diff --git a/.deepsource.toml b/.deepsource.toml index 11ab08068..046b9c445 100644 --- a/.deepsource.toml +++ b/.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" diff --git a/.github/workflows/conda-env-create.yml b/.github/workflows/conda-env-create.yml index e7fcacc83..105cda2ef 100644 --- a/.github/workflows/conda-env-create.yml +++ b/.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: diff --git a/.github/workflows/mypy-type-check.yml b/.github/workflows/mypy-type-check.yml index 336c1de2c..82934ee8c 100644 --- a/.github/workflows/mypy-type-check.yml +++ b/.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: | diff --git a/.github/workflows/pip-install.yml b/.github/workflows/pip-install.yml index f3bf7fee7..c89456ff8 100644 --- a/.github/workflows/pip-install.yml +++ b/.github/workflows/pip-install.yml @@ -3,9 +3,7 @@ name: pip Install on: push: paths: - - "requirements*.yml" - "conda-env-create.yml" - - "requirements/requirement*.txt" - "setup*py" - "setup*cfg" - "pyproject*toml" @@ -13,9 +11,7 @@ on: - ".github/workflows/pip-install.yml" pull_request: paths: - - "requirements*.yml" - "conda-env-create.yml" - - "requirements/requirement*.txt" - "setup*py" - "setup*cfg" - "pyproject*toml" diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2cb795379..468a127e7 100644 --- a/.github/workflows/python-package.yml +++ b/.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 diff --git a/.gitignore b/.gitignore index 66c072da5..9e9456375 100644 --- a/.gitignore +++ b/.gitignore @@ -119,3 +119,6 @@ ENV/ # output zarr generated *.zarr + +# uv lockfile +uv.lock diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0304e94da..535a3ba53 100644 --- a/.pre-commit-config.yaml +++ b/.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 diff --git a/.readthedocs.yml b/.readthedocs.yml index 9ff9f6352..5781204fd 100644 --- a/.readthedocs.yml +++ b/.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 diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index e90cb76a4..04bd8cfb5 100644 --- a/CONTRIBUTING.rst +++ b/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:: diff --git a/MANIFEST.in b/MANIFEST.in index ce5320a51..1deece2a9 100644 --- a/MANIFEST.in +++ b/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 diff --git a/README.md b/README.md index 1d4728011..b99c662cf 100644 --- a/README.md +++ b/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 diff --git a/docs/conf.py b/docs/conf.py index 4d34f4ffd..e0bc23bde 100644 --- a/docs/conf.py +++ b/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. diff --git a/docs/installation.rst b/docs/installation.rst index 340afb5f8..39c85c053 100644 --- a/docs/installation.rst +++ b/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 `_, a fast Python package and project manager, written in Rust. +`uv `_ is a Python package and project manager. First, install uv by following the `official installation guide `_ 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 ------------ diff --git a/docs/requirements.txt b/docs/requirements.txt index b530dce64..e69de29bb 100644 --- a/docs/requirements.txt +++ b/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 diff --git a/pre-commit/missing_imports.py b/pre-commit/missing_imports.py index 4855fda87..f53f0a38e 100644 --- a/pre-commit/missing_imports.py +++ b/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]: diff --git a/pre-commit/requirements_consistency.py b/pre-commit/requirements_consistency.py index ed57f1f9e..88aadb905 100644 --- a/pre-commit/requirements_consistency.py +++ b/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), ] diff --git a/pyproject.toml b/pyproject.toml index 648786293..e51fc73d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,121 @@ +[project] +name = "tiatoolbox" +version = "2.1.2" +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, <3.15" +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", + "Programming Language :: Python :: 3.14", +] +dependencies = [ + "aiohttp>=3.8.1", + "albumentations>=1.3.0", + "albucore <=0.0.28", + "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", + "s3fs>=2024.12.0", + "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>=2025.5.21", + "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>=3.0.8", +] + +[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==0.15.15", + "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 +167,11 @@ 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 diff --git a/requirements/generate_conda_env.py b/requirements/generate_conda_env.py index ae4525d81..763ca79d2 100644 --- a/requirements/generate_conda_env.py +++ b/requirements/generate_conda_env.py @@ -1,4 +1,4 @@ -"""Generate a conda environment YAML from requirements.txt. +"""Generate a conda environment YAML from pyproject.toml. Converts