SingleCellExperiment 0.6.2__tar.gz → 0.6.4__tar.gz

{singlecellexperiment-0.6.2 → singlecellexperiment-0.6.4}/.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-0.6.2 → singlecellexperiment-0.6.4}/CHANGELOG.md

@@ -1,11 +1,15 @@
 # Changelog
 
-## Version 0.6.0 - 0.6.2
+## Version 0.6.0 - 0.6.4
 
 - 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.
+- Fix bug when slicing objects containing row or column pairs.
+- Add getters/setters for `sizeFactors`, modifying this in the column_data of the object.
+- Improve test coverage and fix bugs.
 
 ## Version 0.5.8 - 0.5.9
 

{singlecellexperiment-0.6.2 → singlecellexperiment-0.6.4}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.2
+Version: 0.6.4
 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-0.6.2 → singlecellexperiment-0.6.4}/docs/changelog.md

@@ -1,11 +1,15 @@
 # Changelog
 
-## Version 0.6.0 - 0.6.2
+## Version 0.6.0 - 0.6.4
 
 - 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.
+- Fix bug when slicing objects containing row or column pairs.
+- Add getters/setters for `sizeFactors`, modifying this in the column_data of the object.
+- Improve test coverage and fix bugs.
 
 ## Version 0.5.8 - 0.5.9
 

{singlecellexperiment-0.6.2 → singlecellexperiment-0.6.4}/docs/tutorial.md

@@ -179,6 +179,35 @@ One can access an reduced dimension by index or name:
 sce.reduced_dim(0) # same as se.reduced_dim("random_embeds")
 ```
 
+## Size Factors
+
+In Bioconductor, size factors represent scaling factors used to normalize cell-specific biases (such as differences in sequencing depth). Following the Bioconductor design, `SingleCellExperiment` stores size factors directly inside the column data under the column name `"sizeFactors"`.
+
+You can set, retrieve, and delete size factors using either functional methods or the `size_factors` property:
+
+```{code-cell}
+# Generate mock size factors (e.g. library size scaling factors)
+cell_depths = counts.sum(axis=0)
+if isinstance(cell_depths, np.matrix) or hasattr(cell_depths, "A"):
+    cell_depths = np.array(cell_depths).flatten()
+
+# Scale factors so that their mean is 1
+size_factors = cell_depths / np.mean(cell_depths)
+
+# Set size factors on the experiment
+sce.set_size_factors(size_factors, in_place=True)
+
+# Access size factors
+print("Retrieved size factors:", sce.get_size_factors())
+
+# They reside directly in the column_data under "sizeFactors":
+print("Column data 'sizeFactors':", sce.column_data["sizeFactors"])
+
+# To delete/remove size factors, set them to None
+sce.set_size_factors(None, in_place=True)
+print("After deletion, is 'sizeFactors' in column_data?", "sizeFactors" in sce.column_data.column_names)
+```
+
 ## Subset experiments
 
 You can subset experimental data by using the subset (`[]`) operator. This operation accepts different slice input types, such as a boolean vector, a `slice` object, a list of indices, or names (if available) to subset.

{singlecellexperiment-0.6.2 → singlecellexperiment-0.6.4}/pyproject.toml

@@ -10,7 +10,7 @@ version_scheme = "no-guess-dev"
 [tool.ruff]
 line-length = 120
 src = ["src"]
-exclude = ["tests"]
+# exclude = ["tests"]
 extend-ignore = ["F821"]
 
 [tool.ruff.pydocstyle]

{singlecellexperiment-0.6.2 → singlecellexperiment-0.6.4}/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-0.6.2 → singlecellexperiment-0.6.4}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.2
+Version: 0.6.4
 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-0.6.2 → singlecellexperiment-0.6.4}/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-0.6.4/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-0.6.4/src/SingleCellExperiment.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.6.4",
+  "distance": 0,
+  "node": "g2b7684b0b92219261086934158bbd5c35c2d1e3b",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-06-28"
+}