From 934e1d110b28c3ad348eac05251ef20d34f3073f Mon Sep 17 00:00:00 2001 From: abdol Date: Thu, 30 Apr 2026 16:37:35 +0100 Subject: [PATCH 1/4] :sparkles: Add basic uv support --- pyproject.toml | 121 + uv.lock | 5953 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 6074 insertions(+) create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index 1af1c337a..5e7bb03b6 100644 --- a/pyproject.toml +++ b/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] +# 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file mode 100644 index 000000000..e5ec1c177 --- /dev/null +++ b/tests/test_uv_setup.py @@ -0,0 +1,298 @@ +"""Tests verifying the uv sync development setup is consistent and functional. + +These tests guard against drift between pyproject.toml [project] dependencies +and the requirements/*.txt files, and confirm 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" +REQUIREMENTS_TXT = REPO_ROOT / "requirements" / "requirements.txt" +REQUIREMENTS_DEV_TXT = REPO_ROOT / "requirements" / "requirements_dev.txt" +REQUIREMENTS_DOCS_TXT = REPO_ROOT / "docs" / "requirements.txt" + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _normalize(name: str) -> str: + """Normalize a package name per PEP 503.""" + return re.sub(r"[-_.]+", "-", name.lower()) + + +def _parse_req_line(line: str) -> tuple[str, str] | None: + """Parse one requirements.txt line into (normalized_name, specifier). + + Returns None for blank lines, comments, and -r/-i includes. + """ + line = line.split("#")[0].strip() + if not line or line.startswith("-"): + return None + # Match name (with optional extras) then version specifier + m = re.match(r"^([A-Za-z0-9_.-]+)(\[.*?])?([\s,><=!~^*]+.*)?$", line) + if not m: + return None + name = _normalize(m.group(1)) + spec = re.sub(r"\s+", "", m.group(3) or "") + return name, spec + + +def _parse_requirements_file(path: Path) -> dict[str, str]: + """Return {normalized_name: specifier} from a requirements file.""" + result = {} + for line in path.read_text().splitlines(): + parsed = _parse_req_line(line) + if parsed: + result[parsed[0]] = parsed[1] + return result + + +def _parse_pyproject_deps(deps: list[str]) -> dict[str, str]: + """Return {normalized_name: specifier} from a pyproject.toml dep list. + + Skips self-referential entries like ``tiatoolbox[docs]``. + """ + result = {} + for dep in deps: + dep = dep.strip() + if _normalize(dep.split("[")[0]) == "tiatoolbox": + continue + m = re.match(r"^([A-Za-z0-9_.-]+)(\[.*?])?(.*)?$", dep) + if m: + name = _normalize(m.group(1)) + spec = re.sub(r"\s+", "", m.group(3) or "") + result[name] = spec + return result + + +# --------------------------------------------------------------------------- +# Dependency parity: pyproject.toml ↔ requirements/*.txt +# --------------------------------------------------------------------------- + + +class TestDependencyParity: + """Guard against drift between pyproject.toml and requirements files.""" + + @pytest.fixture(scope="class") + def pyproject(self) -> dict: + """Load pyproject.toml once for the class.""" + return tomllib.loads(PYPROJECT.read_text()) + + def test_runtime_deps_match_requirements_txt(self, pyproject: dict) -> None: + """Every package in requirements.txt must appear in [project].dependencies.""" + req_deps = _parse_requirements_file(REQUIREMENTS_TXT) + proj_deps = _parse_pyproject_deps(pyproject["project"]["dependencies"]) + + missing = set(req_deps) - set(proj_deps) + assert not missing, ( + f"Packages in requirements.txt but missing from pyproject.toml " + f"[project].dependencies: {sorted(missing)}\n" + f"Run `uv sync` users will not get these packages." + ) + + extra = set(proj_deps) - set(req_deps) + assert not extra, ( + f"Packages in pyproject.toml [project].dependencies but missing from " + f"requirements.txt: {sorted(extra)}\n" + f"Conda/pip users installing from requirements.txt will not get these." + ) + + def test_runtime_dep_version_specs_match(self, pyproject: dict) -> None: + """Version specifiers must be identical in both sources (after normalization).""" + req_deps = _parse_requirements_file(REQUIREMENTS_TXT) + proj_deps = _parse_pyproject_deps(pyproject["project"]["dependencies"]) + + mismatches = { + name: (req_deps[name], proj_deps[name]) + for name in req_deps + if name in proj_deps and req_deps[name] != proj_deps[name] + } + assert not mismatches, ( + "Version specifier mismatches between requirements.txt and " + "pyproject.toml [project].dependencies:\n" + + "\n".join( + f" {name}: requirements.txt={r!r} pyproject.toml={p!r}" + for name, (r, p) in sorted(mismatches.items()) + ) + ) + + def test_dev_deps_match_requirements_dev_txt(self, pyproject: dict) -> None: + """Dev packages must match between pyproject.toml [dev] and requirements_dev.txt. + + requirements_dev.txt uses ``-r requirements.txt`` and + ``-r ../docs/requirements.txt`` for transitive deps; those are excluded + from comparison (covered by tiatoolbox[docs] self-reference in pyproject). + """ + req_deps = _parse_requirements_file(REQUIREMENTS_DEV_TXT) + proj_deps = _parse_pyproject_deps( + pyproject["project"]["optional-dependencies"]["dev"] + ) + + missing = set(req_deps) - set(proj_deps) + assert not missing, ( + f"Packages in requirements_dev.txt but missing from pyproject.toml " + f"[project.optional-dependencies.dev]: {sorted(missing)}" + ) + + extra = set(proj_deps) - set(req_deps) + assert not extra, ( + f"Packages in pyproject.toml [dev] but missing from " + f"requirements_dev.txt: {sorted(extra)}" + ) + + def