SingleCellExperiment 0.5.1__tar.gz → 0.5.3__tar.gz

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.6.8
+  rev: v0.8.4
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/CHANGELOG.md

@@ -1,8 +1,12 @@
 # Changelog
 
-## Version 0.5.1
+## Version 0.5.1 - 0.5.3
 
 - Add wrapper class methods to combine experiments by rows or columns.
+- Expand function names for readability, still backwards compatible with the older function and method names.
+- 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
 

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.5.1
+Version: 0.5.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -14,7 +14,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
-Requires-Dist: summarizedexperiment>=0.5.1
+Requires-Dist: summarizedexperiment>=0.5.3
 Provides-Extra: optional
 Requires-Dist: anndata==0.9.2; python_version <= "3.9" and extra == "optional"
 Requires-Dist: anndata>0.9.2; python_version > "3.9" and extra == "optional"

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/docs/changelog.md

@@ -1,8 +1,12 @@
 # Changelog
 
-## Version 0.5.1
+## Version 0.5.1 - 0.5.3
 
 - Add wrapper class methods to combine experiments by rows or columns.
+- Expand function names for readability, still backwards compatible with the older function and method names.
+- 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
 

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/setup.cfg

@@ -24,7 +24,7 @@ package_dir =
 python_requires = >=3.9
 install_requires = 
 	importlib-metadata; python_version<"3.8"
-	summarizedexperiment>=0.5.1
+	summarizedexperiment>=0.5.3
 
 [options.packages.find]
 where = src

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.5.1
+Version: 0.5.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -14,7 +14,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
-Requires-Dist: summarizedexperiment>=0.5.1
+Requires-Dist: summarizedexperiment>=0.5.3
 Provides-Extra: optional
 Requires-Dist: anndata==0.9.2; python_version <= "3.9" and extra == "optional"
 Requires-Dist: anndata>0.9.2; python_version > "3.9" and extra == "optional"

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/src/SingleCellExperiment.egg-info/requires.txt

@@ -1,4 +1,4 @@
-summarizedexperiment>=0.5.1
+summarizedexperiment>=0.5.3
 
 [:python_version < "3.8"]
 importlib-metadata

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/src/singlecellexperiment/SingleCellExperiment.py

@@ -350,7 +350,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
     ######>> reduced_dims <<######
     ##############################
 
-    def get_reduced_dims(self) -> Dict[str, Any]:
+    def get_reduced_dimensions(self) -> Dict[str, Any]:
         """Access dimensionality embeddings.
 
         Returns:
@@ -359,7 +359,11 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         return self._reduced_dims
 
-    def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+    def get_reduced_dims(self) -> Dict[str, Any]:
+        """Alias for :py:meth:`~get_reduced_dimensions`, for back-compatibility."""
+        return self.get_reduced_dimensions()
+
+    def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
         """Set new reduced dimensions.
 
         Args:
@@ -379,25 +383,43 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         output._reduced_dims = reduced_dims
         return output
 
+    def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+        """Alias for :py:meth:`~set_reduced_dimensions`, for back-compatibility."""
+        return self.set_reduced_dimensions(reduced_dims=reduced_dims, in_place=in_place)
+
     @property
     def reduced_dims(self) -> Dict[str, Any]:
-        """Alias for :py:meth:`~get_reduced_dims`."""
-        return self.get_reduced_dims()
+        """Alias for :py:meth:`~get_reduced_dimensions`."""
+        return self.get_reduced_dimensions()
 