pip-style dependencies into conda-forge compatible dependencies. @@ -10,12 +10,13 @@ import os import re +import tomllib from pathlib import Path # ================================ # Config # ================================ -REQ_FILE = "requirements/requirements.txt" +PYPROJECT_FILE = "pyproject.toml" OUT_FILE = "requirements/requirements.conda.generated.yml" PYTHON_VERSION = os.environ.get("PYTHON_VERSION", "3.14") @@ -39,7 +40,7 @@ # Helpers # ================================ def parse_line(line: str) -> tuple[str, str] | None: - """Parse a requirements.txt line into (name, version).""" + """Parse requirement string into (name, version).""" line = line.split("#", 1)[0].strip() if not line: return None @@ -89,15 +90,20 @@ def to_yaml(env: dict) -> str: # ================================ def main() -> None: """Generate conda environment YAML.""" - req_path = Path(REQ_FILE) + pyproject_path = Path(PYPROJECT_FILE) - if not req_path.exists(): - msg = f"{REQ_FILE} not found" + if not pyproject_path.exists(): + msg = f"{PYPROJECT_FILE} not found" raise FileNotFoundError(msg) + with pyproject_path.open("rb") as f: + pyproject = tomllib.load(f) + + raw_deps = pyproject["project"]["dependencies"] + deps: dict[str, str] = {} - for raw_line in req_path.read_text().splitlines(): + for raw_line in raw_deps: parsed = parse_line(raw_line) if not parsed: continue diff --git a/requirements/requirements.conda.yml b/requirements/requirements.conda.yml deleted file mode 100644 index b1b3e4d99..000000000 --- a/requirements/requirements.conda.yml +++ /dev/null @@ -1,13 +0,0 @@ -name: tiatoolbox -channels: - - conda - - conda-forge - - pytorch - - defaults -dependencies: - - cython - - pip>=20.0.2 - - pixman>=0.39.0 - - python>=3.11, <=3.14 - - pip: - - -r requirements.txt diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 4ae080064..e69de29bb 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,44 +0,0 @@ -aiohttp>=3.8.1 -albucore<=0.0.28 -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>=3.10.0 -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 # Used by wsidicom -pyyaml>=6.0 -requests>=2.28.1 -s3fs>=2024.12.0 -scikit-image>=0.26.0 -scikit-learn>=1.2.0 -scipy>=1.8 -shapely>=2.0.0 -SimpleITK>=2.2.1 -simsimd>=6.5.16 # required by conda-package -sphinx>=9.0.0 -tifffile>=2025.5.21 -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>=3.0.8 diff --git a/requirements/requirements_cpu.txt b/requirements/requirements_cpu.txt deleted file mode 100644 index c4aa73ecf..000000000 --- a/requirements/requirements_cpu.txt +++ /dev/null @@ -1,3 +0,0 @@ ---index-url https://download.pytorch.org/whl/cpu -torch -torchvision diff --git a/requirements/requirements_dev.txt b/requirements/requirements_dev.txt index 2f1f3d018..e69de29bb 100644 --- a/requirements/requirements_dev.txt +++ b/requirements/requirements_dev.txt @@ -1,16 +0,0 @@ --r requirements.txt --r ../docs/requirements.txt -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==0.15.15 # This will be updated by pre-commit bot to latest version -toml>=0.10.2 -twine>=4.0.1 -wheel>=0.37.1 diff --git a/setup.py b/setup.py index 93efd37b6..5ad0f473f 100644 --- a/setup.py +++ b/setup.py @@ -12,11 +12,11 @@ with Path("HISTORY.md").open() as history_file: history = history_file.read() -install_requires = [ - line - for line in Path("requirements/requirements.txt").read_text().splitlines() - if line and line[0] not in ("-", "#") -] +import tomllib + +with Path("pyproject.toml").open("rb") as _f: + _pyproject = tomllib.load(_f) +install_requires = _pyproject["project"]["dependencies"] dependency_links = [] diff --git a/tests/test_utils.py b/tests/test_utils.py index a243ae2f7..28518567a 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -4,8 +4,10 @@ import hashlib import json +import platform import re import shutil +import sys from pathlib import Path from typing import TYPE_CHECKING, NoReturn from unittest.mock import patch @@ -1536,6 +1538,16 @@ def test_detect_gpu() -> None: _ = utils.env_detection.has_gpu() +@pytest.mark.skipif( + sys.platform != "darwin" or platform.machine() != "arm64", + reason="MPS is only available on Apple Silicon (macOS arm64).", +) +def test_mps_available_on_apple_silicon() -> None: + """Ensure the uv-installed torch wheel supports MPS on Apple Silicon.""" + assert torch.backends.mps.is_built() + assert torch.backends.mps.is_available() + + def make_simple_dat(centroids: tuple[tuple, tuple] = ((0, 0), (100, 100))) -> dict: """Make a simple dat file with cells at provided centroids.""" polys = [cell_polygon(cent) for cent in centroids] diff --git a/tests/test_uv_setup.py b/tests/test_uv_setup.py new file mode 100644 index 000000000..16c2c239a --- /dev/null +++ b/tests/test_uv_setup.py @@ -0,0 +1,134 @@ +"""Tests verifying the uv sync development