🧑‍💻 Add uv setup workflow

README.md

@@ -103,25 +103,42 @@ Prepare a computer as a convenient platform for further development of the Pytho
     $ cd tiatoolbox
 ```
 
-5. Create virtual environment for TIAToolbox using
+5. Create a virtual environment and install dependencies.
+
+   **Using [uv](https://docs.astral.sh/uv/) (recommended):**
+
+```sh
+    $ uv sync --extra dev
+    $ source .venv/bin/activate   # Linux/macOS
+    $ .venv\Scripts\activate      # Windows
+```
+
+For CPU-only machines (no CUDA GPU):
 
 ```sh
-    $ conda create -n tiatoolbox-dev python=3.11 # select version of your choice
+    $ uv sync --extra dev --index pytorch-cpu=https://download.pytorch.org/whl/cpu
+```
+
+**Using conda:**
+
+```sh
+    $ conda create -n tiatoolbox-dev python=3.11
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```
 
-or
+or (Linux/macOS only):
 
 ```sh
-    $ conda env create -f requirements/requirements.dev.conda.yml # for linux/mac only.
+    $ conda env create -f requirements/requirements.dev.conda.yml
     $ conda activate tiatoolbox-dev
 ```
 
-6. To use the packages installed in the environment, run the command:
+6. To re-enter the environment in a new terminal:
 
 ```sh
-    $ conda activate tiatoolbox-dev
+    $ source .venv/bin/activate   # uv (Linux/macOS)
+    $ conda activate tiatoolbox-dev  # conda
 ```
 
 ### License

pyproject.toml

@@ -1,3 +1,119 @@
+[project]
+name = "tiatoolbox"
+version = "2.0.1"
+description = "Computational pathology toolbox developed by TIA Centre."
+readme = "README.md"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "TIA Centre", email = "TIA@warwick.ac.uk" }]
+requires-python = ">=3.11, <3.14"
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Developers",
+  "Natural Language :: English",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+  # mirror of requirements/requirements.txt — keep in sync
+  "aiohttp>=3.8.1",
+  "albumentations>=1.3.0",
+  "bokeh>=3.8.2",
+  "click>=8.2.0",
+  "dask>=2026.1.2",
+  "defusedxml>=0.7.1",
+  "filelock>=3.9.0",
+  "flask>=2.2.2",
+  "flask-cors>=4.0.0",
+  "glymur>=0.12.7",
+  "huggingface_hub>=0.33.3",
+  "imagecodecs>=2022.9.26",
+  "ipywidgets>=8.1.7",
+  "joblib>=1.1.1",
+  "jupyterlab>=3.5.2",
+  "matplotlib>=3.6.2",
+  "numba>=0.57.0",
+  "numpy>=2.0.0",
+  "opencv-python>=4.6.0",
+  "openslide-bin>=4.0.0.2",
+  "openslide-python>=1.4.0",
+  "pandas>=2.0.0",
+  "pillow>=9.3.0",
+  "pydicom>=2.3.1",
+  "pyyaml>=6.0",
+  "requests>=2.28.1",
+  "scikit-image>=0.26.0",
+  "scikit-learn>=1.2.0",
+  "scipy>=1.8",
+  "shapely>=2.0.0",
+  "simpleitk>=2.2.1",
+  "sphinx>=5.3.0,<9.0.0",
+  "tifffile>=2022.10.10,<=2025.5.10",
+  "timm>=1.0.3",
+  "torch>=2.5.0",
+  "torchvision>=0.15.0",
+  "tqdm>=4.64.1",
+  "transformers>=4.51.1",
+  "umap-learn>=0.5.3",
+  "wsidicom>=0.18.0",
+  "zarr>=2.13.3,<3.0.0",
+]
+
+[project.optional-dependencies]
+docs = [
+  "furo>=2022.12.7",
+  "myst-nb>=0.17.1",
+  "myst-parser>=0.18.1",
+  "sphinx-copybutton>=0.5.1",
+  "sphinx-design>=0.3.0",
+  "sphinx-toolbox>=3.2.0",
+]
+dev = [
+  "tiatoolbox[docs]",
+  "coverage>=7.0.0",
+  "docutils>=0.18.1",
+  "mypy>=1.16",
+  "pip>=22.3",
+  "poetry-bumpversion>=0.3.1",
+  "pre-commit>=2.20.0",
+  "pytest>=7.2.0",
+  "pytest-cov>=4.0.0",
+  "pytest-runner>=6.0",
+  "pytest-xdist[psutil]",
+  "ruff==0.15.9",
+  "toml>=0.10.2",
+  "twine>=4.0.1",
+  "wheel>=0.37.1",
+]
+
+[project.scripts]
+tiatoolbox = "tiatoolbox.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/TissueImageAnalytics/tiatoolbox"
+
+[tool.uv]
+
+[[tool.uv.index]]
+name = "pytorch-cu126"
+url = "https://download.pytorch.org/whl/cu126"
+explicit = true
+
+[[tool.uv.index]]
+name = "pytorch-cpu"
+url = "https://download.pytorch.org/whl/cpu"
+explicit = true
+
+[tool.uv.sources]
+# Linux/Windows get CUDA 12.6 wheels; macOS falls through to PyPI (MPS included)
+torch = [
+  { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
+]
+torchvision = [
+  { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
+]
+
 [tool.pytest.ini_options]
   collect_ignore = ["setup.py", "benchmark/"]
 
@@ -49,6 +165,11 @@ files = [".github/workflows/docker-publish.yml"]
 search = 'TOOLBOX_VER: {current_version}'
 replace = 'TOOLBOX_VER: {new_version}'
 
+[[tool.poetry_bumpversion.replacements]]
+files = ["pyproject.toml"]
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
+
 [tool.ruff]
 lint.select = [
   "A",     # flake8-builtins