Tests

.github/workflows/buildPlugin.yml → .github/workflows/build-and-test.yml

@@ -1,60 +1,60 @@
-# Name of the GitHub Action
-name: Build scipion-em-xmipptomo on Pull Request
+name: Build & test plugin
 
-# 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
+    runs-on: ubuntu-24.04
 
-    # 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: Set up MPI
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: 'openmpi'
 
     - 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
+        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
+        sudo apt-get install -y libfftw3-dev libopenmpi-dev libhdf5-dev libtiff5-dev libsqlite3-dev default-jdk git cmake openmpi-bin ${{ matrix.compiler.cc }} ${{ matrix.compiler.cxx }}
 
     - name: Install CUDA
-      uses: Jimver/cuda-toolkit@master
+      uses: Jimver/cuda-toolkit@v0.2.23
       id: cuda-toolkit
       with:
-        cuda: '11.8.0'
+        cuda: '12.6.0'
         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
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        auto-activate-base: true
+        activate-environment: scipion3
+        python-version: "3.8"
 
     - name: Install Scipion
       working-directory: ${{ github.workspace }}/../
       run: |
-        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
-        pip3 install --user scipion-installer
-        python3 -m scipioninstaller -conda -noXmipp -noAsk scipion
-
+        pip install --user scipion-installer
+        python3 -m scipioninstaller -conda -noAsk scipion
+        scipion/scipion3 run conda install -c conda-forge libstdcxx-ng
 
     - 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
+    # Checkout Xmipp to Pull Request branch if exists
     - name: Conditionally checkout Xmipp to ${{ github.head_ref }}
       working-directory: ${{ github.workspace }}/../xmipp
       env:
@@ -64,49 +64,39 @@ jobs:
           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
+    - name: Compile Xmipp
       working-directory: ${{ github.workspace }}/../xmipp
       env:
         BUILD_TESTS: True
       run: |
-        ../scipion/scipion3 run ./xmipp
-    #TODO: Remove last "cat compileLOG.txt" once there is a new Scipion release
+        ../scipion/scipion3 run ./xmipp --keep-output || (cat compileLOG.txt && false)
 
-    # Checkout scipion-em-xmipp to Pull Request branch if exists, else to devel
+    # Checkout scipion-em-xmipp to Pull Request branch if exists
     - 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
+      uses: actions/checkout@v4
       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
+        pip install --user scipion-testrunner
+        scipion_testrunner ${{ github.workspace }}/../scipion/scipion3 ${{ vars.FOLDER_WITH_VERSION }} --noGpu --testData=testData.json -j=3

.github/workflows/main.yml → .github/workflows/release.yml

@@ -1,45 +1,46 @@
-# Workflow to send master to pypi and tag  the branch:
 # You need to edit FOLDER_WITH_VERSION with the folder that has the __version__ value. 
-
 name: master to pypi with comments and tag
 
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
 on:
   push:
     branches: [ master ]
 
 env:
   FOLDER_WITH_VERSION: xmipptomo
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Checkout repository
+      uses: actions/checkout@main
+
     - name: Set up MPI
-      uses: mpi4py/setup-mpi@v1
+      uses: mpi4py/setup-mpi@master
+      with:
+        mpi: 'openmpi'
+
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@main
       with:
         python-version: '3.8'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
         pip install scipion-pyworkflow 
         pip install scipion-em
         pip install scipion-em-xmipp==20.7rc1
+
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/* -c "${{ secrets.PYPI_COMMENT }}"
+
     - name: Get version and tag
       run: |
         export PACKAGE_VERSION=$(python -c "import $FOLDER_WITH_VERSION; print('VERSION', 'v'+$FOLDER_WITH_VERSION.__version__)" | grep VERSION | sed "s/VERSION //g")

xmipptomo/testData.json

@@ -10,7 +10,7 @@
         "others": [
             {
                 "test": "test_protocol_deep_misalignment_detection.TestDeepMisaligmentDetection",
-                "reason": "Needs DLTK to work, which cannot be installed in GitHub actions due to lack of GPU access."
+                "reason": "Needs DLTK to work, which cannot be installed in GitHub actions due to lack of GPU access"
             },
             {
                 "test": "test_protocol_subtraction_subtomo.TestXmipptomoSubtractionSubtomo",