scatrans 0.9.9.dev2__tar.gz → 0.9.10.dev0__tar.gz

{scatrans-0.9.9.dev2 → scatrans-0.9.10.dev0}/PKG-INFO

@@ -1,128 +1,128 @@
-Metadata-Version: 2.4
-Name: scatrans
-Version: 0.9.9.dev2
-Summary: Single-cell Active Transcription Analysis
-Author: scATrans Developers
-License: Apache-2.0
-Project-URL: Homepage, https://github.com/leelieber2025/scATrans
-Project-URL: Documentation, https://scatrans.readthedocs.io
-Project-URL: Changelog, https://scatrans.readthedocs.io/en/latest/changelog.html
-Keywords: single-cell,RNA-seq,unspliced,nascent RNA,active transcription,bioinformatics
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: scanpy>=1.9
-Requires-Dist: anndata>=0.8
-Requires-Dist: numpy>=1.21
-Requires-Dist: pandas>=1.3
-Requires-Dist: pyarrow>=10.0
-Requires-Dist: scipy>=1.7
-Requires-Dist: scikit-learn>=1.0
-Requires-Dist: joblib>=1.2
-Requires-Dist: statsmodels>=0.13
-Requires-Dist: matplotlib>=3.5
-Requires-Dist: seaborn>=0.12
-Requires-Dist: adjustText>=0.7
-Requires-Dist: importlib_resources>=5.0; python_version < "3.10"
-Provides-Extra: advanced
-Requires-Dist: scvelo>=0.3.0; extra == "advanced"
-Provides-Extra: pseudobulk
-Requires-Dist: pydeseq2>=0.4.0; extra == "pseudobulk"
-Provides-Extra: gene-features
-Requires-Dist: gtfparse>=1.3.0; extra == "gene-features"
-Provides-Extra: memento
-Requires-Dist: memento-de<0.3.0,>=0.1.0; extra == "memento"
-Provides-Extra: gsea
-Requires-Dist: gseapy>=1.1; extra == "gsea"
-Provides-Extra: dev
-Requires-Dist: pytest>=7.0; extra == "dev"
-Requires-Dist: pytest-cov>=4.0; extra == "dev"
-Requires-Dist: ruff>=0.4.0; extra == "dev"
-Requires-Dist: pre-commit>=3.5; extra == "dev"
-Requires-Dist: mypy>=1.10; extra == "dev"
-Dynamic: license-file
-
-# scATrans
-
-[![PyPI version](https://img.shields.io/pypi/v/scatrans.svg)](https://pypi.org/project/scatrans/)
-[![Python versions](https://img.shields.io/pypi/pyversions/scatrans.svg)](https://pypi.org/project/scatrans/)
-[![Documentation Status](https://readthedocs.org/projects/scatrans/badge/?version=latest)](https://scatrans.readthedocs.io/en/latest/?badge=latest)
-[![CI](https://github.com/leelieber2025/scATrans/actions/workflows/ci.yml/badge.svg)](https://github.com/leelieber2025/scATrans/actions/workflows/ci.yml)
-[![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
-
-scATrans is a Python toolkit for single-cell differential analysis. It is
-primarily designed for datasets that contain spliced/unspliced (or
-mature/nascent) RNA layers. In this setting it computes a composite active
-transcription score that integrates differential expression with
-reference-based excess unspliced RNA to rank genes.
-
-It also supports conventional differential expression workflows (no
-velocity data required) using scanpy, PyDESeq2 pseudobulk, linear mixed
-models, or optional Memento. Functional enrichment (ORA, GSEA, GO, KEGG)
-uses bundled gene sets with consistent universe handling, and a set of
-visualization functions is provided.
-
-**📚 Full documentation, tutorials, and the complete API reference are on
-Read the Docs: https://scatrans.readthedocs.io**
-
-## Installation
-
-```bash
-pip install scatrans
-
-# Optional extras: advanced (scVelo) mode, pseudobulk DE (PyDESeq2), Memento, GSEA
-pip install "scatrans[advanced,gene_features,pseudobulk]" gseapy
-```
-
-See [Installation](https://scatrans.readthedocs.io/en/latest/installation.html)
-for extras, source installs, and logging setup.
-
-## Quickstart
-
-```python
-import scatrans as scat
-
