Update test workflow (#675)

* doc: update CITATION.cff

* pinned down more versions. 👛

* Installing mpi locally ⛵

* Using system install of MPI 🎌

* Removed pinning of mpi packages. It's not needed. 🌋

---------

Co-authored-by: anawas <anawas@users.noreply.github.com>

Author: anawas

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Tests
+name: Run Karabo Tests
 
 on:
   schedule: # Every night at 5am
@@ -16,37 +16,66 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
+      
+      - name: Install system MPICH (needed for external mpich) + compat symlink for wsclean
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y mpich libmpich-dev libmpich12
+          arch="$(dpkg-architecture -qDEB_HOST_MULTIARCH)"
+          # wsclean expects libmpicxx.so.12 but Ubuntu provides libmpichcxx.so.12
+          if [ -e "/usr/lib/$arch/libmpichcxx.so.12" ] && [ ! -e "/usr/lib/$arch/libmpicxx.so.12" ]; then
+            sudo ln -s "/usr/lib/$arch/libmpichcxx.so.12" "/usr/lib/$arch/libmpicxx.so.12"
+            sudo ldconfig
+          fi
+          # Optional sanity:
+          ldconfig -p | grep -E 'libmpi\.so\.12|libmpichcxx\.so\.12|libmpicxx\.so\.12' || true
+          which mpirun
+          mpirun --version
+      
       - name: Install Conda
         uses: conda-incubator/setup-miniconda@v3
         with:
           mamba-version: "*"
           channels: conda-forge
           channel-priority: "true"
           conda-remove-defaults: "true"
+          activate-environment: test_karabo
+          python-version: "3.10"
+
       - name: Install Deps
         shell: bash -el {0}
         run: |
           conda create -y -n test_karabo python=3.10
+          conda env update -n test_karabo -f environment.yaml --prune
           conda activate test_karabo
-          conda env update -f environment.yaml
+          pip install --no-binary mpi4py mpi4py==4.1.1
           pip install -e ".[dev]"
           python -m ipykernel install --user --name python3.10
+
+          # Debug since we had problems with mpi installation
+          python -c "import h5py; print('h5py ok')"
+          which wsclean || true
+          ldd "$(which wsclean)" | grep -i mpi || tru  
+
       - name: Test Dev-Tools
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           conda activate test_karabo
           flake8 .
           black --check .
           isort --check .
           mypy .
+
       - name: Test Code
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
-          conda activate test_karabo
           export IS_GITHUB_RUNNER=true RUN_GPU_TESTS=false RUN_NOTEBOOK_TESTS=true
+          conda activate test_karabo
           mpirun -n 2 pytest --only-mpi
           pytest --cov=./ --cov-report=xml
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:

environment.yaml

@@ -1,7 +1,7 @@
 channels:
+  - conda-forge
   - i4ds
   - nvidia/label/cuda-11.7.0
-  - conda-forge
 dependencies:
 # Set dependencies and it's constraints in the package they belong. Otherwise you just cause chaos for future builds.
 # Just Karabo's direct dependencies and Karabo constraints (from our code) should be handled here.