combatlearn 1.1.2__tar.gz → 1.3.0__tar.gz

{combatlearn-1.1.2 → combatlearn-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: combatlearn
-Version: 1.1.2
+Version: 1.3.0
 Summary: Batch-effect harmonization for machine learning frameworks.
 Author-email: Ettore Rocchi <ettoreroc@gmail.com>
 License: MIT
@@ -16,6 +16,7 @@ Requires-Dist: pandas>=1.3
 Requires-Dist: numpy>=1.21
 Requires-Dist: scikit-learn>=1.2
 Requires-Dist: matplotlib>=3.4
+Requires-Dist: seaborn>=0.12
 Requires-Dist: plotly>=5.0
 Requires-Dist: nbformat>=4.2
 Requires-Dist: umap-learn>=0.5
@@ -26,7 +27,7 @@ Requires-Dist: pre-commit>=3.0; extra == "dev"
 Provides-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: myst-nb>=1.1.0; extra == "docs"
 Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
 Requires-Dist: linkify-it-py>=2.0.0; extra == "docs"
 Dynamic: license-file
@@ -61,8 +62,8 @@ pip install combatlearn
 **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/)
+- [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods.html)
+- [API Reference](https://combatlearn.readthedocs.io/en/latest/api.html)
 
 ## Quick start
 
@@ -76,7 +77,7 @@ from combatlearn import ComBat
 df = pd.read_csv("data.csv", index_col=0)
 X, y = df.drop(columns="y"), df["y"]
 
-batch = pd.read_csv("batch.csv", index_col=0, squeeze=True)
+batch = pd.read_csv("batch.csv", index_col=0).squeeze("columns")
 diag = pd.read_csv("diagnosis.csv", index_col=0) # categorical
 age = pd.read_csv("age.csv", index_col=0) # continuous
 
@@ -158,21 +159,31 @@ Pull requests, bug reports, and feature ideas are welcome: feel free to open a P
 
 [Google Scholar](https://scholar.google.com/citations?user=MKHoGnQAAAAJ) | [Scopus](https://www.scopus.com/authid/detail.uri?authorId=57220152522)
 
-## Acknowledgements
 
-This project builds on the excellent work of the ComBat family of harmonisation methods.
-We gratefully acknowledge:
+## Citation
 
-- [**ComBat**](https://rdrr.io/bioc/sva/man/ComBat.html)
-- [**neuroCombat**](https://github.com/Jfortin1/neuroCombat)
-- [**CovBat**](https://github.com/andy1764/CovBat_Harmonization)
+If **combatlearn** is useful in your research, please cite the paper introducing this Python package:
 
-## Citation
+> Rocchi, E., Nicitra, E., Calvo, M. et al. Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy. BMC Microbiol (2026). https://doi.org/10.1186/s12866-025-04657-2
+
+```bibtex
+@article{Rocchi2026,
+  author    = {Rocchi, Ettore and Nicitra, Emanuele and Calvo, Maddalena and Cento, Valeria and Peiretti, Laura and Asif, Zian and Menchinelli, Giulia and Posteraro, Brunella and Sala, Claudia and Colosimo, Claudia and Cricca, Monica and Sambri, Vittorio and Sanguinetti, Maurizio and Castellani, Gastone and Stefani, Stefania},
+  title     = {Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy},
+  journal   = {BMC Microbiology},
+  year      = {2026},
+  doi       = {10.1186/s12866-025-04657-2},
+  url       = {https://doi.org/10.1186/s12866-025-04657-2}
+}
+```
 
-If **combatlearn** is useful in your research, please cite the original papers:
+## Acknowledgements
+
+This project builds on the excellent work of the ComBat family of harmonisation methods.
+Please consider citing 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)
+- [**ComBat**](https://rdrr.io/bioc/sva/man/ComBat.html) - Johnson WE, Li C, Rabinovic A. _Biostatistics_. 2007. doi: [10.1093/biostatistics/kxj037](https://doi.org/10.1093/biostatistics/kxj037)
 
-- Fortin JP, Cullen N, Sheline YI, Taylor WD, Aselcioglu I, Cook PA, Adams P, Cooper C, Fava M, McGrath PJ, McInnis M, Phillips ML, Trivedi MH, Weissman MM, Shinohara RT. Harmonization of cortical thickness measurements across scanners and sites. _Neuroimage_. 2018 Feb 15;167:104-120. doi: [10.1016/j.neuroimage.2017.11.024](https://doi.org/10.1016/j.neuroimage.2017.11.024)
+- [**neuroCombat**](https://github.com/Jfortin1/neuroCombat) - Fortin JP et al. _Neuroimage_. 2018. doi: [10.1016/j.neuroimage.2017.11.024](https://doi.org/10.1016/j.neuroimage.2017.11.024)
 
