SingleCellExperiment 0.6.1__tar.gz → 0.6.3__tar.gz

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.14.5
+  rev: v0.15.6
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/CHANGELOG.md

@@ -1,9 +1,12 @@
 # Changelog
 
-## Version 0.6.0
+## Version 0.6.0 - 0.6.3
 
 - Changed related to SummarizedExperiment and implementation of `CompressedGenomicRangesList` in the genomic ranges package.
 - Update versions of relevant dependency packages.
+- Rename `reduced_dims` to `reduced_dimensions`.
+- Implement coercions to/from RSE/SE.
+- Access data stored in `raw` (if available) as `alternative_experiments`, when initializing `SingleCellExperiment` objects from anndata/h5ad files.
 
 ## Version 0.5.8 - 0.5.9
 

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.1
+Version: 0.6.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
 Author-email: jayaram.kancherla@gmail.com
 License: MIT
-Project-URL: Documentation, https://github.com/BiocPy/SingleCellExperiment
+Project-URL: Documentation, https://biocpy.github.io/SingleCellExperiment/
+Project-URL: Source, https://github.com/BiocPy/SingleCellExperiment
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/docs/changelog.md

@@ -1,9 +1,12 @@
 # Changelog
 
-## Version 0.6.0
+## Version 0.6.0 - 0.6.3
 
 - Changed related to SummarizedExperiment and implementation of `CompressedGenomicRangesList` in the genomic ranges package.
 - Update versions of relevant dependency packages.
+- Rename `reduced_dims` to `reduced_dimensions`.
+- Implement coercions to/from RSE/SE.
+- Access data stored in `raw` (if available) as `alternative_experiments`, when initializing `SingleCellExperiment` objects from anndata/h5ad files.
 
 ## Version 0.5.8 - 0.5.9
 

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/setup.cfg

@@ -9,7 +9,8 @@ long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
 url = https://github.com/BiocPy/SingleCellExperiment
 project_urls = 
-	Documentation = https://github.com/BiocPy/SingleCellExperiment
+	Documentation = https://biocpy.github.io/SingleCellExperiment/
+	Source = https://github.com/BiocPy/SingleCellExperiment
 platforms = any
 classifiers = 
 	Development Status :: 4 - Beta

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.1
+Version: 0.6.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
 Author-email: jayaram.kancherla@gmail.com
 License: MIT
-Project-URL: Documentation, https://github.com/BiocPy/SingleCellExperiment
+Project-URL: Documentation, https://biocpy.github.io/SingleCellExperiment/
+Project-URL: Source, https://github.com/BiocPy/SingleCellExperiment
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/src/SingleCellExperiment.egg-info/SOURCES.txt

@@ -29,6 +29,8 @@ src/SingleCellExperiment.egg-info/SOURCES.txt
 src/SingleCellExperiment.egg-info/dependency_links.txt
 src/SingleCellExperiment.egg-info/not-zip-safe
 src/SingleCellExperiment.egg-info/requires.txt
+src/SingleCellExperiment.egg-info/scm_file_list.json
+src/SingleCellExperiment.egg-info/scm_version.json
 src/SingleCellExperiment.egg-info/top_level.txt
 src/singlecellexperiment/SingleCellExperiment.py
 src/singlecellexperiment/__init__.py

