[pre-commit.ci] auto fixes from pre-commit.com hooks

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BiocPy · Oct 25, 2024 · 1cbbd2c · 1cbbd2c
1 parent cb4fd8c
commit 1cbbd2c
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Showing 11 changed files with 27 additions and 91 deletions.
diff --git a/setup.py b/setup.py
@@ -38,10 +38,7 @@ def build_cmake(self, ext):
                 "lib",
                 "-B",
                 build_temp,
-                "-Dpybind11_DIR="
-                + os.path.join(
-                    os.path.dirname(pybind11.__file__), "share", "cmake", "pybind11"
-                ),
+                "-Dpybind11_DIR=" + os.path.join(os.path.dirname(pybind11.__file__), "share", "cmake", "pybind11"),
                 "-DPYTHON_EXECUTABLE=" + sys.executable,
             ]
             if os.name != "nt":

diff --git a/src/rds2py/PyRdsReader.py b/src/rds2py/PyRdsReader.py
@@ -71,9 +71,7 @@ def _process_object(self, obj: RdsReader) -> Dict[str, Any]:
         except Exception as e:
             raise PyRdsParserError(f"Error processing object: {str(e)}")
 
-    def _handle_r_special_cases(
-        self, data: np.ndarray, rtype: str, size: int
-    ) -> Union[np.ndarray, range]:
+    def _handle_r_special_cases(self, data: np.ndarray, rtype: str, size: int) -> Union[np.ndarray, range]:
         """Handle special R data representations."""
         try:
             # Special handling for R integer containing NA
@@ -82,12 +80,7 @@ def _handle_r_special_cases(
                     return np.array([np.nan if x == self.R_MIN else x for x in data])
 
             # Special handling for R integer sequences
-            if (
-                rtype == "integer"
-                and size == 2
-                and data[0] == self.R_MIN
-                and data[1] < 0
-            ):
+            if rtype == "integer" and size == 2 and data[0] == self.R_MIN and data[1] < 0:
                 if data[1] == self.R_MIN:
                     return [None, None]
                 return range(data[1] * -1)
@@ -106,10 +99,7 @@ def _get_numeric_data(self, obj: RdsReader, rtype: str) -> np.ndarray:
             raise PyRdsParserError(f"Error getting numeric data: {str(e)}")
 
     def _process_vector(self, obj: RdsReader) -> List[Dict[str, Any]]:
-        return [
-            self._process_object(obj.load_vec_element(i))
-            for i in range(obj.get_rsize())
-        ]
+        return [self._process_object(obj.load_vec_element(i)) for i in range(obj.get_rsize())]
 
     def _process_attributes(self, obj: RdsReader) -> Dict[str, Dict[str, Any]]:
         try:

diff --git a/src/rds2py/rdsutils.py b/src/rds2py/rdsutils.py
@@ -37,9 +37,7 @@ def get_class(robj: dict) -> str:
         if "class_name" in robj:
             _inferred_cls_name = robj["class_name"]
             if _inferred_cls_name is not None and (
-                "integer" in _inferred_cls_name
-                or "double" in _inferred_cls_name
-                or _inferred_cls_name == "vector"
+                "integer" in _inferred_cls_name or "double" in _inferred_cls_name or _inferred_cls_name == "vector"
             ):
                 if "attributes" in robj:
                     obj_attr = robj["attributes"]

diff --git a/src/rds2py/read_dict.py b/src/rds2py/read_dict.py
@@ -10,9 +10,7 @@ def parse_vector(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["vector"]:
-        raise RuntimeError(
-            f"`robject` does not contain not a vector/dictionary object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain not a vector/dictionary object, contains `{_cls}`.")
 
     if "names" not in robject["attributes"]:
         return [_dispatcher(x) for x in robject["data"]]

diff --git a/src/rds2py/read_factor.py b/src/rds2py/read_factor.py
@@ -10,9 +10,7 @@ def parse_factor(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["factor"]:
-        raise RuntimeError(
-            f"`robject` does not contain not a factor object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain not a factor object, contains `{_cls}`.")
 
