adding thresdholding segmentation protocols #152
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| # Name of the GitHub Action | |
| name: Build scipion-em-xmipptomo on Pull Request | |
| # Specify when the Action should be triggered: when a pull request is opened against the 'devel' or 'master' branch | |
| on: | |
| pull_request: | |
| branches: [devel, master] | |
| # Define the job that should be run | |
| jobs: | |
| build: | |
| # Specify the machine to run the job on | |
| runs-on: ubuntu-22.04 | |
| # Avoid send statistics | |
| env: | |
| SEND_INSTALLATION_STATISTICS: "False" | |
| # Define the steps to be taken in the job | |
| steps: | |
| - name: Free Disk Space (Ubuntu only) | |
| uses: jlumbroso/free-disk-space@main | |
| - 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 libopencv-dev 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 | |
| working-directory: ${{ github.workspace }}/../ | |
| run: | | |
| wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p ${{ github.workspace }}/../miniconda/ | |
| source ./miniconda/etc/profile.d/conda.sh | |
| conda update -n base -c defaults conda -y | |
| - name: Install Scipion | |
| working-directory: ${{ github.workspace }}/../ | |
| run: | | |
| eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)" | |
| pip3 install --user scipion-installer | |
| python3 -m scipioninstaller -conda -noXmipp -noAsk scipion | |
| # Installing Xmipp's Python dependencies in scipion conda enviroment | |
| - name: Install scons in scipion enviroment | |
| run: | | |
| eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)" | |
| conda activate scipion3 | |
| pip install 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 | |
| # Installing Xmipp | |
| # Log is shown afterwards because new Xmipp's installer does not show error trace if there is any | |
| - name: Compile Xmipp and show log | |
| working-directory: ${{ github.workspace }}/../xmipp | |
| env: | |
| BUILD_TESTS: True | |
| run: | | |
| ../scipion/scipion3 run ./xmipp || (cat compileLOG.txt && false) | |
| cat compileLOG.txt | |
| #TODO: Remove last "cat compileLOG.txt" once there is a new Scipion release | |
| # 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 | |
| # Install scipion-em-xmipp, because scipion-em-xmipptomo depends on it | |
| - 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 | |
| # Currently, test script is being downloaded from scipion-chem, but that should be temporary | |
| # Ideally, the script might be included in scipion core to be able to import it, | |
| # or maybe host it in a separate repository common with useful scripts for all scipion plugins | |
| - name: Run tests | |
| working-directory: ${{ github.workspace }}/${{ vars.FOLDER_WITH_VERSION }} | |
| run: | | |
| wget https://raw.githubusercontent.com/scipion-chem/scipion-chem/devel/pwchem/runTests.py | |
| eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)" | |
| python runTests.py ${{ github.workspace }}/../scipion/scipion3 ${{ vars.FOLDER_WITH_VERSION }} -noGPU -testData=testData.json -j=3 |