combatlearn 1.0.0__tar.gz → 1.1.1__tar.gz

{combatlearn-1.0.0 → combatlearn-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: combatlearn
-Version: 1.0.0
+Version: 1.1.1
 Summary: Batch-effect harmonization for machine learning frameworks.
 Author-email: Ettore Rocchi <ettoreroc@gmail.com>
 License: MIT
@@ -21,14 +21,14 @@ Requires-Dist: nbformat>=4.2
 Requires-Dist: umap-learn>=0.5
 Provides-Extra: dev
 Requires-Dist: pytest>=7; extra == "dev"
-Requires-Dist: pytest-cov>=4.0; extra == "dev"
-Requires-Dist: ruff>=0.1; extra == "dev"
-Requires-Dist: mypy>=1.0; extra == "dev"
+Requires-Dist: ruff>=0.8; extra == "dev"
+Requires-Dist: pre-commit>=3.0; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: mkdocs>=1.5.0; extra == "docs"
-Requires-Dist: mkdocs-material>=9.0.0; extra == "docs"
-Requires-Dist: mkdocstrings[python]>=0.24.0; extra == "docs"
-Requires-Dist: pymdown-extensions>=10.0; extra == "docs"
+Requires-Dist: sphinx>=7.0.0; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.15.0; extra == "docs"
+Requires-Dist: myst-parser>=3.0.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: linkify-it-py>=2.0.0; extra == "docs"
 Dynamic: license-file
 
 # **combatlearn**
@@ -41,7 +41,7 @@ Dynamic: license-file
 [![License](https://img.shields.io/github/license/EttoreRocchi/combatlearn)](https://github.com/EttoreRocchi/combatlearn/blob/main/LICENSE)
 
 <div align="center">
-<p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/logo.png" alt="combatlearn logo" width="350" /></p>
+<p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/source/_static/logo.png" alt="combatlearn logo" width="350" /></p>
 </div>
 
 **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**.
@@ -57,6 +57,14 @@ Dynamic: license-file
 pip install combatlearn
 ```
 
+## Documentation
+
+**Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
+
+The documentation includes:
+- [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods/)
+- [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
+
 ## Quick start
 
 ```python
@@ -103,22 +111,11 @@ print("Best parameters:", grid.best_params_)
 print(f"Best CV AUROC: {grid.best_score_:.3f}")
 ```
 
-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)
-
-## Documentation
-
-**Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
-
-The documentation includes:
-- [Installation Guide](https://combatlearn.readthedocs.io/en/latest/installation/)
-- [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/)
-- [User Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/overview/)
-- [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
-- [Examples](https://combatlearn.readthedocs.io/en/latest/examples/basic-usage/)
+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)
 
 ## `ComBat` parameters
 
-The following section provides a detailed explanation of all parameters available in the scikit-learn-compatible `ComBat` class.
+The following section provides a detailed explanation of all parameters available in the scikit-learn-compatible `ComBat` class. For complete API documentation, see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/).
 
 ### Main Parameters
 
@@ -140,11 +137,17 @@ The following section provides a detailed explanation of all parameters availabl
 | `eps` | float | `1e-8` | Small jitter value added to variances to prevent divide-by-zero errors during standardization. |
 
 
-### Batch Effect Correction Visualization 
+### Batch Effect Correction Visualization
 
 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.
 
-For further details see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
+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).
+
+### Batch Effect Metrics
+
+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.
+
+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).
 
 ## Contributing
 
@@ -167,8 +170,7 @@ We gratefully acknowledge:
 
 ## Citation
 
-If **combatlearn** is useful in your research, please cite the original
-papers:
+If **combatlearn** is useful in your research, please cite the original papers:
 
 - Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. _Biostatistics_. 2007 Jan;8(1):118-27. doi: [10.1093/biostatistics/kxj037](https://doi.org/10.1093/biostatistics/kxj037)
 

{combatlearn-1.0.0 → combatlearn-1.1.1}/README.md

@@ -8,7 +8,7 @@
 [![License](https://img.shields.io/github/license/EttoreRocchi/combatlearn)](https://github.com/EttoreRocchi/combatlearn/blob/main/LICENSE)
 
 <div align="center">
-<p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/logo.png" alt="combatlearn logo" width="350" /></p>
+<p><img src="https://raw.githubusercontent.com/EttoreRocchi/combatlearn/main/docs/source/_static/logo.png" alt="combatlearn logo" width="350" /></p>
 </div>
 
 **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**.
@@ -24,6 +24,14 @@
 pip install combatlearn
 ```
 
+## Documentation
+
+**Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
+
+The documentation includes:
+- [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods/)
+- [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
+
 ## Quick start
 
 ```python
@@ -70,22 +78,11 @@ print("Best parameters:", grid.best_params_)
 print(f"Best CV AUROC: {grid.best_score_:.3f}")
 ```
 
-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)
-
-## Documentation
-
-**Full documentation is available at [combatlearn.readthedocs.io](https://combatlearn.readthedocs.io)**
-
-The documentation includes:
-- [Installation Guide](https://combatlearn.readthedocs.io/en/latest/installation/)
-- [Quick Start Tutorial](https://combatlearn.readthedocs.io/en/latest/quickstart/)
-- [User Guide](https://combatlearn.readthedocs.io/en/latest/user-guide/overview/)
-- [API Reference](https://combatlearn.readthedocs.io/en/latest/api/)
-- [Examples](https://combatlearn.readthedocs.io/en/latest/examples/basic-usage/)
+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)
 
 ## `ComBat` parameters
 
-The following section provides a detailed explanation of all parameters available in the scikit-learn-compatible `ComBat` class.
+The following section provides a detailed explanation of all parameters available in the scikit-learn-compatible `ComBat` class. For complete API documentation, see the [API Reference](https://combatlearn.readthedocs.io/en/latest/api/).
 
 ### Main Parameters
 
@@ -107,11 +104,17 @@ The following section provides a detailed explanation of all parameters availabl
 | `eps` | float | `1e-8` | Small jitter value added to variances to prevent divide-by-zero errors during standardization. |
 
 
-### Batch Effect Correction Visualization 
+### Batch Effect Correction Visualization
 
 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.
 
-For further details see the [notebook demo](https://github.com/EttoreRocchi/combatlearn/blob/main/docs/demo/combatlearn_demo.ipynb).
+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).
+
+### Batch Effect Metrics
+
+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.
+
+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).
 
 ## Contributing
 
@@ -134,8 +137,7 @@ We gratefully acknowledge:
 
 ## Citation
 
-If **combatlearn** is useful in your research, please cite the original
-papers:
+If **combatlearn** is useful in your research, please cite the original papers:
 
 - Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. _Biostatistics_. 2007 Jan;8(1):118-27. doi: [10.1093/biostatistics/kxj037](https://doi.org/10.1093/biostatistics/kxj037)
 

combatlearn-1.1.1/combatlearn/__init__.py

@@ -0,0 +1,5 @@
+from .combat import ComBat
+
+__all__ = ["ComBat"]
+__version__ = "1.1.1"
+__author__ = "Ettore Rocchi"