     data = robject["data"]
 

diff --git a/src/rds2py/read_granges.py b/src/rds2py/read_granges.py
@@ -39,18 +39,10 @@ def parse_genomic_ranges(robject):
 
     _strands = _dispatcher(robject["attributes"]["strand"])
     _seqnames = _dispatcher(robject["attributes"]["seqnames"])
-    _seqinfo_seqnames = _dispatcher(
-        robject["attributes"]["seqinfo"]["attributes"]["seqnames"]
-    )
-    _seqinfo_seqlengths = _dispatcher(
-        robject["attributes"]["seqinfo"]["attributes"]["seqlengths"]
-    )
-    _seqinfo_is_circular = _dispatcher(
-        robject["attributes"]["seqinfo"]["attributes"]["is_circular"]
-    )
-    _seqinfo_genome = _dispatcher(
-        robject["attributes"]["seqinfo"]["attributes"]["genome"]
-    )
+    _seqinfo_seqnames = _dispatcher(robject["attributes"]["seqinfo"]["attributes"]["seqnames"])
+    _seqinfo_seqlengths = _dispatcher(robject["attributes"]["seqinfo"]["attributes"]["seqlengths"])
+    _seqinfo_is_circular = _dispatcher(robject["attributes"]["seqinfo"]["attributes"]["is_circular"])
+    _seqinfo_genome = _dispatcher(robject["attributes"]["seqinfo"]["attributes"]["genome"])
     _seqinfo = SeqInfo(
         seqnames=_seqinfo_seqnames,
         seqlengths=_seqinfo_seqlengths,
@@ -99,9 +91,7 @@ def parse_granges_list(robject):
         _tmp_names = robject["attributes"]["partitioning"]["attributes"]["NAMES"]
         _groups = None if _tmp_names is None else _dispatcher(_tmp_names)
 
-    _partitionends = _dispatcher(
-        robject["attributes"]["partitioning"]["attributes"]["end"]
-    )
+    _partitionends = _dispatcher(robject["attributes"]["partitioning"]["attributes"]["end"])
 
     _grelist = []
 

diff --git a/src/rds2py/read_mae.py b/src/rds2py/read_mae.py
@@ -44,9 +44,7 @@ def parse_multi_assay_experiment(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["MultiAssayExperiment"]:
-        raise RuntimeError(
-            f"`robject` does not contain a 'MultiAssayExperiment' object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain a 'MultiAssayExperiment' object, contains `{_cls}`.")
 
     # parse experiment  names
     _expt_obj = robject["attributes"]["ExperimentList"]["attributes"]["listData"]

diff --git a/src/rds2py/read_matrix.py b/src/rds2py/read_matrix.py
@@ -35,9 +35,7 @@ def _as_sparse_matrix(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["dgCMatrix", "dgRMatrix", "dgTMatrix"]:
-        raise RuntimeError(
-            f"`robject` does not contain not a supported sparse matrix format, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain not a supported sparse matrix format, contains `{_cls}`.")
 
     if _cls == "dgCMatrix":
         mat = csc_matrix(
@@ -98,7 +96,6 @@ def _as_dense_matrix(robject, order: Literal["C", "F"] = "F"):
     """
     _cls = get_class(robject)
 
-
     if order not in ["C", "F"]:
         raise ValueError("order must be either 'C' or 'F'.")
 

diff --git a/src/rds2py/read_rle.py b/src/rds2py/read_rle.py
@@ -20,9 +20,7 @@ def parse_rle(robject: dict):
     _cls = get_class(robject)
 
     if _cls != "Rle":
-        raise RuntimeError(
-            f"`robject` does not contain a 'Rle' object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain a 'Rle' object, contains `{_cls}`.")
 
     data = list(_dispatcher(robject["attributes"]["values"]))
 

diff --git a/src/rds2py/read_sce.py b/src/rds2py/read_sce.py
@@ -10,9 +10,7 @@ def parse_alts_summarized_experiment_by_column(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["SummarizedExperimentByColumn"]:
-        raise RuntimeError(
-            f"`robject` does not contain a 'SummarizedExperimentByColumn' object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain a 'SummarizedExperimentByColumn' object, contains `{_cls}`.")
 
