SingleCellExperiment 0.4.6__tar.gz → 0.5.0__tar.gz

singlecellexperiment-0.5.0/.github/workflows/pypi-publish.yml

@@ -0,0 +1,52 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.12.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

singlecellexperiment-0.5.0/.github/workflows/pypi-test.yml

@@ -0,0 +1,33 @@
+name: Run tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/.pre-commit-config.yaml

@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.4.0
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.3.7
+  rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/CHANGELOG.md

@@ -1,5 +1,21 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
+## Version 0.4.7
+
+- Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).
+- The package now enforces the versions of mudata, anndata and numpy that are compatible with each other.
+
+## Version 0.4.2 - 0.4.6
+
+- Fix issue coercing `SummarizedExperiments` to `AnnData` objects and vice-versa.
+- Handling coercions when matrices are delayed arrays or backed (for `AnnData`).
+- Update sphinx configuration to run snippets in the documentation.
+
 ## Version 0.4.0 to 0.4.1
 
 This is a complete rewrite of the package, following the functional paradigm from our [developer notes](https://github.com/BiocPy/developer_guide#use-functional-discipline).

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.6
+Version: 0.5.0
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -10,26 +10,34 @@ Project-URL: Documentation, https://github.com/BiocPy/SingleCellExperiment
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
-Requires-Python: >=3.8
+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<0.5.0,>=0.4.0
+Requires-Dist: summarizedexperiment>=0.4.5
 Provides-Extra: optional
-Requires-Dist: anndata; 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"
 Requires-Dist: h5py; extra == "optional"
-Requires-Dist: mudata; extra == "optional"
+Requires-Dist: mudata==0.2.3; python_version <= "3.9" and extra == "optional"
+Requires-Dist: mudata>0.2.3; python_version > "3.9" and extra == "optional"
 Requires-Dist: delayedarray; extra == "optional"
 Requires-Dist: hdf5array; extra == "optional"
+Requires-Dist: numpy==1.24.4; python_version <= "3.9" and extra == "optional"
+Requires-Dist: numpy>1.24.4; python_version > "3.9" and extra == "optional"
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
-Requires-Dist: anndata; extra == "testing"
+Requires-Dist: anndata==0.9.2; python_version <= "3.9" and extra == "testing"
+Requires-Dist: anndata>0.9.2; python_version > "3.9" and extra == "testing"
 Requires-Dist: h5py; extra == "testing"
-Requires-Dist: mudata; extra == "testing"
+Requires-Dist: mudata==0.2.3; python_version <= "3.9" and extra == "testing"
+Requires-Dist: mudata>0.2.3; python_version > "3.9" and extra == "testing"
 Requires-Dist: delayedarray; extra == "testing"
 Requires-Dist: hdf5array; extra == "testing"
+Requires-Dist: numpy==1.24.4; python_version <= "3.9" and extra == "testing"
+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/)
@@ -37,20 +45,26 @@ Requires-Dist: hdf5array; extra == "testing"
 
 # SingleCellExperiment
 
-Container class to represent single-cell experiments; follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
+This package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
 
 
 ## Install
 
-Package is published to [PyPI](https://pypi.org/project/singlecellexperiment/)
+To get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)
 
-```shell
+```bash
 pip install singlecellexperiment
 ```
 
 ## Usage
 
-Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `SingleCellExperiment` objects.
+The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+
+- `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
+- `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
+- `row_pairs` or `column_pairs`: Stores relationships between features or cells.
+
+Readers are available to parse h5ad or `AnnData` objects to SCE:
 
 ```python
 import singlecellexperiment
@@ -84,7 +98,8 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
+Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/README.md

@@ -4,20 +4,26 @@
 
 # SingleCellExperiment
 
-Container class to represent single-cell experiments; follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
+This package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
 
 
 ## Install
 
-Package is published to [PyPI](https://pypi.org/project/singlecellexperiment/)
+To get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)
 
-```shell
+```bash
 pip install singlecellexperiment
 ```
 
 ## Usage
 
-Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `SingleCellExperiment` objects.
+The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+
+- `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
+- `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
+- `row_pairs` or `column_pairs`: Stores relationships between features or cells.
+
+Readers are available to parse h5ad or `AnnData` objects to SCE:
 
