Switch to PEP 621 project metadata; build sdist and all wheels in CI

.github/ISSUE_TEMPLATE/release.md

@@ -5,13 +5,14 @@
 - [ ] `git clean -dxf && mkdir dist`
 - [ ] Find the [workflow run](https://github.com/openslide/openslide-python/actions) for the tag; download its docs and wheels artifacts
 - [ ] `unzip /path/to/downloaded/openslide-python-wheels.zip && mv openslide-python-wheels-*/* dist/`
-- [ ] `python setup.py sdist`
 - [ ] `twine upload dist/*`
 - [ ] Recompress tarball with `xz`
 - [ ] Attach release notes to [GitHub release](https://github.com/openslide/openslide-python/releases/new); upload tarballs and wheels
 - [ ] `cd` into website checkout; `rm -r api/python && unzip /path/to/downloaded/openslide-python-docs.zip && mv openslide-python-docs-* api/python`
 - [ ] Update website: `_data/releases.yaml`, `_includes/news.md`
 - [ ] Update Ubuntu PPA
-- [ ] Send mail to -announce and -users
 - [ ] Update Fedora and EPEL packages
+- [ ] Check that [Copr package](https://copr.fedorainfracloud.org/coprs/g/openslide/openslide/builds/) built successfully
+- [ ] Send mail to -announce and -users
+- [ ] Post to [forum.image.sc](https://forum.image.sc/c/announcements/10)
 - [ ] Update MacPorts package

.github/workflows/python.yml

@@ -31,17 +31,48 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.12"
+            sdist: sdist
+          # Python 3.8 is too old to support universal binaries, and
+          # setup-python's Python 3.9 and 3.10 won't build them.  Use the
+          # last upstream patch releases that ship with installers.
+          # https://github.com/actions/setup-python/issues/439#issuecomment-1247646682
+          - os: macos-latest
+            python-version: "3.9"
+            upstream-python: 3.9.13
+          - os: macos-latest
+            python-version: "3.10"
+            upstream-python: 3.10.11
     steps:
     - name: Check out repo
       uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
+      if: matrix.upstream-python == null
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up Python ${{ matrix.python-version }} (macOS fallback)
+      if: matrix.upstream-python != null
+      run: |
+        pkgdir="${{ runner.temp }}/python"
+        mkdir -p "$pkgdir/bin"
+        pkg="$pkgdir/python.pkg"
+        curl -Lfo "$pkg" \
+            "https://www.python.org/ftp/python/${{ matrix.upstream-python }}/python-${{ matrix.upstream-python }}-macos11.pkg"
+        sudo installer -pkg "$pkg" -target /
+        for bin in python pip; do
+            ln -s /usr/local/bin/${bin}3 $pkgdir/bin/${bin}
+        done
+        export PATH="$pkgdir/bin:$PATH"
+        echo "PATH=$PATH" >> $GITHUB_ENV
+        python -V
+        pip -V
     - name: Install Python tools
       run: |
         python -m pip install --upgrade pip
-        pip install jinja2 pytest setuptools
+        pip install auditwheel build jinja2 pytest setuptools
     - name: Install OpenSlide
       run: |
         case "${{ matrix.os }}" in
@@ -52,12 +83,40 @@ jobs:
           brew install openslide
           ;;
         esac
+    - name: Build wheel
+      run: |
+        if [ -z "${{ matrix.sdist }}" ]; then
+            wheel_only=-w
+        fi
+        python -m build $wheel_only
+        case "${{ matrix.os }}" in
+        ubuntu-*)
+            mkdir old
+            mv dist/*.whl old/
+            auditwheel repair --only-plat -w dist old/*whl
+            ;;
+        macos-*)
+            if [ "${{ matrix.python-version }}" != 3.8 -a ! -e dist/*universal2* ]; then
+                echo "Wheel is not universal:"
+                ls dist
+                exit 1
+            fi
+        esac
+        basename=openslide-python-wheels-$GITHUB_RUN_NUMBER-$(echo $GITHUB_SHA | cut -c-10)
+        mkdir -p "artifacts/${basename}"
+        mv dist/* "artifacts/${basename}"
+        echo "basename=${basename}" >> $GITHUB_ENV
     - name: Install
-      run: pip install .
+      run: pip install artifacts/${basename}/*.whl
     - name: Run tests
       run: pytest -v
     - name: Tile slide
       run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs
+    - name: Archive wheel
+      uses: actions/upload-artifact@v3
+      with:
+        name: ${{ env.basename }}
+        path: artifacts
   windows:
     name: Windows
     needs: pre-commit
@@ -80,24 +139,24 @@ jobs:
     - name: Install Python tools
       run: |
         python -m pip install --upgrade pip
-        pip install flask Pillow pytest setuptools wheel
+        pip install build flask pytest
     - name: Install OpenSlide
       run: |
         mkdir -p c:\\openslide
         cd c:\\openslide
         zipname=openslide-win64-${BIN_RELEASE}
-        curl -LO "https://github.com/openslide/openslide-bin/releases/download/v${BIN_RELEASE}/${zipname}.zip"
+        curl -LfO "https://github.com/openslide/openslide-bin/releases/download/v${BIN_RELEASE}/${zipname}.zip"
         7z x ${zipname}.zip
         echo "OPENSLIDE_PATH=c:\\openslide\\${zipname}\\bin" >> $GITHUB_ENV
     - name: Build wheel
       run: |
-        python setup.py bdist_wheel
+        python -m build -w
         basename=openslide-python-wheels-$GITHUB_RUN_NUMBER-$(echo $GITHUB_SHA | cut -c-10)
         mkdir -p "artifacts/${basename}"
         mv dist/*.whl "artifacts/${basename}"
         echo "basename=${basename}" >> $GITHUB_ENV
     - name: Install
-      run: pip install -e .
+      run: pip install artifacts/${basename}/*.whl
     - name: Run tests
       # Reads OPENSLIDE_PATH
       run: pytest -v

