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Merge pull request #237 from bgilbert/setuptools
Switch to PEP 621 project metadata; build sdist and all wheels in CI
2 parents 3bc80e7 + 83b18c7 commit 72eb0d1

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‎.github/ISSUE_TEMPLATE/release.md‎

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

‎.github/workflows/python.yml‎

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

‎.gitignore‎

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/build
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/dist
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/MANIFEST
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/*.egg-info
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*.pyc

‎.isort.cfg‎

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This file was deleted.

‎.pre-commit-config.yaml‎

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

‎.rstcheck.cfg‎

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‎MANIFEST.in‎

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include *.md pytest.ini
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include *.md
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recursive-include doc *.py *.rst
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recursive-include examples *.html *.js *.png *.py
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recursive-include tests *.dcm *.png *.py *.svs *.tiff

‎pyproject.toml‎

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[project]
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name = "openslide-python"
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maintainers = [
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{name = "OpenSlide project", email = "openslide-users@lists.andrew.cmu.edu"}
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]
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description = "Python interface to OpenSlide"
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readme = "README.md"
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license = {text = "GNU Lesser General Public License, version 2.1"}
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keywords = ["OpenSlide", "whole-slide image", "virtual slide", "library"]
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classifiers = [
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"Development Status :: 5 - Production/Stable",
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"Intended Audience :: Developers",
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"Intended Audience :: Healthcare Industry",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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requires-python = ">= 3.8"
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dependencies = ["Pillow"]
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dynamic = ["version"]
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[project.urls]
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Homepage = "https://openslide.org/"
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Documentation = "https://openslide.org/api/python/"
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Repository = "https://github.com/openslide/openslide-python"
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[tool.setuptools]
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packages = ["openslide"]
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[tool.setuptools.dynamic]
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version = {attr = "openslide._version.__version__"}
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[tool.isort]
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profile = "black"
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force_sort_within_sections = true
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[tool.pytest.ini_options]
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minversion = "7.0"
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# don't try to import openslide from the source directory, since it doesn't
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# have the compiled extension module
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addopts = "--import-mode importlib"
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# allow tests to import common module
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pythonpath = "tests"
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[tool.rstcheck]
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ignore_messages = "(Hyperlink target \".*\" is not referenced\\.$)"
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[build-system]
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requires = ["setuptools >= 61.0.0"]
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build-backend = "setuptools.build_meta"

‎pytest.ini‎

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‎setup.py‎

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import os
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from setuptools import Extension, setup
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# Load version string
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_verfile = os.path.join(os.path.dirname(__file__), 'openslide', '_version.py')
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with open(_verfile) as _fh:
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exec(_fh.read()) # instantiates __version__
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with open('README.md') as _fh:
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_long_description = _fh.read()
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setup(
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name='openslide-python',
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version=__version__, # noqa: F821 undefined-name __version__
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packages=[
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'openslide',
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],
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ext_modules=[
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Extension('openslide._convert', ['openslide/_convert.c']),
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],
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test_suite='tests',
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maintainer='OpenSlide project',
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maintainer_email='openslide-users@lists.andrew.cmu.edu',
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description='Python interface to OpenSlide',
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long_description=_long_description,
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long_description_content_type='text/markdown',
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license='GNU Lesser General Public License, version 2.1',
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keywords='openslide whole-slide image virtual slide library',
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url='https://openslide.org/',
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classifiers=[
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'Development Status :: 5 - Production/Stable',
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'Intended Audience :: Developers',
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'Intended Audience :: Healthcare Industry',
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)',
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'Operating System :: MacOS :: MacOS X',
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'Operating System :: Microsoft :: Windows',
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'Operating System :: POSIX :: Linux',
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'Programming Language :: Python',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.8',
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'Programming Language :: Python :: 3.9',
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'Programming Language :: Python :: 3.10',
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'Programming Language :: Python :: 3.11',
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'Programming Language :: Python :: 3.12',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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],
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python_requires='>=3.8',
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install_requires=[
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'Pillow',
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],
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zip_safe=True,
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)

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