-- Chen AA, Beer JC, Tustison NJ, Cook PA, Shinohara RT, Shou H; Alzheimer's Disease Neuroimaging Initiative. Mitigating site effects in covariance for machine learning in neuroimaging data. _Hum Brain Mapp_. 2022 Mar;43(4):1179-1195. doi: [10.1002/hbm.25688](https://doi.org/10.1002/hbm.25688)
+- [**CovBat**](https://github.com/andy1764/CovBat_Harmonization) - Chen AA et al. _Hum Brain Mapp_. 2022. doi: [10.1002/hbm.25688](https://doi.org/10.1002/hbm.25688)

{combatlearn-1.1.2 → combatlearn-1.3.0}/README.md

@@ -28,8 +28,8 @@ pip install combatlearn
 **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/)
+- [Methods Guide](https://combatlearn.readthedocs.io/en/latest/methods.html)
+- [API Reference](https://combatlearn.readthedocs.io/en/latest/api.html)
 
 ## Quick start
 
@@ -43,7 +43,7 @@ from combatlearn import ComBat
 df = pd.read_csv("data.csv", index_col=0)
 X, y = df.drop(columns="y"), df["y"]
 
-batch = pd.read_csv("batch.csv", index_col=0, squeeze=True)
+batch = pd.read_csv("batch.csv", index_col=0).squeeze("columns")
 diag = pd.read_csv("diagnosis.csv", index_col=0) # categorical
 age = pd.read_csv("age.csv", index_col=0) # continuous
 
@@ -125,21 +125,31 @@ Pull requests, bug reports, and feature ideas are welcome: feel free to open a P
 
 [Google Scholar](https://scholar.google.com/citations?user=MKHoGnQAAAAJ) | [Scopus](https://www.scopus.com/authid/detail.uri?authorId=57220152522)
 
-## Acknowledgements
 
-This project builds on the excellent work of the ComBat family of harmonisation methods.
-We gratefully acknowledge:
+## Citation
 
-- [**ComBat**](https://rdrr.io/bioc/sva/man/ComBat.html)
-- [**neuroCombat**](https://github.com/Jfortin1/neuroCombat)
-- [**CovBat**](https://github.com/andy1764/CovBat_Harmonization)
+If **combatlearn** is useful in your research, please cite the paper introducing this Python package:
 
-## Citation
+> Rocchi, E., Nicitra, E., Calvo, M. et al. Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy. BMC Microbiol (2026). https://doi.org/10.1186/s12866-025-04657-2
+
+```bibtex
+@article{Rocchi2026,
+  author    = {Rocchi, Ettore and Nicitra, Emanuele and Calvo, Maddalena and Cento, Valeria and Peiretti, Laura and Asif, Zian and Menchinelli, Giulia and Posteraro, Brunella and Sala, Claudia and Colosimo, Claudia and Cricca, Monica and Sambri, Vittorio and Sanguinetti, Maurizio and Castellani, Gastone and Stefani, Stefania},
+  title     = {Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy},
+  journal   = {BMC Microbiology},
+  year      = {2026},
+  doi       = {10.1186/s12866-025-04657-2},
+  url       = {https://doi.org/10.1186/s12866-025-04657-2}
+}
+```
 
-If **combatlearn** is useful in your research, please cite the original papers:
+## Acknowledgements
+
+This project builds on the excellent work of the ComBat family of harmonisation methods.
+Please consider citing 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)
+- [**ComBat**](https://rdrr.io/bioc/sva/man/ComBat.html) - Johnson WE, Li C, Rabinovic A. _Biostatistics_. 2007. doi: [10.1093/biostatistics/kxj037](https://doi.org/10.1093/biostatistics/kxj037)
 
-- Fortin JP, Cullen N, Sheline YI, Taylor WD, Aselcioglu I, Cook PA, Adams P, Cooper C, Fava M, McGrath PJ, McInnis M, Phillips ML, Trivedi MH, Weissman MM, Shinohara RT. Harmonization of cortical thickness measurements across scanners and sites. _Neuroimage_. 2018 Feb 15;167:104-120. doi: [10.1016/j.neuroimage.2017.11.024](https://doi.org/10.1016/j.neuroimage.2017.11.024)
+- [**neuroCombat**](https://github.com/Jfortin1/neuroCombat) - Fortin JP et al. _Neuroimage_. 2018. doi: [10.1016/j.neuroimage.2017.11.024](https://doi.org/10.1016/j.neuroimage.2017.11.024)
 
-- Chen AA, Beer JC, Tustison NJ, Cook PA, Shinohara RT, Shou H; Alzheimer's Disease Neuroimaging Initiative. Mitigating site effects in covariance for machine learning in neuroimaging data. _Hum Brain Mapp_. 2022 Mar;43(4):1179-1195. doi: [10.1002/hbm.25688](https://doi.org/10.1002/hbm.25688)
+- [**CovBat**](https://github.com/andy1764/CovBat_Harmonization) - Chen AA et al. _Hum Brain Mapp_. 2022. doi: [10.1002/hbm.25688](https://doi.org/10.1002/hbm.25688)

combatlearn-1.3.0/combatlearn/__init__.py

@@ -0,0 +1,5 @@
+from .sklearn_api import ComBat
+
+__all__ = ["ComBat"]
+__version__ = "1.3.0"
+__author__ = "Ettore Rocchi"