setup is consistent and functional. + +These tests confirm that pyproject.toml is well-formed and that a uv-synced +environment can actually import and exercise key tiatoolbox functionality. +""" + +from __future__ import annotations + +import re +import subprocess +import sys +import tomllib +from importlib.metadata import version +from pathlib import Path + +import pytest + +REPO_ROOT = Path(__file__).parent.parent +PYPROJECT = REPO_ROOT / "pyproject.toml" + + +# --------------------------------------------------------------------------- +# Version consistency +# --------------------------------------------------------------------------- + + +class TestVersionConsistency: + """Version must be identical across all authoritative locations.""" + + @pytest.fixture(scope="class") + def pyproject_version(self) -> str: + """Return the version declared in pyproject.toml [project].""" + return tomllib.loads(PYPROJECT.read_text())["project"]["version"] + + @staticmethod + def test_pyproject_version_matches_package(pyproject_version: str) -> None: + """Installed package version must match pyproject.toml [project].version.""" + installed = version("tiatoolbox") + assert installed == pyproject_version, ( + f"Installed tiatoolbox version ({installed!r}) != " + f"pyproject.toml version ({pyproject_version!r}). " + f"Re-install with `uv sync` or `pip install -e .`." + ) + + @staticmethod + def test_pyproject_version_matches_init(pyproject_version: str) -> None: + """tiatoolbox.__version__ must match pyproject.toml [project].version.""" + import tiatoolbox # noqa: PLC0415 + + assert tiatoolbox.__version__ == pyproject_version, ( + f"tiatoolbox.__version__ ({tiatoolbox.__version__!r}) != " + f"pyproject.toml version ({pyproject_version!r}). " + f"Run `poetry version` to bump both simultaneously." + ) + + @staticmethod + def test_pyproject_version_matches_setup_py(pyproject_version: str) -> None: + """setup.py version= must match pyproject.toml [project].version.""" + setup_py = (REPO_ROOT / "setup.py").read_text() + m = re.search(r'version\s*=\s*["\']([^"\']+)["\']', setup_py) + assert m, "Could not find version= in setup.py" + assert m.group(1) == pyproject_version, ( + f"setup.py version ({m.group(1)!r}) != " + f"pyproject.toml version ({pyproject_version!r})." + ) + + +# --------------------------------------------------------------------------- +# uv infrastructure files +# --------------------------------------------------------------------------- + + +def test_pyproject_has_project_table() -> None: + """pyproject.toml must contain a [project] table for uv sync to work.""" + data = tomllib.loads(PYPROJECT.read_text()) + assert "project" in data, "[project] table missing from pyproject.toml" + for field in ("name", "version", "dependencies", "requires-python"): + assert field in data["project"], ( + f"[project].{field} missing from pyproject.toml" + ) + + +# --------------------------------------------------------------------------- +# Functional: key imports and CLI entry point +# --------------------------------------------------------------------------- + + +CRITICAL_IMPORTS = [ + "tiatoolbox", + "tiatoolbox.wsicore.wsireader", + "tiatoolbox.models.engine.semantic_segmentor", + "tiatoolbox.tools.patchextraction", + "tiatoolbox.annotation.storage", + "torch", + "torchvision", + "cv2", + "numpy", + "shapely", + "openslide", + "skimage", + "scipy", +] + + +@pytest.mark.parametrize("module", CRITICAL_IMPORTS) +def test_critical_module_importable(module: str) -> None: + """Each critical module must be importable in the active environment.""" + result = subprocess.run( # noqa: S603 + [sys.executable, "-c", f"import {module}"], + capture_output=True, + check=False, + text=True, + ) + assert result.returncode == 0, ( + f"Failed to import {module!r}.\n" + f"stderr: {result.stderr.strip()}\n" + f"This module may be missing from the uv-synced environment." + ) + + +def test_cli_entry_point() -> None: + """The `tiatoolbox` CLI entry point must respond to --help.""" + result = subprocess.run( + [sys.executable, "-m", "tiatoolbox", "--help"], + capture_output=True, + check=False, + text=True, + ) + assert result.returncode == 0, ( + f"`python -m tiatoolbox --help` failed.\nstderr: {result.stderr.strip()}" + ) + assert "tiatoolbox" in result.stdout.lower(), ( + "Unexpected --help output from tiatoolbox CLI" + ) diff --git a/uv.lock b/uv.lock new file mode 100644 index 000000000..d8ea036c2 --- /dev/null +++ b/uv.lock @@ -0,0 +1,5999 @@ +version = 1 +revision = 3 +requires-python = ">=3.11, <3.14" +resolution-markers = [ + "(python_full_version >= '3.13' and sys_platform == 'linux') or (python_full_version >= '3.13' and sys_platform == 'win32')", + "(python_full_version == '3.12.*' 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