diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index b5c0a17..d4a1558 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -51,7 +51,7 @@ jobs: os: - macos-latest - ubuntu-24.04 - python-version: ["3.10", "3.11"] + python-version: ["3.11"] runs-on: ${{ matrix.os }} permissions: contents: read diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d476094..cb58569 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -95,7 +95,7 @@ We use [pytest](https://docs.pytest.org/) for local testing and [GitHub Actions] ### Getting started -1. [Install Python 3.10+](https://www.python.org/downloads/) +1. [Install Python 3.11](https://www.python.org/downloads/) 1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/) 1. Fork and clone the repository 1. Install the project with development dependencies: diff --git a/README.md b/README.md index 644afc0..948ec5e 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ ![DeepProfiler](figures/logo/banner.png) ----------------- -[![Python 3.10–3.11](https://img.shields.io/badge/python-3.10%20|%203.11-blue)](https://www.python.org/downloads/) +[![Python 3.11](https://img.shields.io/badge/python-3.11-blue)](https://www.python.org/downloads/) [![CI](https://github.com/cytomining/DeepProfiler/actions/workflows/integration-test.yml/badge.svg)](https://github.com/cytomining/DeepProfiler/actions/workflows/integration-test.yml) [![codecov](https://codecov.io/gh/cytomining/DeepProfiler/branch/main/graph/badge.svg)](https://codecov.io/gh/cytomining/DeepProfiler) [![Cell Painting CNN-1 DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7114558.svg)](https://doi.org/10.5281/zenodo.7114558) @@ -10,7 +10,7 @@ > **v0.5.1 is a focused maintenance release.** > Model training, the plugin system, and CometML integration have been removed. > The only supported use case is **feature extraction using the [Cell Painting CNN v1 checkpoint](https://doi.org/10.5281/zenodo.7114558)** (EfficientNet B0). -> This release requires **Python 3.10–3.11** and **TensorFlow 2.10–2.15**. +> This release requires **Python 3.11** and **TensorFlow 2.10–2.15**. > If you need training or used the plugin system, please use the [`v0.3.0` tag](https://github.com/cytomining/DeepProfiler/tree/v0.3.0) and [open an issue](https://github.com/cytomining/DeepProfiler/issues) to let us know your use case. > See [ROADMAP.md](ROADMAP.md) for the full plan. @@ -42,7 +42,7 @@ Features obtained with the Cell Painting CNN are more robust and improve perform ## System requirements -- Python 3.10 or 3.11 +- Python 3.11 - TensorFlow 2.10–2.15 - Linux (Ubuntu 20.04+) recommended - For GPU acceleration, a CUDA-compatible GPU is recommended diff --git a/ROADMAP.md b/ROADMAP.md index 4a7a90f..86124c6 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -28,7 +28,7 @@ The package will be a thin layer over deep learning models, with seamless integr - Migrate to `uv`, dynamic versioning, mypy, ruff - CI/CD with PyPI trusted publishing - Integration test suite: downloads the Zenodo checkpoint and validates the full profiling pipeline end-to-end (`uv run pytest -m integration`) -- **Constraint:** requires Python 3.10–3.11 and TensorFlow 2.10–2.15 (Keras 2); see [README](README.md) +- **Constraint:** requires Python 3.11 and TensorFlow 2.10–2.15 (Keras 2); see [README](README.md) ### 🔜 v0.6.x — PyTorch rewrite (featurizer) - Full rewrite in PyTorch (drop TensorFlow) diff --git a/pyproject.toml b/pyproject.toml index 83acbf6..1b57d63 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,12 +33,11 @@ classifiers = [ "Development Status :: 4 - 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