-# One-liner pipeline: score → filter → GO enrichment
-result = scat.run_default_pipeline(
-    adata,
-    groupby="condition",
-    target_group="Disease",
-    reference_group="Control",
-    sample_col="sample",   # optional; auto-selects pseudobulk when >=3 replicates/group
-    organism="mouse",
-)
-print(result["candidates"].head())
-print(result["enrichment"].head())
-```
-
-See the [Quickstart](https://scatrans.readthedocs.io/en/latest/quickstart.html)
-for a complete end-to-end walkthrough, the
-[Tutorials](https://scatrans.readthedocs.io/en/latest/tutorials/index.html)
-for fully worked, real-data notebooks (with and without RNA-velocity
-layers), and the
-[User Guide](https://scatrans.readthedocs.io/en/latest/user_guide/index.html)
-for DE backends, enrichment, plotting, and advanced options.
-
-## Before reporting results in a paper
-
-`active_score` is a **composite heuristic rank**, not a p-value or FDR on
-its own. See
-[Statistical Guidance](https://scatrans.readthedocs.io/en/latest/statistical_guidance.html)
-for what each output column means, safe vs. unsafe uses, and a reporting
-checklist before you cite scATrans results in a manuscript or supplement.
-
-## License
-
-Software (Python source) is licensed under [Apache License 2.0](LICENSE).
-Bundled gene-set data (GO, KEGG) carries its own licensing terms — see
-[License](https://scatrans.readthedocs.io/en/latest/license.html) before
-commercial use.
+Metadata-Version: 2.4
+Name: scatrans
+Version: 0.9.10.dev0
+Summary: Single-cell Active Transcription Analysis
+Author: scATrans Developers
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/leelieber2025/scATrans
+Project-URL: Documentation, https://scatrans.readthedocs.io
+Project-URL: Changelog, https://scatrans.readthedocs.io/en/latest/changelog.html
+Keywords: single-cell,RNA-seq,unspliced,nascent RNA,active transcription,bioinformatics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scanpy>=1.9
+Requires-Dist: anndata>=0.8
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: pyarrow>=10.0
+Requires-Dist: scipy>=1.7
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: joblib>=1.2
+Requires-Dist: statsmodels>=0.13
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: seaborn>=0.12
+Requires-Dist: adjustText>=0.7
+Requires-Dist: importlib_resources>=5.0; python_version < "3.10"
+Provides-Extra: advanced
+Requires-Dist: scvelo>=0.3.0; extra == "advanced"
+Provides-Extra: pseudobulk
+Requires-Dist: pydeseq2>=0.4.0; extra == "pseudobulk"
+Provides-Extra: gene-features
+Requires-Dist: gtfparse>=1.3.0; extra == "gene-features"
+Provides-Extra: memento
+Requires-Dist: memento-de<0.3.0,>=0.1.0; extra == "memento"
+Provides-Extra: gsea
+Requires-Dist: gseapy>=1.1; extra == "gsea"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.4.0; extra == "dev"
+Requires-Dist: pre-commit>=3.5; extra == "dev"
+Requires-Dist: mypy>=1.10; extra == "dev"
+Dynamic: license-file
+
+# scATrans
+
+[![PyPI version](https://img.shields.io/pypi/v/scatrans.svg)](https://pypi.org/project/scatrans/)
+[![Python versions](https://img.shields.io/pypi/pyversions/scatrans.svg)](https://pypi.org/project/scatrans/)
+[![Documentation Status](https://readthedocs.org/projects/scatrans/badge/?version=latest)](https://scatrans.readthedocs.io/en/latest/?badge=latest)
+[![CI](https://github.com/leelieber2025/scATrans/actions/workflows/ci.yml/badge.svg)](https://github.com/leelieber2025/scATrans/actions/workflows/ci.yml)
+[![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+
