Merge branch 'master' into gabrio

CITATION.bib

@@ -1,6 +1 @@
-@article{orozco2023invertiblenetworks,
-  title={InvertibleNetworks. jl: A Julia package for scalable normalizing flows},
-  author={Orozco, Rafael and Witte, Philipp and Louboutin, Mathias and Siahkoohi, Ali and Rizzuti, Gabrio and Peters, Bas and Herrmann, Felix J},
-  journal={arXiv preprint arXiv:2312.13480},
-  year={2023}
-}
+@article{Orozco2024, doi = {10.21105/joss.06554}, url = {https://doi.org/10.21105/joss.06554}, year = {2024}, publisher = {The Open Journal}, volume = {9}, number = {99}, pages = {6554}, author = {Rafael Orozco and Philipp Witte and Mathias Louboutin and Ali Siahkoohi and Gabrio Rizzuti and Bas Peters and Felix J. Herrmann}, title = {InvertibleNetworks.jl: A Julia package for scalable normalizing flows}, journal = {Journal of Open Source Software} }

CITATION.cff

@@ -0,0 +1,50 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Orozco
+  given-names: Rafael
+- family-names: Witte
+  given-names: Philipp
+- family-names: Louboutin
+  given-names: Mathias
+- family-names: Siahkoohi
+  given-names: Ali
+- family-names: Rizzuti
+  given-names: Gabrio
+- family-names: Peters
+  given-names: Bas
+- family-names: Herrmann
+  given-names: Felix J.
+doi: 10.5281/zenodo.12810006
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Orozco
+    given-names: Rafael
+  - family-names: Witte
+    given-names: Philipp
+  - family-names: Louboutin
+    given-names: Mathias
+  - family-names: Siahkoohi
+    given-names: Ali
+  - family-names: Rizzuti
+    given-names: Gabrio
+  - family-names: Peters
+    given-names: Bas
+  - family-names: Herrmann
+    given-names: Felix J.
+  date-published: 2024-07-30
+  doi: 10.21105/joss.06554
+  issn: 2475-9066
+  issue: 99
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6554
+  title: "InvertibleNetworks.jl: A Julia package for scalable
+    normalizing flows"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06554"
+  volume: 9
+title: "InvertibleNetworks.jl: A Julia package for scalable normalizing
+  flows"

Project.toml

@@ -1,7 +1,7 @@
 name = "InvertibleNetworks"
 uuid = "b7115f24-5f92-4794-81e8-23b0ddb121d3"
 authors = ["Philipp Witte <[email protected]>", "Ali Siahkoohi <[email protected]>", "Mathias Louboutin <[email protected]>", "Gabrio Rizzuti <[email protected]>", "Rafael Orozco <[email protected]>", "Felix J. Herrmann <[email protected]>"]
-version = "2.2.8"
+version = "2.3.1"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -15,6 +15,11 @@ Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
 cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd"
 
 [compat]
+CUDA = "1, 2, 3, 4, 5"
+cuDNN = "1"
+ChainRulesCore = "0.8, 0.9, 0.10, 1"
+Flux = "0.11, 0.12, 0.13, 0.14"
+NNlib = "0.7, 0.8, 0.9"
 TimerOutputs = "0.5"
 Wavelets = "0.9, 0.10"
 

README.md

@@ -1,8 +1,9 @@
 # InvertibleNetworks.jl
 
-| **Documentation** | **Build Status**  |                  |
+| **Documentation** | **Build Status**  |  **JOSS paper**  |
 |:-----------------:|:-----------------:|:----------------:|
-|[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://slimgroup.github.io/InvertibleNetworks.jl/stable/) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://slimgroup.github.io/InvertibleNetworks.jl/dev/)| [![CI](https://github.com/slimgroup/InvertibleNetworks.jl/actions/workflows/runtests.yml/badge.svg)](https://github.com/slimgroup/InvertibleNetworks.jl/actions/workflows/runtests.yml)| [![DOI](https://zenodo.org/badge/239018318.svg)](https://zenodo.org/badge/latestdoi/239018318)
+|[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://slimgroup.github.io/InvertibleNetworks.jl/stable/) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://slimgroup.github.io/InvertibleNetworks.jl/dev/)| [![CI](https://github.com/slimgroup/InvertibleNetworks.jl/actions/workflows/runtests.yml/badge.svg)](https://github.com/slimgroup/InvertibleNetworks.jl/actions/workflows/runtests.yml)|  [![DOI](https://joss.theoj.org/papers/10.21105/joss.06554/status.svg)](https://doi.org/10.21105/joss.06554)
+
 
 Building blocks for invertible neural networks in the [Julia] programming language.
 
@@ -26,7 +27,7 @@ InvertibleNetworks is registered and can be added like any standard Julia packag
 ## Uncertainty-aware image reconstruction
 
 
-Due to its memory scaling InvertibleNetworks.jl has been particularily successful at Bayesian posterior sampling with simulation-based inference. To get started with this application refer to a simple example ([Conditional sampling for MNSIT inpainting](https://github.com/slimgroup/InvertibleNetworks.jl/tree/master/examples/applications/application_conditional_mnist_inpainting.jl)) but feel free to modify this script for your application and please reach out to us if you run into any trouble. 
+Due to its memory scaling InvertibleNetworks.jl, has been particularily successful at Bayesian posterior sampling with simulation-based inference. To get started with this application refer to a simple example ([Conditional sampling for MNSIT inpainting](https://github.com/slimgroup/InvertibleNetworks.jl/tree/master/examples/applications/conditional_sampling/amortized_glow_mnist_inpainting.jl)) but feel free to modify this script for your application and please reach out to us for help. 
 
 ![mnist_sampling_cond](docs/src/figures/mnist_sampling_cond.png)
 
@@ -92,12 +93,7 @@ Y_, logdet = AN.forward(X)
 If you use InvertibleNetworks.jl in your research, we would be grateful if you cite us with the following bibtex:
 
 ```
-@article{orozco2023invertiblenetworks,
-  title={InvertibleNetworks. jl: A Julia package for scalable normalizing flows},
-  author={Orozco, Rafael and Witte, Philipp and Louboutin, Mathias and Siahkoohi, Ali and Rizzuti, Gabrio and Peters, Bas and Herrmann, Felix J},
-  journal={arXiv preprint arXiv:2312.13480},
-  year={2023}
-}
+@article{Orozco2024, doi = {10.21105/joss.06554}, url = {https://doi.org/10.21105/joss.06554}, year = {2024}, publisher = {The Open Journal}, volume = {9}, number = {99}, pages = {6554}, author = {Rafael Orozco and Philipp Witte and Mathias Louboutin and Ali Siahkoohi and Gabrio Rizzuti and Bas Peters and Felix J. Herrmann}, title = {InvertibleNetworks.jl: A Julia package for scalable normalizing flows}, journal = {Journal of Open Source Software} }
 ```