singlecellexperiment-0.6.3/src/SingleCellExperiment.egg-info/scm_file_list.json

@@ -0,0 +1,50 @@
+{
+  "files": [
+    ".coveragerc",
+    ".pre-commit-config.yaml",
+    "README.md",
+    "setup.cfg",
+    "tox.ini",
+    "LICENSE.txt",
+    "setup.py",
+    "pyproject.toml",
+    "CHANGELOG.md",
+    "CONTRIBUTING.md",
+    "AUTHORS.md",
+    ".readthedocs.yml",
+    ".gitignore",
+    "docs/readme.md",
+    "docs/Makefile",
+    "docs/authors.md",
+    "docs/requirements.txt",
+    "docs/tutorial.md",
+    "docs/contributing.md",
+    "docs/license.md",
+    "docs/changelog.md",
+    "docs/conf.py",
+    "docs/index.md",
+    "docs/_static/.gitignore",
+    "src/singlecellexperiment/__init__.py",
+    "src/singlecellexperiment/SingleCellExperiment.py",
+    "src/singlecellexperiment/_combineutils.py",
+    "src/singlecellexperiment/_ioutils.py",
+    "src/singlecellexperiment/io/tenx.py",
+    "src/singlecellexperiment/io/__init__.py",
+    "src/singlecellexperiment/io/h5ad.py",
+    "tests/test_sce_methods.py",
+    "tests/test_sce.py",
+    "tests/conftest.py",
+    "tests/test_sce_slice.py",
+    "tests/test_sce_io.py",
+    "tests/test_sce_combine_rows.py",
+    "tests/test_sce_combine_cols.py",
+    "tests/data/mocks.py",
+    "tests/data/adata.h5ad",
+    "tests/data/tenx.sub.h5",
+    "tests/data/raw_feature_bc_matrix/matrix.mtx",
+    "tests/data/raw_feature_bc_matrix/features.tsv",
+    "tests/data/raw_feature_bc_matrix/barcodes.tsv",
+    ".github/workflows/run-tests.yml",
+    ".github/workflows/publish-pypi.yml"
+  ]
+}

singlecellexperiment-0.6.3/src/SingleCellExperiment.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.6.3",
+  "distance": 0,
+  "node": "ge5f7e11fcea4daa04c4699ed04d87fdb8e9ed3ec",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-06-24"
+}

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/src/singlecellexperiment/SingleCellExperiment.py

@@ -6,6 +6,7 @@ from warnings import warn
 
 import biocframe
 import biocutils as ut
+from summarizedexperiment import SummarizedExperiment
 from summarizedexperiment._combineutils import (
     check_assays_are_equal,
     merge_assays,
@@ -1194,14 +1195,18 @@ class SingleCellExperiment(RangedSummarizedExperiment):
     def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
         """Create a ``SingleCellExperiment`` from :py:class:`~anndata.AnnData`.
 
-         Args:
+        If the input contains any data in the ``uns`` attribute, the
+        `metadata` slot of the ``SingleCellExperiment`` will contain a key ``uns``.
+
+        If the input contains ``raw`` data, the ``SingleCellExperiment``
+        will contain an alternative experiment called ``raw``.
+
+        Args:
             input:
                 Input data.
 
         Returns:
-            A ``SingleCellExperiment`` object. If the input contains any data
-            in the ``uns`` attribute, the `metadata` slot of the ``SingleCellExperiment``
-            will contain a key ``uns``.
+            A ``SingleCellExperiment`` object.
         """
 
         layers = OrderedDict()
@@ -1216,6 +1221,15 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         obsp = _to_normal_dict(input.obsp)
         _metadata = {"uns": input.uns} if input.uns is not None else None
 
+        alt_expts = None
+        if input.raw is not None:
+            raw_se = SummarizedExperiment(
+                assays={"X": input.raw.X.transpose()},
+                row_data=biocframe.BiocFrame.from_pandas(input.raw.var),
+                column_data=biocframe.BiocFrame.from_pandas(input.obs),
+            )
+            alt_expts = {"raw": raw_se}
+
         return cls(
             assays=layers,
             row_data=biocframe.BiocFrame.from_pandas(input.var),
@@ -1224,6 +1238,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             reduced_dimensions=obsm,
             row_pairs=varp,
             column_pairs=obsp,
+            alternative_experiments=alt_expts,
         )
 
     ###############################
@@ -1277,6 +1292,86 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """Wrapper around :py:func:`~combine_columns`."""
         return combine_columns(self, *other)
 