test_docs_deps_match_requirements_docs_txt(self, pyproject: dict) -> None: + """Docs packages must match between pyproject.toml [docs] and docs/requirements.txt.""" + req_deps = _parse_requirements_file(REQUIREMENTS_DOCS_TXT) + proj_deps = _parse_pyproject_deps( + pyproject["project"]["optional-dependencies"]["docs"] + ) + + missing = set(req_deps) - set(proj_deps) + assert not missing, ( + f"Packages in docs/requirements.txt but missing from pyproject.toml " + f"[project.optional-dependencies.docs]: {sorted(missing)}" + ) + + extra = set(proj_deps) - set(req_deps) + assert not extra, ( + f"Packages in pyproject.toml [docs] but missing from " + f"docs/requirements.txt: {sorted(extra)}" + ) + + +# --------------------------------------------------------------------------- +# 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"] + + def test_pyproject_version_matches_package(self, 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 .`." + ) + + def test_pyproject_version_matches_init(self, 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." + ) + + def test_pyproject_version_matches_setup_py(self, 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_python_version_file_exists() -> None: + """.python-version must exist and declare Python 3.x.""" + pv_file = REPO_ROOT / ".python-version" + assert pv_file.exists(), ".python-version not found — run `echo '3.11' > .python-version`" + content = pv_file.read_text().strip() + assert re.match(r"^3\.\d+", content), ( + f".python-version contains {content!r}, expected e.g. '3.11'" + ) + + +def test_uv_lockfile_exists() -> None: + """uv.lock must be committed so `uv sync --frozen` works in CI.""" + assert (REPO_ROOT / "uv.lock").exists(), ( + "uv.lock not found. Generate it with `uv lock` and commit the result." + ) + + +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}"], # noqa: S603 + capture_output=True, + 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( # noqa: S603 + [sys.executable, "-m", "tiatoolbox", "--help"], # noqa: S603 + capture_output=True, + 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" + ) From 6821d414da7f24e49c23bbe9ada14fbaf0f2b2f3 Mon Sep 17 00:00:00 2001 From: abdol Date: Thu, 30 Apr 2026 16:38:48 +0100 Subject: [PATCH 3/4] :memo: Update README with uv install steps --- README.md | 29 +++++++++++++++++++++++------ 1 file changed, 23 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 711ef4e75..149f4dc30 100644 --- a/README.md +++ b/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 From edd9bfd3c7230da6d2ec6bd371ee545c076b671a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 30 Apr 2026 15:43:43 +0000 Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- README.md | 6 +++--- tests/test_uv_setup.py | 16 ++++++++++------ 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 149f4dc30..a9f38e9b8 100644 --- a/README.md +++ b/README.md @@ -113,13 +113,13 @@ Prepare a computer as a convenient platform for further development of the Pytho $ .venv\Scripts\activate # Windows ``` - For CPU-only machines (no CUDA GPU): +For CPU-only machines (no CUDA GPU): ```sh $ uv sync --extra dev --index pytorch-cpu=https://download.pytorch.org/whl/cpu ``` - **Using conda:** +**Using conda:** ```sh $ conda create -n tiatoolbox-dev python=3.11 @@ -127,7 +127,7 @@ Prepare a computer as a convenient platform for further development of the Pytho $ pip install -r requirements/requirements_dev.txt ``` - or (Linux/macOS only): +or (Linux/macOS only): ```sh $ conda env create -f requirements/requirements.dev.conda.yml diff --git a/tests/test_uv_setup.py b/tests/test_uv_setup.py index e5ec1c177..43521d820 100644 --- a/tests/test_uv_setup.py +++ b/tests/test_uv_setup.py @@ -38,7 +38,7 @@ def _parse_req_line(line: str) -> tuple[str, str] | None: Returns None for blank lines, comments, and -r/-i includes. """ - line = line.split("#")[0].strip() + line = line.split("#", maxsplit=1)[0].strip() if not line or line.startswith("-"): return None # Match name (with optional extras) then version specifier @@ -224,7 +224,9 @@ def test_pyproject_version_matches_setup_py(self, pyproject_version: str) -> Non def test_python_version_file_exists() -> None: """.python-version must exist and declare Python 3.x.""" pv_file = REPO_ROOT / ".python-version" - assert pv_file.exists(), ".python-version not found — run `echo '3.11' > .python-version`" + assert pv_file.exists(), ( + ".python-version not found — run `echo '3.11' > .python-version`" + ) content = pv_file.read_text().strip() assert re.match(r"^3\.\d+", content), ( f".python-version contains {content!r}, expected e.g. '3.11'" @@ -243,7 +245,9 @@ def test_pyproject_has_project_table() -> None: 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" + assert field in data["project"], ( + f"[project].{field} missing from pyproject.toml" + ) # --------------------------------------------------------------------------- @@ -272,7 +276,7 @@ def test_pyproject_has_project_table() -> None: 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}"], # noqa: S603 + [sys.executable, "-c", f"import {module}"], capture_output=True, text=True, ) @@ -285,8 +289,8 @@ def test_critical_module_importable(module: str) -> None: def test_cli_entry_point() -> None: """The `tiatoolbox` CLI entry point must respond to --help.""" - result = subprocess.run( # noqa: S603 - [sys.executable, "-m", "tiatoolbox", "--help"], # noqa: S603 + result = subprocess.run( + [sys.executable, "-m", "tiatoolbox", "--help"], capture_output=True, text=True, )