From f9263ba210765e6ff61892dbb24d3e5a1197527d Mon Sep 17 00:00:00 2001
From: Martin Salinas <ssalinasmartin@gmail.com>
Date: Sat, 31 Aug 2024 17:52:15 +0200
Subject: [PATCH] Fixed test action

---
 .../{buildPlugin.yml => build-and-test.yml}   | 50 +++++++------------
 1 file changed, 19 insertions(+), 31 deletions(-)
 rename .github/workflows/{buildPlugin.yml => build-and-test.yml} (57%)

diff --git a/.github/workflows/buildPlugin.yml b/.github/workflows/build-and-test.yml
similarity index 57%
rename from .github/workflows/buildPlugin.yml
rename to .github/workflows/build-and-test.yml
index 052d5c0..c73a068 100644
--- a/.github/workflows/buildPlugin.yml
+++ b/.github/workflows/build-and-test.yml
@@ -1,30 +1,29 @@
-# 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: 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 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
     
     - name: Install CUDA
       uses: Jimver/cuda-toolkit@master
@@ -35,26 +34,23 @@ jobs:
         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@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: ${{ github.workspace }}/../
       run: |
-        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
-        pip3 install --user scipion-installer
+        pip 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
+    - name: Install Scons in Scipion's enviroment
       run: |
-        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
-        conda activate scipion3
-        pip install scons
+        pip install --user scons
         
     - name: Cloning Xmipp
       working-directory: ${{ github.workspace }}/../
@@ -70,16 +66,13 @@ 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 || (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 }}
@@ -93,7 +86,6 @@ jobs:
           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
@@ -108,12 +100,8 @@ jobs:
       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