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scaramallionscaramallion
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Update interface and deploy builds (#11)
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‎.github/workflows/pytest-builds.yml‎

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name: Run pytest
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name: unit-tests
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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jobs:
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pytest:

‎.github/workflows/release-wheels.yml‎

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name: Build wheels and deploy to PyPI
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name: release-deploy
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on:
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release:
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types: [ published ]
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jobs:
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build_wheels:
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name: Build wheels for ${{ matrix.os }}
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build-sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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timeout-minutes: 10
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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- uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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- uses: actions/setup-python@v2
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name: Install Python
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with:
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python-version: '3.10'
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- name: Build sdist
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run: |
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python -m pip install -U pip
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python -m pip install -U setuptools-rust
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python -m pip install .
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python setup.py sdist
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- name: Store artifacts
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uses: actions/upload-artifact@v2
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with:
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name: wheels
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path: ./dist
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build-wheels:
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name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }}
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runs-on: ${{ matrix.os }}
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env:
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CIBW_SKIP: "cp36-* *-musl*"
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ["3.10"]
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include:
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# Windows 32 bit
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- os: windows-latest
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python: 37
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platform_id: win32
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- os: windows-latest
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python: 38
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platform_id: win32
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- os: windows-latest
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python: 39
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platform_id: win32
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- os: windows-latest
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python: 310
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platform_id: win32
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# Windows 64 bit
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- os: windows-latest
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python: 37
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platform_id: win_amd64
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- os: windows-latest
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python: 38
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platform_id: win_amd64
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- os: windows-latest
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python: 39
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platform_id: win_amd64
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- os: windows-latest
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python: 310
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platform_id: win_amd64
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# Linux 64 bit manylinux2010
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- os: ubuntu-latest
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python: 37
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2010
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- os: ubuntu-latest
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python: 38
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2010
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- os: ubuntu-latest
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python: 39
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2010
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- os: ubuntu-latest
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python: 310
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2010
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# Linux 64 bit manylinux2014
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- os: ubuntu-latest
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python: 37
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: 38
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: 39
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: 310
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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# MacOS x86_64
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- os: macos-latest
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python: 37
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platform_id: macosx_x86_64
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- os: macos-latest
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python: 38
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platform_id: macosx_x86_64
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- os: macos-latest
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python: 39
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platform_id: macosx_x86_64
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- os: macos-latest
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python: 310
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platform_id: macosx_x86_64
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# MacOS arm64
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- os: macos-latest
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python: 38
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platform_id: macosx_arm64
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- os: macos-latest
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python: 39
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platform_id: macosx_arm64
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- os: macos-latest
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python: 310
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platform_id: macosx_arm64
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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# Install rust
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- uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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# Install Python
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- uses: actions/setup-python@v2
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name: Install Python
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install requirements
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run: |
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pip install -U pip
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pip install cibuildwheel==2.3.1
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pip install setuptools-rust
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python-version: '3.9'
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- name: Build sdist
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- name: Install cibuildwheel
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run: |
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python setup.py sdist
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python -m pip install -U pip
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python -m pip install -U setuptools-rust
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python -m pip install cibuildwheel==2.3.1
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- name: Build wheels
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env:
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CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
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CIBW_ARCHS: all
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CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.manylinux_image }}
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CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.manylinux_image }}
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CIBW_BUILD_VERBOSITY: 1
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CIBW_BEFORE_ALL: |
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curl -sSf https://sh.rustup.rs | sh -s -- --default-toolchain stable -y && rustup target add i686-pc-windows-msvc
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CIBW_ENVIRONMENT: 'PATH="$PATH:$HOME/.cargo/bin"'
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run: |
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python --version
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python -m cibuildwheel --output-dir dist
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env:
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CIBW_BEFORE_ALL: |
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curl -sSf https://sh.rustup.rs | sh -s -- --default-toolchain stable -y && rustup target add i686-pc-windows-msvc
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CIBW_ENVIRONMENT: 'PATH="$PATH:$HOME/.cargo/bin"'
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- uses: actions/upload-artifact@v2
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- name: Store artifacts
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uses: actions/upload-artifact@v2
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with:
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name: wheels
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path: ./dist
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test-package:
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name: Test built package
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needs: [ build-wheels, build-sdist ]
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runs-on: ubuntu-latest
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timeout-minutes: 30
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.7', '3.8', '3.9', '3.10']
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steps:
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- uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Download the wheels
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uses: actions/download-artifact@v2
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with:
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name: wheels
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path: dist/
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- name: Install from package wheels and test
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run: |
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python -m venv testwhl
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source testwhl/bin/activate
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python -m pip install -U pip
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python -m pip install -U pytest pydicom pylibjpeg
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python -m pip uninstall -y pylibjpeg-rle
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python -m pip install git+https://github.com/pydicom/pylibjpeg-data
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python -m pip install -U --find-links dist/ pylibjpeg-rle
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python -c "import pytest; pytest.main(['--pyargs', 'rle.tests'])"
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deactivate
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- name: Install from package tarball and test
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run: |
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python -m venv testsrc
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source testsrc/bin/activate
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python -m pip install -U pip
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python -m pip install -U pytest pydicom pylibjpeg
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python -m pip uninstall -y pylibjpeg-rle
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python -m pip install git+https://github.com/pydicom/pylibjpeg-data
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export PATH="$PATH:$HOME/.cargo/bin"
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python -m pip install -U dist/pylibjpeg-rle-*.tar.gz
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python -c "import pytest; pytest.main(['--pyargs', 'rle.tests'])"
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deactivate
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# The pypi upload fails with non-linux containers, so grab the uploaded
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# artifacts and run using those
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# See: https://github.com/pypa/gh-action-pypi-publish/discussions/15
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deploy:
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name: Upload wheels to PyPI
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needs:
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- build_wheels
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needs: [ test-package ]
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runs-on: ubuntu-latest
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steps:
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name: wheels
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path: dist/
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#- name: Publish package to Test PyPi
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# uses: pypa/gh-action-pypi-publish@master
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# with:
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# user: __token__
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# password: ${{ secrets.TEST_PYPI_PASSWORD }}
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# repository_url: https://test.pypi.org/legacy/
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- name: Publish package to PyPi
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uses: pypa/gh-action-pypi-publish@master
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with:

