remove setup.py, replacing it with pyproject.toml

.pre-commit-config.yaml

@@ -15,23 +15,22 @@ repos:
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/pyproject_.toml"]
+        args: ["--settings-path=python/cucim/pyproject.toml"]
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
         files: (python|legate)/.*
-        args: ["--config", "python/cucim/pyproject_.toml"]
+        args: ["--config", "python/cucim/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.0.278
     hooks:
       - id: ruff
         files: python/.*$
-        args: ["--exclude", "__init__.py"]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4
     hooks:
       - id: codespell
-        args: ["--toml", "python/cucim/pyproject_.toml"]
+        args: ["--toml", "python/cucim/pyproject.toml"]
         additional_dependencies:
           - tomli

conda/recipes/cucim/build.sh

@@ -18,6 +18,6 @@ cp -P python/install/lib/* python/cucim/src/cucim/clara/
 pushd python/cucim
 
 echo "PYTHON: ${PYTHON}"
-$PYTHON setup.py install
+$PYTHON -m pip install .
 
 popd

python/cucim/pyproject.toml

@@ -0,0 +1,241 @@
+# Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
+# See file LICENSE for terms.
+
+[build-system]
+build-backend = "setuptools.build_meta"
+# TODO: generate this list with `rapids-dependency-file-generator`
+requires = [
+    "setuptools>=24.2.0",
+    "wheel",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+
+[project]
+name = "cucim"
+version = "23.12.00"
+description = "cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitives for N-Dimensional images with a focus on biomedical imaging."
+# TODO: tried also adding CHANGELOG.md as in setup.py's long_description, but ruff complained about it
+readme = { file = "README.md", content-type = "text/markdown" }
+# readme = [
+#     { file = "README.md", content-type = "text/markdown" },
+#     { file = "CHANGELOG.md", content-type = "text/markdown" },
+# ]
+authors = [
+    { name = "NVIDIA Corporation" },
+]
+license = { text = "Apache 2.0" }
+requires-python = ">=3.8"
+#TODO: add dependencies.yaml and generate this by `rapids-dependency-file-generator` instead
+dependencies = [
+    "click",
+    "numpy",
+    "lazy_loader>=0.1",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Healthcare Industry",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: POSIX :: Linux",
+    "Environment :: Console",
+    "Environment :: GPU :: NVIDIA CUDA :: 11.0",
+    "Environment :: GPU :: NVIDIA CUDA :: 12.0",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+
+[project.urls]
+Homepage = "https://developer.nvidia.com/multidimensional-image-processing"
+Documentation = "https://docs.rapids.ai/api/cucim/stable/"
+Changelog = "https://github.com/rapidsai/cucim/blob/branch-23.12/CHANGELOG.md"
+Source = "https://github.com/rapidsai/cucim"
+Tracker = "https://github.com/rapidsai/cucim/issues"
+
+[project.optional-dependencies]
+test = [
+    "cupy-cuda11x>=12.0.0",
+    "scipy",
+    "scikit-image>=0.19",
+    "pytest",
+    "pytest-lazy-fixture",
+    "gputil",
+    "openslide-python",
+] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../dependencies.yaml and run `rapids-dependency-file-generator`.
+developer = [
+    "black",
+    "isort",
+    "pre-commit",
+    "ruff",
+]
+docs = [
+    "Sphinx==4.5.0",
+    "sphinx-autobuild",
+    "sphinx-book-theme",
+    "sphinxcontrib-bibtex<2.0.0",  # https://github.com/executablebooks/jupyter-book/issues/1137
+    "sphinx-copybutton",
+    "sphinx-panels",
+    "sphinx-thebe",
+    "sphinx-togglebutton",
+    "sphinxemoji",
+    "ablog",
+    "docutils==0.16", # 0.17 causes error. https://github.com/executablebooks/MyST-Parser/issues/343
+    "pydata_sphinx_theme",
+    "myst-parser",
+    "myst-nb",
+    "ipywidgets",
+    "nbclient",
+    "plotly<5",
+    "pandas",
+    "matplotlib",
+    "cupy-cuda110",
+    "numpy",
+    "scipy",
+    "scikit-image",
+]
+
+[project.entry-points."console_scripts"]
+cucim = "cucim.clara.cli:main"
+
+[tool.setuptools]
+license-files = ["LICENSE"]
+# By default, include-package-data is true in pyproject.toml, so you do
+# NOT have to specify this line.
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src/cucim"]
+
+[tool.setuptools.package-data]
+mypkg = ["*.pyi", "*.h", "*.cu"]
+
+[tool.isort]
+profile = "black"
+force_single_line = false
+line_length = 80
+forced_separate = "test_cucim"
+force_grid_wrap = 0
+multi_line_output = 3
+order_by_type = true
+combine_as_imports = true
+include_trailing_comma = true
+known_first_party = [
+    "cucim",
+]
+default_section = "THIRDPARTY"
+sections = [
+    "FUTURE",
+    "STDLIB",
+    "THIRDPARTY",
+    "FIRSTPARTY",
+    "LOCALFOLDER",
+]
+skip = [
+    "3rdparty",
+    "thirdparty",
+    ".eggs",
+    ".git",
+    ".hg",
+    ".mypy_cache",
+    ".tox",
+    ".venv",
+    "ci",
+    "cpp",
+    "_build",
+    "build",
+    "build-debug",
+    "build-release",
+    "_deps",
+    "dist",
+]
+
+[tool.pytest.ini_options]
+# If a pytest section is found in one of the possible config files
+# (pytest.ini, tox.ini or setup.cfg), then pytest will not look for any others,
+# so if you add a pytest config section elsewhere,
+# you will need to delete this section from setup.cfg.
+norecursedirs = "migrations"
+python_files = [
+    "test_*.py",
+    "*_test.py",
+    "tests.py",
+]
+addopts = [
+    "-ra",
+    "--strict-markers",
+    # --doctest-modules",
+    # --doctest-glob=\*.rst",
+    "--tb=short",
+    "--ignore-glob=build*",
+]
+testpaths = [
+    "src",
+    "tests",
+]
+
+[tool.ruff]
+# see: https://docs.astral.sh/ruff/rules/
+select = ["E", "F", "W"]
+fixable = ["ALL"]
+exclude = [
+    # TODO: Remove this in a follow-up where we fix __all__.
+    ".tox",
+    ".eggs",
+    "ci/templates",
+    "build",
+    "dist",
+    ".git",
+    "__pycache__",
+    "doc/conf.py",
+    "doc/sphinxext",
+    "__init__.py",
+]
+line-length = 80
+
+[tool.ruff.per-file-ignores]
+# "src/cucim/skimage/util/tests/test_shape.py" = ["E201", "E202"]
+
+[tool.black]
+line-length = 80
+target-version = ["py39"]
+include = '\.py?$'
+exclude = '''
+/(
+    3rdparty |
+    thirdparty |
+    \.eggs |
+    \.git |
+    \.hg |
+    \.mypy_cache |
+    \.tox |
+    \.venv |
+    _build |
+    _deps |
+    cpp |
+    ci |
+    build |
+    build-debug |
+    build-release |
+    dist |
+    docker |
+    docs |
+)/
+'''
+
+[tool.codespell]
+# note: pre-commit passes explicit lists of files here, which this skip file list doesn't override -
+# this is only to allow you to run codespell interactively
+# e.g. via
+#   codespell --toml python/cucim/pyproject.toml . -i 3 -w
+skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
+# ignore-regex = ""
+ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,nd,paeth,unser,wronly"
+quiet-level = 3
+
+# to undo: ./test_data/input/LICENSE-3rdparty