combatlearn 1.1.0__tar.gz → 1.1.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (18) hide show
  1. {combatlearn-1.1.0 → combatlearn-1.1.2}/PKG-INFO +13 -19
  2. {combatlearn-1.1.0 → combatlearn-1.1.2}/README.md +5 -11
  3. combatlearn-1.1.2/combatlearn/__init__.py +5 -0
  4. {combatlearn-1.1.0 → combatlearn-1.1.2}/combatlearn/combat.py +358 -375
  5. {combatlearn-1.1.0 → combatlearn-1.1.2}/combatlearn.egg-info/PKG-INFO +13 -19
  6. {combatlearn-1.1.0 → combatlearn-1.1.2}/combatlearn.egg-info/SOURCES.txt +2 -0
  7. combatlearn-1.1.2/combatlearn.egg-info/requires.txt +19 -0
  8. combatlearn-1.1.2/dev_requirements.txt +3 -0
  9. combatlearn-1.1.2/docs_requirements.txt +5 -0
  10. {combatlearn-1.1.0 → combatlearn-1.1.2}/pyproject.toml +16 -15
  11. {combatlearn-1.1.0 → combatlearn-1.1.2}/tests/test_combat.py +66 -69
  12. combatlearn-1.1.0/combatlearn/__init__.py +0 -5
  13. combatlearn-1.1.0/combatlearn.egg-info/requires.txt +0 -19
  14. {combatlearn-1.1.0 → combatlearn-1.1.2}/LICENSE +0 -0
  15. {combatlearn-1.1.0 → combatlearn-1.1.2}/combatlearn.egg-info/dependency_links.txt +0 -0
  16. {combatlearn-1.1.0 → combatlearn-1.1.2}/combatlearn.egg-info/top_level.txt +0 -0
  17. {combatlearn-1.1.0 → combatlearn-1.1.2}/requirements.txt +0 -0
  18. {combatlearn-1.1.0 → combatlearn-1.1.2}/setup.cfg +0 -0
{combatlearn-1.1.0 → combatlearn-1.1.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: combatlearn
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- Version: 1.1.0
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+ Version: 1.1.2
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  Summary: Batch-effect harmonization for machine learning frameworks.
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  Author-email: Ettore Rocchi <ettoreroc@gmail.com>
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  License: MIT
@@ -21,14 +21,14 @@ Requires-Dist: nbformat>=4.2
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  Requires-Dist: umap-learn>=0.5
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  Provides-Extra: dev
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  Requires-Dist: pytest>=7; extra == "dev"
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- Requires-Dist: pytest-cov>=4.0; extra == "dev"
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- Requires-Dist: ruff>=0.1; extra == "dev"
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- Requires-Dist: mypy>=1.0; extra == "dev"
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+ Requires-Dist: ruff>=0.8; extra == "dev"
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+ Requires-Dist: pre-commit>=3.0; extra == "dev"
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  Provides-Extra: docs
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- Requires-Dist: mkdocs>=1.5.0; extra == "docs"
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- Requires-Dist: mkdocs-material>=9.0.0; extra == "docs"
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- Requires-Dist: mkdocstrings[python]>=0.24.0; extra == "docs"
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- Requires-Dist: pymdown-extensions>=10.0; extra == "docs"
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+ Requires-Dist: sphinx>=7.0.0; extra == "docs"
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+ Requires-Dist: pydata-sphinx-theme>=0.15.0; extra == "docs"
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+ Requires-Dist: myst-parser>=3.0.0; extra == "docs"
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+ Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
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+ Requires-Dist: linkify-it-py>=2.0.0; extra == "docs"
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  Dynamic: license-file
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  # **combatlearn**
@@ -36,12 +36,11 @@ Dynamic: license-file
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  [![Python versions](https://img.shields.io/badge/python-%3E%3D3.10-blue?logo=python)](https://www.python.org/)
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  [![Test](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml/badge.svg)](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml)
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  [![Documentation](https://readthedocs.org/projects/combatlearn/badge/?version=latest)](https://combatlearn.readthedocs.io)
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- [![PyPI Downloads](https://static.pepy.tech/badge/combatlearn)](https://pepy.tech/projects/combatlearn)
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  [![PyPI Version](https://img.shields.io/pypi/v/combatlearn?cacheSeconds=300)](https://pypi.org/project/combatlearn/)
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  [![License](https://img.shields.io/github/license/EttoreRocchi/combatlearn)](https://github.com/EttoreRocchi/combatlearn/blob/main/LICENSE)
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  <div align="center">
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- <p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/logo.png" alt="combatlearn logo" width="350" /></p>
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+ <p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/source/_static/logo.png" alt="combatlearn logo" width="350" /></p>
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  </div>
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  **combatlearn** makes the popular _ComBat_ (and _CovBat_) batch-effect correction algorithm available for use into machine learning frameworks. It lets you harmonise high-dimensional data inside a scikit-learn `Pipeline`, so that cross-validation and grid-search automatically take batch structure into account, **without data leakage**.
