🧑‍💻 Add uv setup workflow

.deepsource.toml

@@ -7,7 +7,7 @@ exclude_patterns = ["docs/*.py", "**/__init__.py"]
 [[analyzers]]
 name = "python"
 enabled = true
-dependency_file_paths = ["requirements/requirements_dev.txt"]
+dependency_file_paths = ["pyproject.toml"]
 
   [analyzers.meta]
   runtime_version = "3.x.x"

.github/workflows/conda-env-create.yml

@@ -7,15 +7,11 @@ permissions:
 
 on:
   push:
-    paths:
-      - "requirements/requirements*.txt"
-      - "requirements/generate_conda_env.py"
-      - ".github/workflows/conda-env-create.yml"
+    paths: [ "requirements/generate_conda_env.py", "conda-env-create.yml", "pyproject.toml"]
   pull_request:
-    paths:
-      - "requirements/requirements*.txt"
-      - "requirements/generate_conda_env.py"
-      - ".github/workflows/conda-env-create.yml"
+    paths: [ "requirements/generate_conda_env.py", "conda-env-create.yml", "pyproject.toml"]
+  schedule: # Run on the 1st of every month at midnight
+    - cron: "0 0 1 * *"
 
 jobs:
   conda_solve:

.github/workflows/mypy-type-check.yml

@@ -37,7 +37,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install uv
         uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        uv pip install --system -r requirements/requirements_dev.txt
+        uv pip install --system -e ".[dev]"
 
     - name: Debug typing environment
       run: |

.github/workflows/pip-install.yml

@@ -3,19 +3,15 @@ name: pip Install
 on:
   push:
     paths:
-      - "requirements*.yml"
       - "conda-env-create.yml"
-      - "requirements/requirement*.txt"
       - "setup*py"
       - "setup*cfg"
       - "pyproject*toml"
       - "MANIFEST*in"
       - ".github/workflows/pip-install.yml"
   pull_request:
     paths:
-      - "requirements*.yml"
       - "conda-env-create.yml"
-      - "requirements/requirement*.txt"
       - "setup*py"
       - "setup*cfg"
       - "pyproject*toml"

.github/workflows/python-package.yml

@@ -36,7 +36,7 @@ jobs:
         python -m pip install ruff==0.15.15 pytest pytest-cov pytest-runner
         pip install uv
         uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        uv pip install --system -r requirements/requirements.txt
+        uv pip install --system -e .
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v4
       with:
@@ -114,7 +114,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install uv
         uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
-        uv pip install --system -r requirements/requirements.txt
+        uv pip install --system -e .
         uv pip install --system build
     - name: Build package
       run: python -m build

.gitignore

@@ -119,3 +119,6 @@ ENV/
 
 # output zarr generated
 *.zarr
+
+# uv lockfile
+uv.lock

.pre-commit-config.yaml

@@ -45,7 +45,6 @@ repos:
       - id: detect-private-key      # Detects the presence of private keys.
       - id: end-of-file-fixer       # Ensures that a file is either empty, or ends with one newline.
       - id: mixed-line-ending       # Replaces or checks mixed line endings.
-      - id: requirements-txt-fixer  # Sorts entries in requirements.txt.
       - id: trailing-whitespace     # Trims trailing whitespace.
       - id: file-contents-sorter    # Sorts the lines in specified files (defaults to alphabetical).
         files: whitelist.txt

.readthedocs.yml

@@ -13,15 +13,19 @@ build:
   apt_packages:
     - libopenjp2-7-dev
     - libopenjp2-tools
+  jobs:
+    pre_install:
+      # Install CPU-only PyTorch before the package so pip doesn't pull in CUDA wheels
+      - pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
+# Install tiatoolbox with docs extras (pyproject.toml is the single source of truth)
 python:
   install:
-      # Install PyTorch CPU version first
-      - requirements: requirements/requirements_cpu.txt
-      - requirements: docs/requirements.txt
-      - requirements: requirements/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

CONTRIBUTING.rst

@@ -58,11 +58,26 @@ Ready to contribute? Here's how to set up ``tiatoolbox`` for local development.
 
     $ git clone git@github.com:your_name_here/tiatoolbox.git
 
-3. Install your local copy into a virtual environment. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Set up the development environment. Using ``conda``::
 
-    $ mkvirtualenv tiatoolbox
     $ cd tiatoolbox/
-    $ python setup.py develop
+    $ conda create -n tiatoolbox-dev python=3.11
+    $ conda activate tiatoolbox-dev
+    $ pip install -e ".[dev]"
+
+   Alternatively, using ``uv``::
+
+    $ uv sync --extra dev
+
+   This creates a ``.venv`` directory with Python 3.11 and all development
+   dependencies installed. Activate it with::
+
+    $ source .venv/bin/activate        # Linux/macOS
+    $ .venv\Scripts\activate           # Windows
+
+   For CPU-only machines (no CUDA GPU)::
+
+    $ uv sync --extra dev --index pytorch-cpu=https://download.pytorch.org/whl/cpu
 
 4. Create a branch for local development::
 

MANIFEST.in

@@ -3,7 +3,6 @@ include CONTRIBUTING.rst
 include HISTORY.md
 include LICENSE
 include README.md
-include requirements/requirements.txt
 include make.bat
 include Makefile
 include conf.py

