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add option to remove small connected components in postprocesssing #226

add option to remove small connected components in postprocesssing

add option to remove small connected components in postprocesssing #226

Workflow file for this run

name: Run basic tests on all OS
on:
push:
paths-ignore:
- '**.md'
jobs:
run-tests:
strategy:
matrix:
# os: [ubuntu-latest, windows-latest, macos-latest] # fails on windows until https://github.com/MIC-DKFZ/nnUNet/issues/2396 is resolved
os: [ubuntu-latest, macos-latest]
python-version: ["3.10"]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies on Ubuntu
if: runner.os == 'Linux'
run: |
python -m pip install --upgrade pip
pip install pytest Cython fury
pip install torch==2.0.0 -f https://download.pytorch.org/whl/cpu
pip install .
- name: Install dependencies on Windows / MacOS
if: runner.os == 'Windows' || runner.os == 'macOS'
run: |
python -m pip install --upgrade pip
pip install pytest Cython
pip install torch==2.0.0
pip install .
- name: Run test script
run: python tests/tests_os.py