diff --git a/.napari/DESCRIPTION.md b/.napari/DESCRIPTION.md index 0c4fbc77..2ad7586e 100644 --- a/.napari/DESCRIPTION.md +++ b/.napari/DESCRIPTION.md @@ -98,7 +98,7 @@ more detailed documentation if you have it. ## Additional Install Steps -**Python >= 3.8 required** +**Python >= 3.10 required** Requires manual installation of **pytorch** and **MONAI**. diff --git a/README.md b/README.md index ba94612e..d5b4cb89 100644 --- a/README.md +++ b/README.md @@ -3,11 +3,12 @@ [![PyPI](https://img.shields.io/pypi/v/napari-cellseg3d.svg?color=green)](https://pypi.org/project/napari-cellseg3d) +[![Python versions](https://img.shields.io/pypi/pyversions/napari-cellseg3d)](https://pypi.org/project/napari-cellseg3d) [![Downloads](https://static.pepy.tech/badge/napari-cellseg3d)](https://pepy.tech/project/napari-cellseg3d) [![Downloads](https://static.pepy.tech/badge/napari-cellseg3d/month)](https://pepy.tech/project/napari-cellseg3d) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/AdaptiveMotorControlLab/CellSeg3D/raw/main/LICENSE) [![codecov](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3D/branch/main/graph/badge.svg?token=hzUcn3XN8F)](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3D) -Code style: black +[![Code style:Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) cellseg3d logo @@ -65,7 +66,16 @@ F1-score is computed from the Intersection over Union (IoU) with ground truth la Read the [article here !](https://elifesciences.org/articles/99848) -### **New version: v0.2.2** +### **New version: v0.2.3** + +- v0.2.3: + - Python 3.10-12 support added + - Several fixes to deprecation errors on newer Python versions + - Upgraded packaging to use only pyproject.toml + - Added uv.lock to repository for more reproducible installs + +> [!WARNING] +> If you are still getting errors related to `in_channels` on the SwinUNetR model, please open an issue and report your MONAI version. Thanks! - v0.2.2: @@ -102,7 +112,7 @@ Previous additions: ## Requirements -**Compatible with Python 3.8 to 3.10.** +**Compatible with Python 3.10 to 3.12.** Requires **[napari]**, **[PyTorch]** and **[MONAI]**. Compatible with Windows, MacOS and Linux. Installation of the plugin itself should not take more than 30 minutes, depending on your internet connection, diff --git a/napari_cellseg3d/code_models/models/model_SwinUNetR.py b/napari_cellseg3d/code_models/models/model_SwinUNetR.py index 8c59e93a..350b8a36 100644 --- a/napari_cellseg3d/code_models/models/model_SwinUNetR.py +++ b/napari_cellseg3d/code_models/models/model_SwinUNetR.py @@ -45,7 +45,6 @@ def __init__( **kwargs, ) if "img_size" in sig.parameters: - # since MONAI API changes depending on py3.8 or py3.9 init_kwargs["img_size"] = input_img_size if "dropout_prob" in kwargs: init_kwargs["drop_rate"] = kwargs["dropout_prob"] diff --git a/pyproject.toml b/pyproject.toml index edc9afbd..eb3629dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,7 +70,7 @@ dev = [ "twine", ] docs = [ - "jupyter-book", + "jupyter-book<2", ] onnx-cpu = [ "onnx", "onnxruntime" ] onnx-gpu = [ "onnx", "onnxruntime-gpu" ]