+    #######################
+    ######>> to rse <<#####
+    #######################
+
+    def to_rangedsummarizedexperiment(self) -> RangedSummarizedExperiment:
+        """Coerce to :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`.
+
+        Returns:
+            A ``RangedSummarizedExperiment`` object.
+        """
+        return RangedSummarizedExperiment(
+            assays=self._assays,
+            row_ranges=self._row_ranges,
+            row_data=self._rows,
+            column_data=self._cols,
+            row_names=self._row_names,
+            column_names=self._column_names,
+            metadata=self._metadata,
+            _validate=False,
+        )
+
+    def to_rse(self) -> RangedSummarizedExperiment:
+        """Alias for :py:meth:`~to_rangedsummarizedexperiment`."""
+        return self.to_rangedsummarizedexperiment()
+
+    @classmethod
+    def from_rangedsummarizedexperiment(cls, rse: RangedSummarizedExperiment) -> SingleCellExperiment:
+        """Coerce from :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`.
+
+        Args:
+            rse:
+                A ``RangedSummarizedExperiment`` object.
+
+        Returns:
+            A ``SingleCellExperiment`` object.
+        """
+        return cls(
+            assays=rse.assays,
+            row_ranges=rse.row_ranges,
+            row_data=rse.row_data,
+            column_data=rse.col_data,
+            row_names=rse.row_names,
+            column_names=rse.column_names,
+            metadata=rse.metadata,
+        )
+
+    @classmethod
+    def from_rse(cls, rse: RangedSummarizedExperiment) -> SingleCellExperiment:
+        """Alias for :py:meth:`~from_rangedsummarizedexperiment`."""
+        return cls.from_rangedsummarizedexperiment(rse)
+
+    ########################
+    ######>> from se <<#####
+    ########################
+
+    @classmethod
+    def from_summarizedexperiment(cls, se: SummarizedExperiment) -> SingleCellExperiment:
+        """Coerce from :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
+
+        Args:
+            se:
+                A ``SummarizedExperiment`` object.
+
+        Returns:
+            A ``SingleCellExperiment`` object.
+        """
+        return cls(
+            assays=se.assays,
+            row_data=se.row_data,
+            column_data=se.col_data,
+            row_names=se.row_names,
+            column_names=se.column_names,
+            metadata=se.metadata,
+        )
+
+    @classmethod
+    def from_se(cls, se: SummarizedExperiment) -> SingleCellExperiment:
+        """Alias for :py:meth:`~from_summarizedexperiment`."""
+        return cls.from_summarizedexperiment(se)
+
 
 ############################
 ######>> combine ops <<#####

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/tests/test_sce_io.py

@@ -198,6 +198,16 @@ def test_SCE_randomAnnData():
     assert tse is not None
     assert isinstance(tse, SingleCellExperiment)
 
+    # set raw
+    adata.raw = adata.copy()
+    tse = singlecellexperiment.SingleCellExperiment.from_anndata(adata)
+
+    assert tse is not None
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.alternative_experiments is not None
+    assert "raw" in tse.alternative_experiments
+    assert isinstance(tse.alternative_experiments["raw"], SummarizedExperiment)
+    assert tse.alternative_experiments["raw"].shape == (d, n)
 
 def test_SCE_to_mudata():
     tse = SingleCellExperiment(

{singlecellexperiment-0.6.1 → singlecellexperiment-0.6.3}/tests/test_sce_methods.py

@@ -5,7 +5,7 @@ from biocframe import BiocFrame
 import numpy as np
 import pandas as pd
 import pytest
-from summarizedexperiment import SummarizedExperiment
+from summarizedexperiment import SummarizedExperiment, RangedSummarizedExperiment
 
 from singlecellexperiment import SingleCellExperiment
 from singlecellexperiment.SingleCellExperiment import SingleCellExperiment as sce
@@ -90,3 +90,45 @@ def test_SCE_props():
 
     assert tse.reduced_dim_names is not None
     assert len(tse.reduced_dim_names) == 1
+
+def test_SCE_to_RSE():
+    tse = SingleCellExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    rse = tse.to_rangedsummarizedexperiment()
+    assert isinstance(rse, RangedSummarizedExperiment)
+    assert not isinstance(rse, SingleCellExperiment)
+    assert rse.shape == tse.shape
+    assert rse.row_ranges is not None
+
+def test_RSE_to_SCE():
+    rse = RangedSummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    tse = SingleCellExperiment.from_rangedsummarizedexperiment(rse)
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.shape == rse.shape
+    assert tse.row_ranges is not None
+
+def test_SCE_to_SE():
+    tse = SingleCellExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    se = tse.to_summarizedexperiment()
+    assert isinstance(se, SummarizedExperiment)
+    assert not isinstance(se, SingleCellExperiment)
+    assert se.shape == tse.shape
+    assert se.row_data is not None
+    assert "seqnames" in se.row_data.column_names
+
+def test_SE_to_SCE():
+    se = SummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data
+    )
+
+    tse = SingleCellExperiment.from_summarizedexperiment(se)
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.shape == se.shape