Numpy 2 compatibility fix #57
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| build-macos: | |
| runs-on: | |
| - macos-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| lfs: true | |
| - name: Brew Update | |
| run: brew update >/dev/null | |
| - name: Reinstall | |
| run: brew reinstall xz curl | |
| continue-on-error: true | |
| - name: Install Deps | |
| run: brew install boost zlib curl samtools bzip2 xz && brew link --overwrite [email protected] | |
| - name: Pip install | |
| run: sudo python3 -m pip install --user --upgrade pip setuptools && sudo python3 -m pip install --user numpy && sudo python3 -m pip install --user -e ./python | |
| - name: make | |
| run: > | |
| export ZLIB_PATH=$(ls /usr/local/Cellar/zlib/*/lib/libz.a) | |
| LZMA_PATH=$(ls /usr/local/Cellar/xz/*/lib/liblzma.a) && | |
| make -f test_data/Makefile.osx | |
| - name: Download Tests | |
| run: > | |
| cd test_data && | |
| wget https://storage.googleapis.com/agraubert/broadinstitute/rnaseqc/test_inputs.tar.gz && | |
| tar xzf test_inputs.tar.gz && | |
| cd .. | |
| - name: Run Tests | |
| run: sudo bash -c "PYTHONPATH=$(pwd) make -f test_data/Makefile.osx test" | |
| build-linux: | |
| runs-on: | |
| - ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| lfs: true | |
| - name: Install deps | |
| run: > | |
| sudo apt-get update && sudo apt-get install -y cmake python3 python3-dev | |
| libboost-filesystem-dev libboost-regex-dev libboost-system-dev libbz2-dev | |
| liblzma-dev libpthread-stubs0-dev wget zlib1g-dev g++ && | |
| curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && sudo | |
| python3 get-pip.py && python3 -m pip install --upgrade pip && | |
| python3 -m pip install numpy && python3 -m pip install -e ./python && | |
| python3 -m pip install --force-reinstall matplotlib | |
| - name: make | |
| run: make -f test_data/Makefile.linux | |
| - name: Download Tests | |
| run: > | |
| cd test_data && | |
| wget https://storage.googleapis.com/agraubert/broadinstitute/rnaseqc/test_inputs.tar.gz && | |
| tar xzf test_inputs.tar.gz && | |
| cd .. | |
| - name: Run Tests | |
| run: make -f test_data/Makefile.linux test |