     objs = {}
 
@@ -39,42 +37,28 @@ 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)
 
     # check red. dims, alternative expts
     robj_reduced_dims = None
     robj_alt_exps = None
-    col_attrs = list(
-        _dispatcher(
-            robject["attributes"]["int_colData"]["attributes"]["listData"][
-                "attributes"
-            ]["names"]
-        )
-    )
+    col_attrs = list(_dispatcher(robject["attributes"]["int_colData"]["attributes"]["listData"]["attributes"]["names"]))
 
     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.get("data", None) is not None:
             robj_reduced_dims = _dispatcher(idx_value)
 
         if idx_col == "altExps":
-            alt_names = list(
-                _dispatcher(idx_value["attributes"]["listData"]["attributes"]["names"])
-            )
+            alt_names = list(_dispatcher(idx_value["attributes"]["listData"]["attributes"]["names"]))
             robj_alt_exps = {}
             for idx, altn in enumerate(alt_names):
-                robj_alt_exps[altn] = _dispatcher(
-                    idx_value["attributes"]["listData"]["data"][idx]
-                )["se"]
+                robj_alt_exps[altn] = _dispatcher(idx_value["attributes"]["listData"]["data"][idx])["se"]
 
         # ignore colpairs for now, does anyone even use this ?
         # if col == "colPairs":

diff --git a/src/rds2py/read_se.py b/src/rds2py/read_se.py
@@ -43,37 +43,27 @@ def parse_summarized_experiment(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["SummarizedExperiment"]:
-        raise RuntimeError(
-            f"`robject` does not contain a 'SummarizedExperiment' object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain a 'SummarizedExperiment' object, contains `{_cls}`.")
     # parse assays  names
     robj_asys = {}
     assay_dims = None
     asy_names = list(
         _dispatcher(
-            robject["attributes"]["assays"]["attributes"]["data"]["attributes"][
-                "listData"
-            ]["attributes"]["names"]
+            robject["attributes"]["assays"]["attributes"]["data"]["attributes"]["listData"]["attributes"]["names"]
         )
     )
     for idx, asyname in enumerate(asy_names):
-        idx_asy = robject["attributes"]["assays"]["attributes"]["data"]["attributes"][
-            "listData"
-        ]["data"][idx]
+        idx_asy = robject["attributes"]["assays"]["attributes"]["data"]["attributes"]["listData"]["data"][idx]
 
         robj_asys[asyname] = _dispatcher(idx_asy)
         if assay_dims is None:
             assay_dims = robj_asys[asyname].shape
 
     # parse coldata
-    robj_coldata = _sanitize_empty_frame(
-        _dispatcher(robject["attributes"]["colData"]), assay_dims[1]
-    )
+    robj_coldata = _sanitize_empty_frame(_dispatcher(robject["attributes"]["colData"]), assay_dims[1])
 
     # parse rowdata
-    robj_rowdata = _sanitize_empty_frame(
-        _dispatcher(robject["attributes"]["elementMetadata"]), assay_dims[0]
-    )
+    robj_rowdata = _sanitize_empty_frame(_dispatcher(robject["attributes"]["elementMetadata"]), assay_dims[0])
 
     return SummarizedExperiment(
         assays=_sanitize_assays(robj_asys),
@@ -99,9 +89,7 @@ def parse_ranged_summarized_experiment(robject: dict):
     _cls = get_class(robject)
 
     if _cls not in ["RangedSummarizedExperiment"]:
-        raise RuntimeError(
-            f"`robject` does not contain a 'RangedSummarizedExperiment' object, contains `{_cls}`."
-        )
+        raise RuntimeError(f"`robject` does not contain a 'RangedSummarizedExperiment' object, contains `{_cls}`.")
 
     robject["class_name"] = "SummarizedExperiment"
     _se = _dispatcher(robject)