     @reduced_dims.setter
     def reduced_dims(self, reduced_dims: Dict[str, Any]):
-        """Alias for :py:meth:`~set_reduced_dims`."""
+        """Alias for :py:meth:`~set_reduced_dimensions`."""
         warn(
-            "Setting property 'reduced_dims' is an in-place operation, use 'set_reduced_dims' instead",
+            "Setting property 'reduced_dims' is an in-place operation, use 'set_reduced_dimensions' instead",
             UserWarning,
         )
-        self.set_reduced_dims(reduced_dims, in_place=True)
+        self.set_reduced_dimensions(reduced_dims, in_place=True)
+
+    @property
+    def reduced_dimensions(self) -> Dict[str, Any]:
+        """Alias for :py:meth:`~get_reduced_dimensions`."""
+        return self.get_reduced_dimensions()
+
+    @reduced_dimensions.setter
+    def reduced_dimensions(self, reduced_dims: Dict[str, Any]):
+        """Alias for :py:meth:`~set_reduced_dimensions`."""
+        warn(
+            "Setting property 'reduced_dimensions' is an in-place operation, use 'set_reduced_dimensions' instead",
+            UserWarning,
+        )
+        self.set_reduced_dimensions(reduced_dims, in_place=True)
 
     ####################################
     ######>> reduced_dims_names <<######
     ####################################
 
-    def get_reduced_dim_names(self) -> List[str]:
+    def get_reduced_dimension_names(self) -> List[str]:
         """Access reduced dimension names.
 
         Returns:
@@ -405,7 +427,11 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         return list(self._reduced_dims.keys())
 
-    def set_reduced_dim_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def get_reduced_dim_names(self) -> Dict[str, Any]:
+        """Alias for :py:meth:`~get_reduced_dimension_names`, for back-compatibility."""
+        return self.get_reduced_dimension_names()
+
+    def set_reduced_dimension_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
         """Replace :py:attr:`~.reduced_dims`'s names.
 
         Args:
@@ -431,29 +457,47 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         output._reduced_dims = new_reduced_dims
         return output
 
+    def set_reduced_dim_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+        """Alias for :py:meth:`~set_reduced_dimension_names`, for back-compatibility."""
+        return self.set_reduced_dimension_names(names=names, in_place=in_place)
+
     @property
     def reduced_dim_names(self) -> List[str]:
-        """Alias for :py:meth:`~get_reduced_dim_names`."""
-        return self.get_reduced_dim_names()
+        """Alias for :py:meth:`~get_reduced_dimension_names`."""
+        return self.get_reduced_dimension_names()
 
     @reduced_dim_names.setter
     def reduced_dim_names(self, names: List[str]):
-        """Alias for :py:meth:`~set_reduced_dim_names`."""
+        """Alias for :py:meth:`~set_reduced_dimension_names`."""
+        warn(
+            "Renaming names of property 'reduced_dims' is an in-place operation, use 'set_reduced_dimension_names' instead",
+            UserWarning,
+        )
+        self.set_reduced_dimension_names(names, in_place=True)
+
+    @property
+    def reduced_dimension_names(self) -> List[str]:
+        """Alias for :py:meth:`~get_reduced_dimension_names`."""
+        return self.get_reduced_dimension_names()
+
+    @reduced_dimension_names.setter
+    def reduced_dimension_names(self, names: List[str]):
+        """Alias for :py:meth:`~set_reduced_dimension_names`."""
         warn(
-            "Renaming names of property 'reduced_dims' is an in-place operation, use 'set_reduced_dim_names' instead",
+            "Renaming names of property 'reduced_dims' is an in-place operation, use 'set_reduced_dimension_names' instead",
             UserWarning,
         )
-        self.set_reduced_dim_names(names, in_place=True)
+        self.set_reduced_dimension_names(names, in_place=True)
 
     ####################################
     ######>> reduced_dim getter <<######
     ####################################
 
-    def reduced_dim(self, dimension: Union[str, int]) -> Any:
+    def get_reduced_dimension(self, name: Union[str, int]) -> Any:
         """Access an embedding by name.
 
         Args:
-            dimension:
+            name:
                 Name or index position of the reduced dimension.
 
         Raises:
@@ -465,21 +509,53 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         Returns:
             The embedding.
         """
-        if isinstance(dimension, int):
-            if dimension < 0:
+        if isinstance(name, int):
+            if name < 0:
                 raise IndexError("Index cannot be negative.")
 
-            if dimension > len(self.reduced_dim_names):
+            if name > len(self.reduced_dim_names):
                 raise IndexError("Index greater than the number of reduced dimensions.")
 