‎README.md‎

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[![Build Status](https://github.com/pydicom/pylibjpeg-rle/workflows/unit-tests/badge.svg)](https://github.com/pydicom/pylibjpeg-rle/actions?query=workflow%3Aunit-tests)
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[![codecov](https://codecov.io/gh/pydicom/pylibjpeg-rle/branch/master/graph/badge.svg)](https://codecov.io/gh/pydicom/pylibjpeg-rle)
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[![PyPI version](https://badge.fury.io/py/pylibjpeg-rle.svg)](https://badge.fury.io/py/pylibjpeg-rle)
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[![Python versions](https://img.shields.io/pypi/pyversions/pylibjpeg-rle.svg)](https://img.shields.io/pypi/pyversions/pylibjpeg-rle.svg)
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## pylibjpeg-rle
37

@@ -18,7 +22,7 @@ Make sure [Python](https://www.python.org/), [Git](https://git-scm.com/) and
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```bash
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git clone https://github.com/pydicom/pylibjpeg-rle
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cd pylibjpeg-rle
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python -m setup.py develop
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python -m pip install .
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```
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### Supported Transfer Syntaxes
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#### Decoding
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##### With pylibjpeg
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Because pydicom defaults to its own RLE decoder you must specify the use
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of pylibjpeg when decompressing:
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```python
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from pydicom import dcmread
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from pydicom.data import get_testdata_file
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ds = dcmread(get_testdata_file("OBXXXX1A_rle.dcm"))
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ds.decompress("pylibjpeg")
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arr = ds.pixel_array
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```
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‎docs/release_notes/v1.3.0.rst‎

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.. _v1.3.0:
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1.3.0
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=====
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Enhancements
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............
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* Update decoding interface to allow passing kwargs instead of a dataset

‎pyproject.toml‎

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[build-system]
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requires = [
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"setuptools>=18.0",
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"setuptools-rust",
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"wheel"
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"wheel",
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]

‎rle/_version.py‎

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import re
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__version__ = '1.2.0'
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__version__ = '1.3.0'
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VERSION_PATTERN = r"""

‎rle/tests/test_handler.py‎

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@pytest.mark.skipif(not HAVE_PYDICOM, reason="No pydicom")
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class TestDecodePixelData:
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"""Tests for the plugin's decoder interface."""
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def test_no_dataset_kwargs_raises(self):
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"""Test plugin decoder with no dataset or kwargs raises"""
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ds = INDEX["OBXXXX1A_rle.dcm"]['ds']
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assert ds.file_meta.TransferSyntaxUID == RLELossless
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assert 8 == ds.BitsAllocated
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assert 1 == ds.SamplesPerPixel
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assert 0 == ds.PixelRepresentation
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assert 600 == ds.Rows
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assert 800 == ds.Columns
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assert 1 == getattr(ds, 'NumberOfFrames', 1)
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frame = next(generate_pixel_data_frame(ds.PixelData))
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msg = r"Either `ds` or `\*\*kwargs` must be used"
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with pytest.raises(ValueError, match=msg):
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decode_pixel_data(frame)
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def test_u8_1s_1f(self):
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"""Test plugin decoder for 8 bit, 1 sample, 1 frame data."""
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ds = INDEX["OBXXXX1A_rle.dcm"]['ds']

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