SingleCellExperiment 0.5.7__tar.gz → 0.5.8__tar.gz

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.9.3
+  rev: v0.9.10
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/CHANGELOG.md

@@ -1,16 +1,22 @@
 # Changelog
 
+## Version 0.5.8
+
+- Rename `reduced_dims` to `reduced_dimensions`. Constructor accepts both these arguments for backwards compatibility.
+- Additionally, SCE's constructor takes kwargs for future proofing any additional attributes in the upstream classes.
+
 ## Version 0.5.7
+
 - Support reading outputs from CellRanger version 3 and later in `read_tenx_mtx`.
   - Handle both `genes.csv` and `features.csv` for gene annotations.
 
 ## Version 0.5.6
 
-- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the ``withDimnames`` parameter in the R implementation.
+- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the `withDimnames` parameter in the R implementation.
   - On **getters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **replaced** with the
-  column names of the main experiment.
+    column names of the main experiment.
   - On **setters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **checked** with the
-  column names of the main experiment and an Exception is raised if they do not match.
+    column names of the main experiment and an Exception is raised if they do not match.
 
 ## Version 0.5.1 - 0.5.5
 
@@ -19,7 +25,6 @@
 - Add getters and setters to replace a specific alternative experiment or reduced dimension.
 - Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils's subset functions to perform these operations.
 
-
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.7
+Version: 0.5.8
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/docs/changelog.md

@@ -1,16 +1,22 @@
 # Changelog
 
+## Version 0.5.8
+
+- Rename `reduced_dims` to `reduced_dimensions`. Constructor accepts both these arguments for backwards compatibility.
+- Additionally, SCE's constructor takes kwargs for future proofing any additional attributes in the upstream classes.
+
 ## Version 0.5.7
+
 - Support reading outputs from CellRanger version 3 and later in `read_tenx_mtx`.
   - Handle both `genes.csv` and `features.csv` for gene annotations.
 
 ## Version 0.5.6
 
-- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the ``withDimnames`` parameter in the R implementation.
+- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the `withDimnames` parameter in the R implementation.
   - On **getters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **replaced** with the
-  column names of the main experiment.
+    column names of the main experiment.
   - On **setters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **checked** with the
-  column names of the main experiment and an Exception is raised if they do not match.
+    column names of the main experiment and an Exception is raised if they do not match.
 
 ## Version 0.5.1 - 0.5.5
 
@@ -19,7 +25,6 @@
 - Add getters and setters to replace a specific alternative experiment or reduced dimension.
 - Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils's subset functions to perform these operations.
 
-
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.7
+Version: 0.5.8
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/src/singlecellexperiment/SingleCellExperiment.py

@@ -94,7 +94,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
     parent experiment. Otherwise, these cells do not share the same sample or annotations
     and cannot be set in alternative experiments!
 
-    Note: Validation checks do not apply to ``row_pairs`` or ``col_pairs``.
+    Note: Validation checks do not apply to ``row_pairs`` or ``column_pairs``.
     """
 
     def __init__(
@@ -106,13 +106,15 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
         metadata: Optional[dict] = None,
-        reduced_dims: Optional[Dict[str, Any]] = None,
+        reduced_dimensions: Optional[Dict[str, Any]] = None,
+        reduced_dims: Optional[Dict[str, Any]] = None,  # deprecated name
         main_experiment_name: Optional[str] = None,
         alternative_experiments: Optional[Dict[str, Any]] = None,
         row_pairs: Optional[Any] = None,
         column_pairs: Optional[Any] = None,
         alternative_experiment_check_dim_names: bool = True,
         validate: bool = True,
+        **kwargs,
     ) -> None:
         """Initialize a single-cell experiment.
 
@@ -157,7 +159,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
                 Additional experimental metadata describing the methods.
                 Defaults to None.
 
-            reduced_dims:
+            reduced_dimensions:
                 Slot for low-dimensionality embeddings.
 
                 Usually a dictionary with the embedding method as keys (e.g., t-SNE, UMAP)
@@ -165,6 +167,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
                 Embeddings may be represented as a matrix or a data frame, must contain a shape.
 
+            reduced_dims:
+                Will be deprecated in the future versions. Use py:attr:`~reduced_dimensions` instead.
+
             main_experiment_name:
                 A string, specifying the main experiment name.
 
@@ -195,6 +200,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
             validate:
                 Internal use only.
+
+            kwargs:
+                Additional arguments.
         """
 
         super().__init__(
@@ -206,10 +214,20 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             column_names=column_names,
             metadata=metadata,
             validate=validate,
+            **kwargs,
         )
         self._main_experiment_name = main_experiment_name
 
-        self._reduced_dims = reduced_dims if reduced_dims is not None else {}
+        _dims = None
+        if reduced_dimensions is not None and reduced_dims is not None:
+            raise ValueError("Either 'reduced_dims' or 'reduced_dimensions' should be provided, but not both.")
+        elif reduced_dims is not None:
+            warn("'reduced_dims' is deprecated, use 'reduced_dimensions' instead.", DeprecationWarning)
+            _dims = reduced_dims
+        elif reduced_dimensions is not None:
+            _dims = reduced_dimensions
+
+        self._reduced_dims = _dims if _dims is not None else {}
 
         self._alternative_experiments = alternative_experiments if alternative_experiments is not None else {}
 
@@ -551,6 +569,10 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """Alias for :py:meth:`~get_reduced_dimension`, for back-compatibility."""
         return self.get_reduced_dimension(name=name)
 
+    def reduced_dimension(self, name: Union[str, int]) -> Any:
+        """Alias for :py:meth:`~get_reduced_dimension`, for back-compatibility."""
+        return self.get_reduced_dimension(name=name)
+
     def set_reduced_dimension(self, name: str, embedding: Any, in_place: bool = False) -> "SingleCellExperiment":
         """Add or replace :py:attr:`~singlecellexperiment.SingleCellExperiment.reduced_dimension`'s.
 

{singlecellexperiment-0.5.7 → singlecellexperiment-0.5.8}/tests/test_sce.py

@@ -172,3 +172,48 @@ def test_SCE_different_alt_names():
             column_data=pd.DataFrame(index = ["ChIP", "Input", "Input"] * 2),
             alternative_experiments={"alt": rse},
         )
+
+def test_SCE_dims():
+    embeds = np.random.rand(counts.shape[1], 4)
+    tse = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dimensions={
+            "something": embeds
+        }
+    )
+
+    assert tse is not None
+    assert isinstance(tse, sce)
+    assert tse.get_reduced_dimension_names() == ["something"]
+
+    tse2 = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dims={
+            "something": embeds
+        }
+    )
+
+    assert tse2 is not None
+    assert isinstance(tse2, sce)
+    assert tse2.get_reduced_dimension_names() == ["something"]
+
+    print(tse.get_reduced_dimension("something"), tse2.get_reduced_dimension("something"))
+
+    assert np.allclose(tse.get_reduced_dimension("something"), tse2.get_reduced_dimension("something"))
+
+    with pytest.raises(Exception, match="Either 'reduced_dims' or 'reduced_dimensions' should be provided, but not both."):
+        SingleCellExperiment(
+            assays={"counts": counts},
+            row_data=row_data,
+            column_data=col_data,
+            reduced_dims={
+                "something": embeds
+            },
+            reduced_dimensions={
+                "something": embeds
+            }
+        )