updating CLtomo #70
Workflow file for this run
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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 | |
# Define the steps to be taken in the job | |
steps: | |
# Installing dependencies | |
- 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 | |
# Installing CUDA | |
- name: Install CUDA | |
uses: Jimver/[email protected] | |
id: cuda-toolkit | |
with: | |
cuda: '11.8.0' | |
method: network | |
sub-packages: '["nvcc", "toolkit"]' | |
# Installing Miniconda | |
- 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 | |
# Installing Scipion | |
- 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 | |
# Cloning Xmipp | |
- 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@v4 | |
with: | |
ref: ${{ github.head_ref }} | |
# Install plugin from the pull request using the Scipion3 installp command | |
- name: Install plugin from pull request | |
working-directory: ${{ github.workspace }} | |
run: | | |
# Install the repository from the pull request | |
../scipion/scipion3 installp -p . --devel |