diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e366c4..ba90a22 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,19 @@ and this project adheres to [Semantic Versioning][]. [keep a changelog]: https://keepachangelog.com/en/1.0.0/ [semantic versioning]: https://semver.org/spec/v2.0.0.html -## [1.0.0b1] - 2023-02-21 +## [1.0.1] - 2024-05-10 + +### :warning: Deprecation Warning + +- The MrVI implementation has been moved to `scvi-tools` (`from scvi.external import MRVI`), + and this package will no longer be maintained. + +### Added + +- Adds deprecation warning in the form of a FutureWarning on import. +- Various fixes and UX improvements to the model kwargs, DE, and DA functions. + +## [1.0.0b1] - 2024-02-21 ### :warning: Breaking Changes diff --git a/README.md b/README.md index 0a026b2..ac576d8 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Multi-resolution Variational Inference. -🚧 :warning: This is a soft launch of the new `mrvi` package. We are working on docs and tutorials. :warning: 🚧 +🚧 :warning: [DEPRECATED] For the latest version of MrVI, please use the implementation in the `scvi-tools` package (`from scvi.external import MRVI`). This package will no longer be maintained. :warning: 🚧 ## Getting started @@ -128,7 +128,12 @@ If you found a bug, please use the [issue tracker][issue-tracker]. ## Citation -> t.b.a +> **Deep generative modeling of sample-level heterogeneity in single-cell genomics** +> +> Pierre Boyeau, Justin Hong, Adam Gayoso, Martin Kim, Jose L. McFaline-Figueroa, Michael I. Jordan, +> Elham Azizi, Can Ergen, & Nir Yosef +> +> _bioRxiv_ 2024 May 10. doi: [10.1101/2022.10.04.510898](https://doi.org/10.1101/2022.10.04.510898). [scverse-discourse]: https://discourse.scverse.org/ [issue-tracker]: https://github.com/justjhong/mrvi/issues diff --git a/pyproject.toml b/pyproject.toml index 0ec75bf..e932be8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ requires = ["hatchling"] [project] name = "mrvi" -version = "1.0.0b1" +version = "1.0.1" description = "Multi-resolution Variational Inference" readme = "README.md" requires-python = ">=3.9" @@ -14,7 +14,7 @@ authors = [ {name = "Justin Hong"}, {name = "Pierre Boyeau"}, {name = "Adam Gayoso"}, - {name = "Can Ergan"}, + {name = "Can Ergen"}, {name = "Martin Kim"}, ] maintainers = [ diff --git a/src/mrvi/__init__.py b/src/mrvi/__init__.py index d53e676..f4ac438 100644 --- a/src/mrvi/__init__.py +++ b/src/mrvi/__init__.py @@ -1,9 +1,16 @@ +import warnings from importlib.metadata import version from ._model import MrVI from ._module import MrVAE from ._types import MrVIReduction +warnings.warn( + "This package is deprecated. For the latest version of MrVI, please install `scvi-tools` and import the model class via `scvi.external.MRVI`.", + FutureWarning, + stacklevel=2, +) + __all__ = [ "MrVI", "MrVAE",