removed conda from ci pipeline

brown-ccv · Jun 12, 2024 · c05a59f · c05a59f
1 parent ab74e65
commit c05a59f
Showing 1 changed file with 49 additions and 15 deletions.
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -12,16 +12,16 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9]
+        os: [ubuntu-24.04,macos-14]
+        python-version: [3.8,3.9]
 
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: test
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        id: cp310
+        with:    
           python-version: ${{ matrix.python-version }}
-          fetch-depth: 2
       - name: Install ubuntu dependencies
         shell: bash -el {0}
         run: |
@@ -30,24 +30,58 @@ jobs:
             sudo apt-get update
             sudo apt-get install libopenmpi-dev openmpi-bin
           fi;
+      - name: Install MacOs dependencies
+        shell: bash -el {0}
+        run: |
+          if [ "${{ matrix.os }}" == "macos-latest" ]; then
+              brew install open-mpi
+          fi;
       - name: Install dependencies
         shell: bash -el {0}
         run: |
-          python -m pip install --upgrade pip
-          conda install --yes -c conda-forge mpi4py openmpi
+           '${{ steps.cp310.outputs.python-path }}' -m pip install --upgrade pip
+           '${{ steps.cp310.outputs.python-path }}' -m pip install mpi4py openmpi
+      - name: Check MPI version
+        shell: bash -el {0}
+        run: |
+          mpiexec --version
+      - name: Check Python version
+        shell: bash -el {0}
+        run: |
+            '${{ steps.cp310.outputs.python-path }}' --version
       - name: Install HNN-core
         shell: bash -el {0}
         run: |
-          pip install --verbose '.[opt, parallel, test, gui]'
-      - name: Lint with flake8
+          '${{ steps.cp310.outputs.python-path }}' -m pip install --verbose '.[opt, parallel, test, gui]'
+      - name: Set Env Variables
         shell: bash -el {0}
         run: |
-          flake8 --count hnn_core
-      - name: Test with pytest
+          if [ "${{ matrix.os }}" == "macos-latest" ]; then
+            echo "List /opt/homebrew/lib"
+            ls /opt/homebrew/lib
+            echo "MPI_LIB_NRN_PATH=/opt/homebrew/lib/libmpi.dylib" >> $GITHUB_ENV
+          fi;
+      # - name: Run MPI application
+      #   shell: bash -el {0}
+      #   run: |
+      #       mpiexec -np 2 '${{ steps.cp310.outputs.python-path }}' ./hnn_core/mpi_test.py
+      - name: Verify NEURON installation
         shell: bash -el {0}
         run: |
-          python -m pytest ./hnn_core/tests/  --cov=hnn_core --cov-report=xml
-      - name:  Upload coverage to Codecov
+          nrniv -python -nobanner -mpi '${{ steps.cp310.outputs.python-path }}' "from neuron import h; print(h)"
+      # - name: Run MPI application with NEURON
+      #   shell: bash -el {0}
+      #   run: |
+      #     mpiexec -np 2 -verbose nrniv -python -mpi -nobanner '${{ steps.cp310.outputs.python-path }}' ./hnn_core/mpi_test.py
+      # - name: Lint with flake8
+      #   shell: bash -el {0}
+      #   run: |
+      #     flake8 --count hnn_core
+      - name: Test with pytest
         shell: bash -el {0}
         run: |
-          bash <(curl -s https://codecov.io/bash) -f ./coverage.xml
+          '${{ steps.cp310.outputs.python-path }}' -m pytest ./hnn_core/tests/  --cov=hnn_core --cov-report=xml
+      # - name:  Upload coverage to Codecov
+      #   shell: bash -el {0}
+      #   run: |
+      #     bash <(curl -s https://codecov.io/bash) -f ./coverage.xml