@@ -62,16 +61,11 @@ pip install combatlearn
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  **Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
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  The documentation includes:
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- - [Installation Guide](https://combatlearn.readthedocs.io/en/latest/installation/)
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- - [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/)
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- - [User Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/overview/)
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+ - [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods/)
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  - [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
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- - [Examples](https://combatlearn.readthedocs.io/en/latest/examples/basic-usage/)
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  ## Quick start
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- For more details, see the [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/).
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-
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  ```python
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  import pandas as pd
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  from sklearn.pipeline import Pipeline
@@ -116,7 +110,7 @@ print("Best parameters:", grid.best_params_)
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  print(f"Best CV AUROC: {grid.best_score_:.3f}")
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  ```
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- For a full example of how to use **combatlearn** see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb)
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+ For a full example of how to use **combatlearn** see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb)
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  ## `ComBat` parameters
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@@ -146,13 +140,13 @@ The following section provides a detailed explanation of all parameters availabl
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  The `plot_transformation` method allows to visualize the **ComBat** transformation effect using dimensionality reduction, showing the before/after comparison of data transformed by `ComBat` using PCA, t-SNE, or UMAP to reduce dimensions for visualization.
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- For further details see the [Visualization Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/visualization/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
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+ For further details see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb).
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  ### Batch Effect Metrics
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  The `compute_batch_metrics` method provides quantitative assessment of batch correction quality. It computes metrics including Silhouette coefficient, Davies-Bouldin index, kBET, LISI, and variance ratio for batch effect quantification, as well as k-NN preservation and distance correlation for structure preservation.
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- For further details see the [Metrics Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/metrics/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
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+ For further details see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb).
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  ## Contributing
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{combatlearn-1.1.0 → combatlearn-1.1.2}/README.md RENAMED
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  [![Python versions](https://img.shields.io/badge/python-%3E%3D3.10-blue?logo=python)](https://www.python.org/)
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  [![Test](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml/badge.svg)](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml)
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  [![Documentation](https://readthedocs.org/projects/combatlearn/badge/?version=latest)](https://combatlearn.readthedocs.io)
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- [![PyPI Downloads](https://static.pepy.tech/badge/combatlearn)](https://pepy.tech/projects/combatlearn)
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  [![PyPI Version](https://img.shields.io/pypi/v/combatlearn?cacheSeconds=300)](https://pypi.org/project/combatlearn/)
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  [![License](https://img.shields.io/github/license/EttoreRocchi/combatlearn)](https://github.com/EttoreRocchi/combatlearn/blob/main/LICENSE)
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  <div align="center">
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- <p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/logo.png" alt="combatlearn logo" width="350" /></p>
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+ <p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/source/_static/logo.png" alt="combatlearn logo" width="350" /></p>
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  </div>
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  **combatlearn** makes the popular _ComBat_ (and _CovBat_) batch-effect correction algorithm available for use into machine learning frameworks. It lets you harmonise high-dimensional data inside a scikit-learn `Pipeline`, so that cross-validation and grid-search automatically take batch structure into account, **without data leakage**.
@@ -29,16 +28,11 @@ pip install combatlearn
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  **Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
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  The documentation includes:
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- - [Installation Guide](https://combatlearn.readthedocs.io/en/latest/installation/)
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- - [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/)
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- - [User Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/overview/)
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+ - [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods/)
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  - [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
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- - [Examples](https://combatlearn.readthedocs.io/en/latest/examples/basic-usage/)
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  ## Quick start
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- For more details, see the [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/).
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  ```python
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  import pandas as pd
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  from sklearn.pipeline import Pipeline
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  print(f"Best CV AUROC: {grid.best_score_:.3f}")
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  ```
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- For a full example of how to use **combatlearn** see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb)
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+ For a full example of how to use **combatlearn** see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb)
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  ## `ComBat` parameters
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  The `plot_transformation` method allows to visualize the **ComBat** transformation effect using dimensionality reduction, showing the before/after comparison of data transformed by `ComBat` using PCA, t-SNE, or UMAP to reduce dimensions for visualization.
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- For further details see the [Visualization Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/visualization/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
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+ For further details see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb).
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  ### Batch Effect Metrics
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  The `compute_batch_metrics` method provides quantitative assessment of batch correction quality. It computes metrics including Silhouette coefficient, Davies-Bouldin index, kBET, LISI, and variance ratio for batch effect quantification, as well as k-NN preservation and distance correlation for structure preservation.
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- For further details see the [Metrics Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/metrics/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
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+ For further details see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/) and the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/source/demo/combatlearn_demo.ipynb).
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  ## Contributing
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combatlearn-1.1.2/combatlearn/__init__.py ADDED
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+ from .combat import ComBat
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+ __all__ = ["ComBat"]
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+ __version__ = "1.1.2"
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+ __author__ = "Ettore Rocchi"