Merge pull request #103 from YosefLab/jhong/deprecate

Add deprecation warnings for 1.0.1

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
 

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

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 = [

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",