Merge pull request #78 from klarman-cell-observatory/yiming

Fix issue on subclasses of UnimodalData
lilab-bcb · Nov 16, 2021 · b353dc0 · b353dc0
2 parents e54cf57 + 167805d
commit b353dc0
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Showing 4 changed files with 16 additions and 16 deletions.
diff --git a/pegasusio/citeseq_data.py b/pegasusio/citeseq_data.py
@@ -23,10 +23,10 @@ def __init__(
         feature_metadata: Union[dict, pd.DataFrame],
         matrices: Dict[str, csr_matrix],
         metadata: dict,
-        barcode_multiarrays: Dict[str, np.ndarray] = dict(),
-        feature_multiarrays: Dict[str, np.ndarray] = dict(),
-        barcode_multigraphs: Dict[str, csr_matrix] = dict(),
-        feature_multigraphs: Dict[str, csr_matrix] = dict(),
+        barcode_multiarrays: Dict[str, np.ndarray] = None,
+        feature_multiarrays: Dict[str, np.ndarray] = None,
+        barcode_multigraphs: Dict[str, csr_matrix] = None,
+        feature_multigraphs: Dict[str, csr_matrix] = None,
         cur_matrix: str = "raw.count",
     ) -> None:
         assert metadata["modality"] == "citeseq"

diff --git a/pegasusio/cyto_data.py b/pegasusio/cyto_data.py
@@ -22,10 +22,10 @@ def __init__(
         feature_metadata: Union[dict, pd.DataFrame],
         matrices: Dict[str, np.ndarray],
         metadata: dict,
-        barcode_multiarrays: Dict[str, np.ndarray] = dict(),
-        feature_multiarrays: Dict[str, np.ndarray] = dict(),
-        barcode_multigraphs: Dict[str, csr_matrix] = dict(),
-        feature_multigraphs: Dict[str, csr_matrix] = dict(),
+        barcode_multiarrays: Dict[str, np.ndarray] = None,
+        feature_multiarrays: Dict[str, np.ndarray] = None,
+        barcode_multigraphs: Dict[str, csr_matrix] = None,
+        feature_multigraphs: Dict[str, csr_matrix] = None,
         cur_matrix: str = "raw.data",
     ) -> None:
         assert metadata["modality"] == "cyto"

diff --git a/pegasusio/nanostring_data.py b/pegasusio/nanostring_data.py
@@ -20,10 +20,10 @@ def __init__(
         feature_metadata: Union[dict, pd.DataFrame],
         matrices: Dict[str, np.ndarray],
         metadata: dict,
-        barcode_multiarrays: Dict[str, np.ndarray] = dict(),
-        feature_multiarrays: Dict[str, np.ndarray] = dict(),
-        barcode_multigraphs: Dict[str, csr_matrix] = dict(),
-        feature_multigraphs: Dict[str, csr_matrix] = dict(),
+        barcode_multiarrays: Dict[str, np.ndarray] = None,
+        feature_multiarrays: Dict[str, np.ndarray] = None,
+        barcode_multigraphs: Dict[str, csr_matrix] = None,
+        feature_multigraphs: Dict[str, csr_matrix] = None,
         cur_matrix: str = "Q3Norm",
     ) -> None:
         assert metadata["modality"] == "nanostring"

diff --git a/pegasusio/vdj_data.py b/pegasusio/vdj_data.py
@@ -66,10 +66,10 @@ def __init__(
         feature_metadata: Union[dict, pd.DataFrame],
         matrices: Dict[str, csr_matrix],
         metadata: dict,
-        barcode_multiarrays: Dict[str, np.ndarray] = dict(),
-        feature_multiarrays: Dict[str, np.ndarray] = dict(),
-        barcode_multigraphs: Dict[str, csr_matrix] = dict(),
-        feature_multigraphs: Dict[str, csr_matrix] = dict(),
+        barcode_multiarrays: Dict[str, np.ndarray] = None,
+        feature_multiarrays: Dict[str, np.ndarray] = None,
+        barcode_multigraphs: Dict[str, csr_matrix] = None,
+        feature_multigraphs: Dict[str, csr_matrix] = None,
         cur_matrix: str = "umis",
     ) -> None:
         assert metadata["modality"] in {"tcr", "bcr"}