+scATrans is a Python toolkit for single-cell differential analysis. It is
+primarily designed for datasets that contain spliced/unspliced (or
+mature/nascent) RNA layers. In this setting it computes a composite active
+transcription score that integrates differential expression with
+reference-based excess unspliced RNA to rank genes.
+
+It also supports conventional differential expression workflows (no
+velocity data required) using scanpy, PyDESeq2 pseudobulk, linear mixed
+models, or optional Memento. Functional enrichment (ORA, GSEA, GO, KEGG)
+uses bundled gene sets with consistent universe handling, and a set of
+visualization functions is provided.
+
+**📚 Full documentation, tutorials, and the complete API reference are on
+Read the Docs: https://scatrans.readthedocs.io**
+
+## Installation
+
+```bash
+pip install scatrans
+
+# Optional extras: advanced (scVelo) mode, pseudobulk DE (PyDESeq2), Memento, GSEA
+pip install "scatrans[advanced,gene_features,pseudobulk]" gseapy
+```
+
+See [Installation](https://scatrans.readthedocs.io/en/latest/installation.html)
+for extras, source installs, and logging setup.
+
+## Quickstart
+
+```python
+import scatrans as scat
+
+# One-liner pipeline: score → filter → GO enrichment
+result = scat.run_default_pipeline(
+    adata,
+    groupby="condition",
+    target_group="Disease",
+    reference_group="Control",
+    sample_col="sample",   # optional; auto-selects pseudobulk when >=3 replicates/group
+    organism="mouse",
+)
+print(result["candidates"].head())
+print(result["enrichment"].head())
+```
+
+See the [Quickstart](https://scatrans.readthedocs.io/en/latest/quickstart.html)
+for a complete end-to-end walkthrough, the
+[Tutorials](https://scatrans.readthedocs.io/en/latest/tutorials/index.html)
+for fully worked, real-data notebooks (with and without RNA-velocity
+layers), and the
+[User Guide](https://scatrans.readthedocs.io/en/latest/user_guide/index.html)
+for DE backends, enrichment, plotting, and advanced options.
+
+## Before reporting results in a paper
+
+`active_score` is a **composite heuristic rank**, not a p-value or FDR on
+its own. See
+[Statistical Guidance](https://scatrans.readthedocs.io/en/latest/statistical_guidance.html)
+for what each output column means, safe vs. unsafe uses, and a reporting
+checklist before you cite scATrans results in a manuscript or supplement.
+
+## License
+
+Software (Python source) is licensed under [Apache License 2.0](LICENSE).
+Bundled gene-set data (GO, KEGG) carries its own licensing terms — see
+[License](https://scatrans.readthedocs.io/en/latest/license.html) before
+commercial use.

{scatrans-0.9.9.dev2 → scatrans-0.9.10.dev0}/setup.cfg

@@ -1,5 +1,5 @@
-[egg_info]
-egg_base = .
-tag_build = 
-tag_date = 0
-
+[egg_info]
+egg_base = .
+tag_build = 
+tag_date = 0
+

{scatrans-0.9.9.dev2 → scatrans-0.9.10.dev0}/src/scatrans/_version.py

@@ -1,24 +1,24 @@
-# file generated by vcs-versioning
-# don't change, don't track in version control
-from __future__ import annotations
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-version: str
-__version__: str
-__version_tuple__: tuple[int | str, ...]
-version_tuple: tuple[int | str, ...]
-commit_id: str | None
-__commit_id__: str | None
-
-__version__ = version = '0.9.9.dev2'
-__version_tuple__ = version_tuple = (0, 9, 9, 'dev2')
-
-__commit_id__ = commit_id = None
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.9.10.dev0'
+__version_tuple__ = version_tuple = (0, 9, 10, 'dev0')
+
+__commit_id__ = commit_id = 'g84717a676'