This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build scipion-em-xmipptomo on Pull Request | |
| on: | |
| pull_request: | |
| branches: [devel, master] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| SEND_INSTALLATION_STATISTICS: "False" | |
| steps: | |
| - name: Free Disk Space (Ubuntu only) | |
| uses: jlumbroso/free-disk-space@main | |
| - name: Set up MPI | |
| uses: mpi4py/setup-mpi@master | |
| with: | |
| mpi: 'openmpi' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libfftw3-dev libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip libsqlite3-dev default-jdk git cmake libopencv-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 | |
| python3 -m scipioninstaller -conda -noXmipp -noAsk scipion | |
| - name: Install Scons in Scipion's enviroment | |
| run: | | |
| pip install --user scons | |
| - name: Cloning Xmipp | |
| working-directory: ${{ github.workspace }}/../ | |
| run: git clone https://github.com/I2PC/xmipp.git | |
| # Checkout Xmipp to Pull Request branch if exists, by default stays in devel | |
| - 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 | |
| # Log is shown afterwards because new Xmipp's installer does not show error trace if there is any | |
| - name: Compile Xmipp | |
| working-directory: ${{ github.workspace }}/../xmipp | |
| env: | |
| BUILD_TESTS: True | |
| run: | | |
| ../scipion/scipion3 run ./xmipp || (cat compileLOG.txt && false) | |
| # Checkout scipion-em-xmipp to Pull Request branch if exists, else to devel | |
| - name: Conditionally checkout scipion-em-xmipp to ${{ github.head_ref }} | |
| working-directory: ${{ github.workspace }}/../xmipp/src/scipion-em-xmipp | |
| env: | |
| BRANCH_NAME: ${{ github.head_ref }} | |
| run: | | |
| if [ $(git ls-remote --heads https://github.com/I2PC/scipion-em-xmipp.git $BRANCH_NAME | wc -l) -eq 1 ]; then | |
| git checkout $BRANCH_NAME | |
| else | |
| git checkout devel | |
| fi | |
| - name: Install scipion-em-xmipp | |
| working-directory: ${{ github.workspace }}/../xmipp/src/scipion-em-xmipp | |
| run: ${{ github.workspace }}/../scipion/scipion3 installp -p . --devel --noBin | |
| # Check out the repository in the pull request | |
| - name: Checkout repository | |
| uses: actions/checkout@main | |
| with: | |
| ref: ${{ github.head_ref }} | |
| - name: Install plugin from pull request | |
| working-directory: ${{ github.workspace }} | |
| run: ../scipion/scipion3 installp -p . --devel | |
| - name: Run tests | |
| working-directory: ${{ github.workspace }}/${{ vars.FOLDER_WITH_VERSION }} | |
| run: | | |
| pip install --user scipion-testrunner | |
| scipion_testrunner ${{ github.workspace }}/../scipion/scipion3 ${{ vars.FOLDER_WITH_VERSION }} --noGpu --testData=testData.json -j=3 |