementMetadata': {'type': 'S4', 'package_name': 'S4Vectors', 'class_name': 'DFrame', 'attributes': {'rownames': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'nrows': {'type': 'integer', 'data': array([200], dtype=int32), 'attributes': {}, 'class_name': 'integer_vector'}, 'listData': {'type': 'vector', 'data': [{'type': 'string', 'data': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2', 'chr2'], 'class_name': 'string_vector'}], 'attributes': {'names': {'type': 'string', 'data': ['seqs'], 'class_name': 'string_vector'}}, 'class_name': 'vector'}, 'elementType': {'type': 'string', 'data': ['ANY'], 'class_name': 'string_vector'}, 'elementMetadata': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}, 'assays': {'type': 'S4', 'package_name': 'SummarizedExperiment', 'class_name': 'SimpleAssays', 'attributes': {'data': {'type': 'S4', 'package_name': 'S4Vectors', 'class_name': 'SimpleList', 'attributes': {'listData': {'type': 'vector', 'data': [{'type': 'double', 'data': array([5984.7896784 , 4351.34643709, 2763.82637297, ...,   20.0651535 ,
-       2590.73635628, 4687.51702976]), 'attributes': {'dim': {'type': 'integer', 'data': array([200,   6], dtype=int32), 'attributes': {}, 'class_name': 'integer_vector'}}, 'class_name': 'double_vector'}], 'attributes': {'names': {'type': 'string', 'data': ['counts'], 'class_name': 'string_vector'}}, 'class_name': 'vector'}, 'elementType': {'type': 'string', 'data': ['ANY'], 'class_name': 'string_vector'}, 'elementMetadata': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}}}, 'NAMES': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}
+       2590.73635628, 4687.51702976]), 'attributes': {'dim': {'type': 'integer', 'data': array([200,   6], dtype=int32), 'attributes': {}, 'class_name': 'integer_vector'}}, 'class_name': 'double_vector'}], 'attributes': {'names': {'type': 'string', 'data': ['counts'], 'class_name': 'string_vector'}}, 'class_name': 'vector'}, 'elementType': {'type': 'string', 'data': ['ANY'], 'class_name': 'string_vector'}, 'elementMetadata': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}}}, 'NAMES': {'type': 'other', 'data': None, 'attributes': None, 'class_name': None}, 'metadata': {'type': 'vector', 'data': [], 'attributes': {}, 'class_name': 'vector'}}}