.gitignore

@@ -1,5 +1,4 @@
 /build
 /dist
-/MANIFEST
 /*.egg-info
 *.pyc

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ exclude: '^(COPYING\.LESSER|examples/deepzoom/static/.*\.js)$'
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
       - id: check-merge-conflict
@@ -14,7 +14,7 @@ repos:
         exclude: '^\.github/.*\.md$'
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.14.0
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         name: Modernize python code
@@ -27,7 +27,7 @@ repos:
         name: Reorder python imports with isort
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.1
     hooks:
       - id: black
         name: Format python code with black
@@ -57,7 +57,7 @@ repos:
     hooks:
       - id: rstcheck
         name: Validate reStructuredText syntax
-        additional_dependencies: [sphinx]
+        additional_dependencies: [sphinx, toml]
 
   - repo: meta
     hooks:

MANIFEST.in

@@ -1,4 +1,4 @@
-include *.md pytest.ini
+include *.md
 recursive-include doc *.py *.rst
 recursive-include examples *.html *.js *.png *.py
 recursive-include tests *.dcm *.png *.py *.svs *.tiff

pyproject.toml

@@ -0,0 +1,60 @@
+[project]
+name = "openslide-python"
+maintainers = [
+    {name = "OpenSlide project", email = "[email protected]"}
+]
+description = "Python interface to OpenSlide"
+readme = "README.md"
+license = {text = "GNU Lesser General Public License, version 2.1"}
+keywords = ["OpenSlide", "whole-slide image", "virtual slide", "library"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "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",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+requires-python = ">= 3.8"
+dependencies = ["Pillow"]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://openslide.org/"
+Documentation = "https://openslide.org/api/python/"
+Repository = "https://github.com/openslide/openslide-python"
+
+[tool.setuptools]
+packages = ["openslide"]
+
+[tool.setuptools.dynamic]
+version = {attr = "openslide._version.__version__"}
+
+[tool.isort]
+profile = "black"
+force_sort_within_sections = true
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+# don't try to import openslide from the source directory, since it doesn't
+# have the compiled extension module
+addopts = "--import-mode importlib"
+# allow tests to import common module
+pythonpath = "tests"
+
+[tool.rstcheck]
+ignore_messages = "(Hyperlink target \".*\" is not referenced\\.$)"
+
+[build-system]
+requires = ["setuptools >= 61.0.0"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -1,54 +1,7 @@
-import os
-
 from setuptools import Extension, setup
 
-# Load version string
-_verfile = os.path.join(os.path.dirname(__file__), 'openslide', '_version.py')
-with open(_verfile) as _fh:
-    exec(_fh.read())  # instantiates __version__
-
-with open('README.md') as _fh:
-    _long_description = _fh.read()
-
 setup(
-    name='openslide-python',
-    version=__version__,  # noqa: F821  undefined-name __version__
-    packages=[
-        'openslide',
-    ],
     ext_modules=[
         Extension('openslide._convert', ['openslide/_convert.c']),
     ],
-    test_suite='tests',
-    maintainer='OpenSlide project',
-    maintainer_email='[email protected]',
-    description='Python interface to OpenSlide',
-    long_description=_long_description,
-    long_description_content_type='text/markdown',
-    license='GNU Lesser General Public License, version 2.1',
-    keywords='openslide whole-slide image virtual slide library',
-    url='https://openslide.org/',
-    classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Healthcare Industry',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: POSIX :: Linux',
-        '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',
-        'Programming Language :: Python :: 3.12',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-    ],
-    python_requires='>=3.8',
-    install_requires=[
-        'Pillow',
-    ],
-    zip_safe=True,
 )