README.md

@@ -71,7 +71,21 @@ The [bash](https://www.gnu.org/software/bash) shell is available on all commonly
 
 ### Install Python package
 
+#### Using `pip`
+
 If you wish to use our programs, perhaps without developing them further, run the command `pip install tiatoolbox` or `pip install --ignore-installed --upgrade tiatoolbox` to upgrade from an existing installation.
+
+#### Using `uv`
+
+Alternatively, you can install the latest stable release with [uv](https://docs.astral.sh/uv/):
+
+```sh
+    $ uv venv
+    $ source .venv/bin/activate   # Linux/macOS
+    $ .venv\Scripts\activate      # Windows
+    $ uv pip install tiatoolbox
+```
+
 Detailed installation instructions can be found in the [documentation](https://tia-toolbox.readthedocs.io/en/latest/installation.html).
 
 To understand better how the programs work, study the jupyter notebooks referred to under the heading **Examples Taster**.
@@ -103,25 +117,35 @@ 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/):**
 
 ```sh
-    $ conda create -n tiatoolbox-dev python=3.11 # select version of your choice
-    $ conda activate tiatoolbox-dev
-    $ pip install -r requirements/requirements_dev.txt
+    $ uv sync --extra dev
+    $ source .venv/bin/activate   # Linux/macOS
+    $ .venv\Scripts\activate      # Windows
 ```
 
-or
+For CPU-only machines (no CUDA GPU):
 
 ```sh
-    $ conda env create -f requirements/requirements.dev.conda.yml # for linux/mac only.
-    $ conda activate tiatoolbox-dev
+    $ uv sync --extra dev --index pytorch-cpu=https://download.pytorch.org/whl/cpu
 ```
 
-6. To use the packages installed in the environment, run the command:
+**Using conda:**
 
 ```sh
+    $ conda create -n tiatoolbox-dev python=3.11
     $ conda activate tiatoolbox-dev
+    $ pip install -e ".[dev]"
+```
+
+6. To re-enter the environment in a new terminal:
+
+```sh
+    $ source .venv/bin/activate   # uv (Linux/macOS)
+    $ conda activate tiatoolbox-dev  # conda
 ```
 
 ### License

docs/conf.py

@@ -114,7 +114,6 @@
     "_build",
     "Thumbs.db",
     ".DS_Store",
-    "requirements/requirements*.txt",
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.

docs/installation.rst

@@ -118,13 +118,43 @@ An alternate way to install using conda on Windows could be to install it in `WS
 Using uv
 --------
 
-To install using `uv <https://docs.astral.sh/uv/>`_, a fast Python package and project manager, written in Rust.
+`uv <https://docs.astral.sh/uv/>`_ is a Python package and project manager. First, install uv by following the `official installation guide <https://docs.astral.sh/uv/getting-started/installation/#installing-uv>`_ for your platform (macOS, Linux, and Windows).
+
+**End-user installation**
+
+Create a virtual environment and install the latest stable release from PyPI:
 
 .. code-block:: console
 
-    $ pip install uv
+    $ uv venv
+    $ source .venv/bin/activate   # Linux/macOS
+    $ .venv\Scripts\activate      # Windows
     $ uv pip install tiatoolbox
 
+To upgrade an existing installation to the latest stable release:
+
+.. code-block:: console
+
+    $ uv pip install --upgrade tiatoolbox
+
+**Development setup (from source)**
+
+Clone the repository and create a virtual environment with all development dependencies:
+
+.. code-block:: console
+
+    $ git clone https://github.com/TissueImageAnalytics/tiatoolbox.git
+    $ cd tiatoolbox
+    $ uv sync --extra dev
+    $ source .venv/bin/activate   # Linux/macOS
+    $ .venv\Scripts\activate      # Windows
+
+On CPU-only machines (no CUDA GPU):
+
+.. code-block:: console
+
+    $ uv sync --extra dev --index pytorch-cpu=https://download.pytorch.org/whl/cpu
+
 From Sources
 ------------
 

docs/requirements.txt

@@ -1,6 +0,0 @@
-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>=4.2.0

pre-commit/missing_imports.py

@@ -35,14 +35,7 @@
     "ipython": ["IPython"],
 }
 
-REQUIREMENTS_FILES = (
-    "requirements/requirements.txt",
-    "requirements/requirements_dev.txt",
-    "requirements/requirements.conda.yml",
-    "requirements/requirements.dev.conda.yml",
-    "requirements/requirements.win64.conda.yml",
-    "setup.py",
-)
+REQUIREMENTS_FILES = ("setup.py",)
 
 
 def find_source_files(base_dir: Path) -> list[Path]:

pre-commit/requirements_consistency.py

@@ -11,10 +11,6 @@
 from pkg_resources import Requirement
 
 REQUIREMENTS_FILES = [
-    ("requirements/requirements.txt", "requirements/requirements_dev.txt"),
-    ("requirements/requirements.conda.yml", "requirements/requirements.dev.conda.yml"),
-    ("requirements/requirements.win64.conda.yml", None),
-    ("docs/requirements.txt", None),
     ("setup.py", None),
 ]