-            return self._reduced_dims[self.reduced_dim_names[dimension]]
-        elif isinstance(dimension, str):
-            if dimension not in self._reduced_dims:
-                raise AttributeError(f"Reduced dimension: {dimension} does not exist.")
+            return self._reduced_dims[self.reduced_dim_names[name]]
+        elif isinstance(name, str):
+            if name not in self._reduced_dims:
+                raise AttributeError(f"Reduced dimension: {name} does not exist.")
+
+            return self._reduced_dims[name]
+
+        raise TypeError(f"'dimension' must be a string or integer, provided '{type(name)}'.")
+
+    def reduced_dim(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.
+
+        Args:
+            name:
+                New or existing embedding or dimension name.
+
+            embedding:
+                Embeddings may be represented as a matrix or a data frame, must contain a shape.
 
-            return self._reduced_dims[dimension]
+            in_place:
+                Whether to modify the ``SingleCellExperiment`` in place.
+
+        Returns:
+            A modified ``SingleCellExperiment`` object, either as a copy of the original
+            or as a reference to the (in-place-modified) original.
+        """
+        output = self._define_output(in_place)
 
-        raise TypeError(f"'dimension' must be a string or integer, provided '{type(dimension)}'.")
+        _tmp_red_dims = output._reduced_dims
+        if in_place is False:
+            _tmp_red_dims = _tmp_red_dims.copy()
+        _tmp_red_dims[name] = embedding
+
+        _validate_reduced_dims(_tmp_red_dims, self._shape)
+        output._reduced_dims = _tmp_red_dims
+        return output
 
     ################################
     ######>> main_expt_name <<######
@@ -629,7 +705,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
     ######>> alternative_experiment getter <<######
     ###############################################
 
-    def alternative_experiment(self, name: Union[str, int]) -> Any:
+    def get_alternative_experiment(self, name: Union[str, int]) -> Any:
         """Access alternative experiment by name.
 
         Args:
@@ -661,6 +737,42 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
         raise TypeError(f"'name' must be a string or integer, provided '{type(name)}'.")
 
+    def alternative_experiment(self, name: Union[str, int]) -> Any:
+        """Alias for :py:meth:`~get_alternative_experiment`, for back-compatibility."""
+        return self.get_alternative_experiment(name=name)
+
+    def set_alternative_experiment(
+        self, name: str, alternative_experiment: Any, in_place: bool = False
+    ) -> "SingleCellExperiment":
+        """Add or replace :py:attr:`~singlecellexperiment.SingleCellExperiment.alternative_experiment`'s.
+
+        Args:
+            name:
+                New or existing alternative experiment name.
+
+            alternative_experiment:
+                Alternative experiments must contain the same cells (rows) as the primary experiment.
+                Is a subclasses of
+                :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
+
+            in_place:
+                Whether to modify the ``SingleCellExperiment`` in place.
+
+        Returns:
+            A modified ``BasSingleCellExperimenteSE`` object, either as a copy of the original
+            or as a reference to the (in-place-modified) original.
+        """
+        output = self._define_output(in_place)
+
+        _tmp_alt_expt = output._alternative_experiments
+        if in_place is False:
+            _tmp_alt_expt = _tmp_alt_expt.copy()
+        _tmp_alt_expt[name] = alternative_experiment
+
+        _validate_alternative_experiments(_tmp_alt_expt, self._shape)
+        output._alternative_experiments = _tmp_alt_expt
+        return output
+
     ###########################
     ######>> row_pairs <<######
     ###########################
@@ -868,41 +980,40 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         rows: Optional[Union[str, int, bool, Sequence]],
         columns: Optional[Union[str, int, bool, Sequence]],
     ) -> "SingleCellExperiment":
-        """Alias for :py:attr:`~__getitem__`, for back-compatibility."""
+        """Alias for :py:attr:`~__getitem__`."""
 
