release v1.0.1 (post publication)

Author: quentinblampey

CHANGELOG.md

@@ -1,6 +1,8 @@
-## [1.0.1] - xxxx-xx-xx
+## [1.0.2] - xxxx-xx-xx
 
-🎉 Novae is now published in XXX
+## [1.0.1] - 2025-12-10
+
+🎉 Novae is now [published in Nature Methods](https://www.nature.com/articles/s41592-025-02899-6)!
 
 ### Added
 - Full dataset added to [our Hugging Face Hub](https://huggingface.co/datasets/MICS-Lab/novae)

README.md

@@ -22,7 +22,7 @@
 Novae is a deep learning model for spatial domain assignments of spatial transcriptomics data (at both single-cell or spot resolution). It works across multiple gene panels, tissues, and technologies. Novae offers several additional features, including: (i) native batch-effect correction, (ii) analysis of spatially variable genes and pathways, and (iii) architecture analysis of tissue slides.
 
 > [!NOTE]
-> Novae was developed by the authors of [`sopa`](https://github.com/gustaveroussy/sopa) and is part of the [`scverse`](https://scverse.org/) ecosystem.
+> Novae was developed by the authors of [`sopa`](https://github.com/gustaveroussy/sopa) and is part of the [`scverse`](https://scverse.org/) ecosystem. Read our article [here](https://www.nature.com/articles/s41592-025-02899-6).
 
 ## Documentation
 
@@ -67,15 +67,9 @@ model.assign_domains(adata)
 
 ## Cite us
 
-You can cite our [preprint](https://www.biorxiv.org/content/10.1101/2024.09.09.612009v1) as below:
+Our article is published in [Nature Methods](https://www.nature.com/articles/s41592-025-02899-6). You can cite Novae as below:
 
 ```txt
-@article{blampeyNovae2024,
-  title = {Novae: A Graph-Based Foundation Model for Spatial Transcriptomics Data},
-  author = {Blampey, Quentin and Benkirane, Hakim and Bercovici, Nadege and Andre, Fabrice and Cournede, Paul-Henry},
-  year = {2024},
-  pages = {2024.09.09.612009},
-  publisher = {bioRxiv},
-  doi = {10.1101/2024.09.09.612009},
-}
+Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data.
+Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6
 ```

docs/cite_us.md

@@ -1,16 +1,10 @@
 ## LaTeX citation
 
-You can cite our [preprint](https://www.biorxiv.org/content/10.1101/2024.09.09.612009v1) as below:
+Our article is published in [Nature Methods](https://www.nature.com/articles/s41592-025-02899-6). You can cite Novae as below:
 
 ```txt
-@article{blampeyNovae2024,
-  title = {Novae: A Graph-Based Foundation Model for Spatial Transcriptomics Data},
-  author = {Blampey, Quentin and Benkirane, Hakim and Bercovici, Nadege and Andre, Fabrice and Cournede, Paul-Henry},
-  year = {2024},
-  pages = {2024.09.09.612009},
-  publisher = {bioRxiv},
-  doi = {10.1101/2024.09.09.612009},
-}
+Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data.
+Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6
 ```
 
 This library has been developed by Quentin Blampey, PhD researcher in biomathematics and deep learning. The following institutions funded this work:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "novae"
-version = "1.0.0"
+version = "1.0.1"
 description = "Graph-based foundation model for spatial transcriptomics data"
 authors = [{ name = "Quentin Blampey", email = "[email protected]" }]
 requires-python = ">=3.11"