New protocol: micrographs defocus sampler #985
Workflow file for this run
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| name: Build plugin | |
| on: | |
| pull_request: | |
| branches: [devel, master] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| # Avoid send statistics | |
| env: | |
| SEND_INSTALLATION_STATISTICS: OFF | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@main | |
| with: | |
| ref: ${{ github.head_ref }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libfftw3-dev libopenmpi-dev openmpi-bin libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip libsqlite3-dev default-jdk git cmake libopenmpi-dev make cmake | |
| - name: Install CUDA | |
| uses: Jimver/cuda-toolkit@master | |
| id: cuda-toolkit | |
| with: | |
| cuda: '11.8.0' | |
| method: network | |
| sub-packages: '["nvcc", "toolkit"]' | |
| - name: Install Miniconda | |
| uses: conda-incubator/setup-miniconda@main | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| activate-environment: scipion3 | |
| python-version: "3.8" | |
| - name: Install Scipion | |
| working-directory: ${{ github.workspace }}/../ | |
| run: | | |
| pip install --user scipion-installer | |
| python -m scipioninstaller -conda -noAsk scipion | |
| - name: Cloning Xmipp | |
| working-directory: ${{ github.workspace }}/../ | |
| run: git clone https://github.com/I2PC/xmipp.git | |
| - name: Conditionally checkout Xmipp to ${{ github.head_ref }} | |
| working-directory: ${{ github.workspace }}/../xmipp | |
| env: | |
| BRANCH_NAME: ${{ github.head_ref }} | |
| run: | | |
| if [ $(git ls-remote --heads https://github.com/I2PC/xmipp.git $BRANCH_NAME | wc -l) -eq 1 ]; then | |
| git checkout $BRANCH_NAME | |
| fi | |
| - name: Compile Xmipp and show log | |
| working-directory: ${{ github.workspace }}/../xmipp | |
| env: | |
| BUILD_TESTS: True | |
| BRANCH_NAME: ${{ github.head_ref }} | |
| SEND_INSTALLATION_STATISTICS: OFF | |
| run: ../scipion/scipion3 run ./xmipp -b $BRANCH_NAME --keep-output || (cat compilation.log && false) |