         slicer = self._generic_slice(rows=rows, columns=columns)
+        do_slice_rows = not (isinstance(slicer.row_indices, slice) and slicer.row_indices == slice(None))
+        do_slice_cols = not (isinstance(slicer.col_indices, slice) and slicer.col_indices == slice(None))
 
         new_row_ranges = None
-        if slicer.row_indices != slice(None):
+        if do_slice_rows:
             new_row_ranges = self._row_ranges[slicer.row_indices]
 
         new_reduced_dims = {}
         for rdim, rmat in self._reduced_dims.items():
-            if slicer.col_indices != slice(None):
+            if do_slice_cols:
                 rmat = rmat[slicer.col_indices, :]
 
             new_reduced_dims[rdim] = rmat
 
         new_alt_expts = {}
         for altname, altexpt in self._alternative_experiments.items():
-            if slicer.row_indices != slice(None):
-                altexpt = altexpt[slicer.row_indices, :]
-
-            if slicer.col_indices != slice(None):
+            if do_slice_cols:
                 altexpt = altexpt[:, slicer.col_indices]
 
             new_alt_expts[altname] = altexpt
 
         new_row_pairs = {}
         for rname, rpair in self._row_pairs.items():
-            if slicer.row_indices != slice(None):
+            if do_slice_rows:
                 rpair = rpair[slicer.row_indices, :]
 
             new_row_pairs[rname] = rpair
 
         new_col_pairs = {}
         for cname, cpair in self._column_pairs.items():
-            if slicer.col_indices != slice(None):
+            if do_slice_cols:
                 cpair = cpair[:, slicer.col_indices]
 
             new_col_pairs[cname] = cpair

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/tests/test_sce.py

@@ -118,3 +118,28 @@ def test_SCE_creation_with_alts_should_fail():
             column_data=col_data,
             alternative_experiments={"alt": tse},
         )
+
+def test_SCE_creation_modifications():
+    rse = SummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data
+    )
+
+    tse = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        alternative_experiments={"alt": rse},
+    )
+
+    assert tse is not None
+    assert isinstance(tse, sce)
+
+    with pytest.raises(Exception):
+        tse.set_reduced_dimension("something", np.random.rand(ncols - 1, 4), in_place=False)
+
+    nassay_tse = tse.set_reduced_dimension("something", np.random.rand(tse.shape[1], 4), in_place=False)
+
+    assert nassay_tse.get_reduced_dimension_names() != tse.get_reduced_dimension_names()
+
+    tse.set_reduced_dimension("something", np.random.rand(tse.shape[1], 4), in_place=True)
+    assert nassay_tse.get_reduced_dimension_names() == tse.get_reduced_dimension_names()

{singlecellexperiment-0.5.1 → singlecellexperiment-0.5.3}/tests/test_sce_slice.py

@@ -66,6 +66,31 @@ def test_SCE_slice():
 
     assert tse_slice.assay("counts").shape == (10, 3)
 
+def test_SCE_slice_with_numpy():
+    tse = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dims={"random_embeds": np.random.rand(ncols, 5)},
+    )
+
+    tse_slice = tse[np.arange(10), 0:3]
+    assert tse_slice is not None
+    assert isinstance(tse_slice, sce)
+
+    assert len(tse_slice.row_data) == 10
+    assert len(tse_slice.col_data) == 3
+
+    assert tse_slice.assay("counts").shape == (10, 3)
+
+    tse_slice = tse[np.arange(10), np.arange(3)]
+    assert tse_slice is not None
+    assert isinstance(tse_slice, sce)
+
+    assert len(tse_slice.row_data) == 10
+    assert len(tse_slice.col_data) == 3
+
+    assert tse_slice.assay("counts").shape == (10, 3)
 
 def test_SCE_creation_with_alts_slice():
     trse = SummarizedExperiment(
@@ -91,4 +116,4 @@ def test_SCE_creation_with_alts_slice():
 
     assert tsce_slice.assay("counts").shape == (10, 3)
     alt_exp = tsce_slice.alternative_experiments["alt"]
-    assert alt_exp.shape == (10, 3)
+    assert alt_exp.shape == (200, 3)