 ```python
 import singlecellexperiment
@@ -51,7 +57,8 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
+Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/docs/changelog.md

@@ -1,5 +1,21 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
+## Version 0.4.7
+
+- Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).
+- The package now enforces the versions of mudata, anndata and numpy that are compatible with each other.
+
+## Version 0.4.2 - 0.4.6
+
+- Fix issue coercing `SummarizedExperiments` to `AnnData` objects and vice-versa.
+- Handling coercions when matrices are delayed arrays or backed (for `AnnData`).
+- Update sphinx configuration to run snippets in the documentation.
+
 ## Version 0.4.0 to 0.4.1
 
 This is a complete rewrite of the package, following the functional paradigm from our [developer notes](https://github.com/BiocPy/developer_guide#use-functional-discipline).

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/docs/conf.py

@@ -72,6 +72,7 @@ extensions = [
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -79,7 +80,8 @@ templates_path = ["_templates"]
 
 
 # Enable markdown
-extensions.append("myst_parser")
+# extensions.append("myst_parser")
+extensions.append("myst_nb")
 
 # Configure MyST-Parser
 myst_enable_extensions = [
@@ -167,9 +169,11 @@ pygments_style = "sphinx"
 todo_emit_warnings = True
 
 autodoc_default_options = {
-    'special-members': True,
-    'undoc-members': False,
-    'exclude-members': '__weakref__, __dict__, __str__, __module__, __init__'
+    # 'members': 'var1, var2',
+    # 'member-order': 'bysource',
+    "special-members": True,
+    "undoc-members": True,
+    "exclude-members": "__weakref__, __dict__, __str__, __module__",
 }
 
 autosummary_generate = True
@@ -309,7 +313,8 @@ intersphinx_mapping = {
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
     "biocframe": ("https://biocpy.github.io/BiocFrame", None),
     "genomicranges": ("https://biocpy.github.io/GenomicRanges", None),
-    "singlecellexperiment": ("https://biocpy.github.io/SingleCellExperiment", None),
+    "summarizedexperiment": ("https://biocpy.github.io/SummarizedExperiment", None),
+    "biocutils": ("https://biocpy.github.io/BiocUtils", None),
 }
 
 print(f"loading configurations for {project} {version} ...", file=sys.stderr)

singlecellexperiment-0.5.0/docs/index.md

@@ -0,0 +1,37 @@
+# SingleCellExperiment
+
+This package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
+
+
+## Install
+
+To get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)
+
+```bash
+pip install singlecellexperiment
+```
+
+## Contents
+
+```{toctree}
+:maxdepth: 2
+
+Overview <tutorial>
+Module Reference <api/modules>
+Contributions & Help <contributing>
+License <license>
+Authors <authors>
+Changelog <changelog>
+```
+
+
+## Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+
+[Sphinx]: http://www.sphinx-doc.org/
+[Markdown]: https://daringfireball.net/projects/markdown/
+[reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+[MyST]: https://myst-parser.readthedocs.io/en/latest/

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/docs/readme.md

@@ -4,20 +4,26 @@
 
 # SingleCellExperiment
 
-Container class to represent single-cell experiments; follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
+This package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).
 
 
 ## Install
 
-Package is published to [PyPI](https://pypi.org/project/singlecellexperiment/)
+To get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)
 
-```shell
+```bash
 pip install singlecellexperiment
 ```
 
 ## Usage
 
-Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `SingleCellExperiment` objects.
+The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+
+- `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
+- `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
+- `row_pairs` or `column_pairs`: Stores relationships between features or cells.
+
+Readers are available to parse h5ad or `AnnData` objects to SCE:
 
 ```python
 import singlecellexperiment
@@ -51,7 +57,8 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
+Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 

{singlecellexperiment-0.4.6 → singlecellexperiment-0.5.0}/docs/requirements.txt

@@ -1,7 +1,9 @@
 furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
+sphinx-autodoc-typehints