SingleCellExperiment 0.5.0__tar.gz → 0.5.2__tar.gz

singlecellexperiment-0.5.0/.github/workflows/pypi-test.yml → singlecellexperiment-0.5.2/.github/workflows/run-tests.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches: [master]
   pull_request:
-    branches: [master]
 
 jobs:
   build:

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/.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-0.5.0 → singlecellexperiment-0.5.2}/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## Version 0.5.1 - 0.5.2
+
+- 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.
+
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.5.0
+Version: 0.5.2
 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>=0.4.5
+Requires-Dist: summarizedexperiment>=0.5.1
 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"
@@ -41,7 +41,7 @@ Requires-Dist: numpy>1.24.4; python_version > "3.9" and extra == "testing"
 
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)
-![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/run-tests.yml/badge.svg)
 
 # SingleCellExperiment
 

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/README.md

@@ -1,6 +1,6 @@
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)
-![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/run-tests.yml/badge.svg)
 
 # SingleCellExperiment
 

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/docs/changelog.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## Version 0.5.1 - 0.5.2
+
+- 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.
+
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/docs/readme.md

@@ -1,6 +1,6 @@
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)
-![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/run-tests.yml/badge.svg)
 
 # SingleCellExperiment
 

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/setup.cfg

@@ -24,7 +24,7 @@ package_dir =
 python_requires = >=3.9
 install_requires = 
 	importlib-metadata; python_version<"3.8"
-	summarizedexperiment>=0.4.5
+	summarizedexperiment>=0.5.1
 
 [options.packages.find]
 where = src

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.5.0
+Version: 0.5.2
 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>=0.4.5
+Requires-Dist: summarizedexperiment>=0.5.1
 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"
@@ -41,7 +41,7 @@ Requires-Dist: numpy>1.24.4; python_version > "3.9" and extra == "testing"
 
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)
-![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/run-tests.yml/badge.svg)
 
 # SingleCellExperiment
 

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/src/SingleCellExperiment.egg-info/SOURCES.txt

@@ -11,8 +11,8 @@ pyproject.toml
 setup.cfg
 setup.py
 tox.ini
-.github/workflows/pypi-publish.yml
-.github/workflows/pypi-test.yml
+.github/workflows/publish-pypi.yml
+.github/workflows/run-tests.yml
 docs/Makefile
 docs/authors.md
 docs/changelog.md

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/src/SingleCellExperiment.egg-info/requires.txt

@@ -1,4 +1,4 @@
-summarizedexperiment>=0.4.5
+summarizedexperiment>=0.5.1
 
 [:python_version < "3.8"]
 importlib-metadata

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/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_dimensions' instead",
+            UserWarning,
+        )
+        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_dims' is an in-place operation, use 'set_reduced_dims' instead",
+            "Setting property 'reduced_dimensions' 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)
 
     ####################################
     ######>> 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.
+
+            in_place:
+                Whether to modify the ``SingleCellExperiment`` in place.
 
-            return self._reduced_dims[dimension]
+        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 <<######
     ###########################
@@ -1027,6 +1139,26 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
         return MuData(expts)
 
+    ############################
+    ######>> combine ops <<#####
+    ############################
+
+    def relaxed_combine_rows(self, *other) -> "SingleCellExperiment":
+        """Wrapper around :py:func:`~relaxed_combine_rows`."""
+        return relaxed_combine_rows(self, *other)
+
+    def relaxed_combine_columns(self, *other) -> "SingleCellExperiment":
+        """Wrapper around :py:func:`~relaxed_combine_columns`."""
+        return relaxed_combine_columns(self, *other)
+
+    def combine_rows(self, *other) -> "SingleCellExperiment":
+        """Wrapper around :py:func:`~combine_rows`."""
+        return combine_rows(self, *other)
+
+    def combine_columns(self, *other) -> "SingleCellExperiment":
+        """Wrapper around :py:func:`~combine_columns`."""
+        return combine_columns(self, *other)
+
 
 ############################
 ######>> combine ops <<#####

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/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-0.5.0 → singlecellexperiment-0.5.2}/tests/test_sce_combine_cols.py

@@ -27,6 +27,15 @@ def test_combine_columns(experiments):
     assert len(combined.alternative_experiments) == 0
     assert len(combined.column_data["A"]) == 20
 
+    combined2 = experiments.se_unnamed.combine_columns(
+        experiments.se_unnamed_2
+    )
+    assert combined2 is not None
+    assert isinstance(combined2, SingleCellExperiment)
+    assert len(combined2.alternative_experiments) == 0
+    assert len(combined2.column_data["A"]) == 20
+
+
 
 def test_relaxed_combine_columns(experiments):
     ncols = 10
@@ -48,6 +57,12 @@ def test_relaxed_combine_columns(experiments):
     assert len(combined.alternative_experiments) == 0
     assert len(combined.row_data["A"]) == 100
 
+    combined2 = experiments.se_unnamed.relaxed_combine_columns(test2)
+    assert combined2 is not None
+    assert isinstance(combined2, SingleCellExperiment)
+    assert len(combined2.alternative_experiments) == 0
+    assert len(combined2.row_data["A"]) == 100
+
 
 def test_combine_with_alts(experiments):
     combined = biocutils.combine_columns(

{singlecellexperiment-0.5.0 → singlecellexperiment-0.5.2}/tests/test_sce_combine_rows.py

@@ -25,6 +25,11 @@ def test_combine_rows(experiments):
     assert len(combined.alternative_experiments) == 0
     assert len(combined.row_data["A"]) == 200
 
+    combined2 = experiments.se_unnamed.combine_rows(experiments.se_unnamed_2)
+    assert combined2 is not None
+    assert isinstance(combined2, SingleCellExperiment)
+    assert len(combined2.alternative_experiments) == 0
+    assert len(combined2.row_data["A"]) == 200
 
 def test_relaxed_combine_rows(experiments):
     ncols = 10
@@ -46,6 +51,12 @@ def test_relaxed_combine_rows(experiments):
     assert len(combined.alternative_experiments) == 0
     assert len(combined.row_data["A"]) == 200
 
+    combined2 = experiments.se_unnamed.relaxed_combine_rows(test2)
+    assert combined2 is not None
+    assert isinstance(combined2, SingleCellExperiment)
+    assert len(combined2.alternative_experiments) == 0
+    assert len(combined2.row_data["A"]) == 200
+
 
 def test_combine_with_alts(experiments):
     combined = biocutils.combine_rows(