build: Adding support for python3.14 [WIP]

.github/workflows/test_linux.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ["3.11", "3.12", "3.13"]
+        python: ["3.12", "3.13", "3.14"]
 
     name: integration
 

.github/workflows/test_linux_resolution.yml

@@ -33,7 +33,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ["3.11", "3.12", "3.13"]
+        python: ["3.12", "3.13", "3.14"]
         install-flags: ["--prerelease if-necessary-or-explicit"]
 
     name: integration

.github/workflows/test_macos.yml

@@ -34,7 +34,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-14]
-        python: ["3.11", "3.12", "3.13"]
+        python: ["3.12", "3.13", "3.14"]
 
     name: integration
 

.github/workflows/test_windows.yml

@@ -34,7 +34,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest]
-        python: ["3.11", "3.12", "3.13"]
+        python: ["3.12", "3.13", "3.14"]
 
     name: integration
 

CHANGELOG.md

@@ -10,6 +10,7 @@ to [Semantic Versioning]. The full commit history is available in the [commit lo
 #### Added
 
 - Added dispersion tests, including support for {class}`scvi.external.SCVIVA`, {pr}`3677`.
+- Add support for Python 3.14 {pr}`3563`.
 
 #### Fixed
 

docs/developer/code.md

@@ -24,7 +24,8 @@ up a local development environment:
     ```
 
 4. Install the development dependencies and the package in editable mode into a virtual
-    environment with Python 3.11–3.13:
+    environment with Python 3.12 - 3.14:
+
 
     ```bash
     pip install -e ".[dev]"

docs/extensions/typed_returns.py

@@ -12,7 +12,7 @@
     from collections.abc import Generator, Iterable
 
 
-def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+def _process_return(lines: Iterable[str]) -> Generator[str]:
     for line in lines:
         if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
             yield f"-{m['param']} (:class:`~{m['type']}`)"

docs/installation.md

@@ -40,15 +40,16 @@ Don't know how to get started with virtual environments or `conda`/`pip`? Check
 ### Virtual environment
 
 A virtual environment can be created with either `conda` or `venv`. We recommend using a fresh `conda` environment.
-We currently support Python 3.11–3.13.
+We currently support Python 3.12 - 3.14.
+
 
 For `conda`, we recommend using the [Miniforge](https://github.com/conda-forge/miniforge) or
 [Mamba](https://mamba.readthedocs.io/en/latest/) distribution, which are generally lighter and
 faster than the official distribution and comes with conda-forge as the default channel
 (where scvi-tools is hosted).
 
 ```bash
-conda create -n scvi-env python=3.13  # any python 3.11 to 3.13
+conda create -n scvi-env python=3.13  # any python 3.12 to 3.14
 conda activate scvi-env
 ```
 

pyproject.toml

@@ -7,7 +7,7 @@ name = "scvi-tools"
 version = "1.4.1"
 description = "Deep probabilistic analysis of single-cell omics data."
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 license = {file = "LICENSE"}
 authors = [
     {name = "The scvi-tools development team"},
@@ -24,9 +24,9 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: POSIX :: Linux",
@@ -142,7 +142,7 @@ markers = [
 src = ["src"]
 line-length = 99
 indent-width = 4
-target-version = "py312"
+target-version = "py313"
 
 # Exclude a variety of commonly ignored directories.
 exclude = [