IGNORE - PR to test CI

.github/workflows/linux_unit_test.yml

@@ -0,0 +1,78 @@
+name: Unit tests
+
+on:
+  push:
+    branches: ['**']
+  pull_request:
+    branches: ['**']
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: ['3.9.10']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:    
+          python-version: '3.9.10'
+      - name: Install ubuntu dependencies
+        shell: bash -el {0}
+        run: |
+            sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+            sudo apt-get update
+            sudo apt-get install libopenmpi-dev openmpi-bin
+      - name: Check MPI version
+        shell: bash -el {0}
+        run: |
+            mpiexec --version
+      - name: Check Python version
+        shell: bash -el {0}
+        run: |
+            python --version
+
+      - name: Install dependencies
+        shell: bash -el {0}
+        run: |
+           python -m pip install --upgrade pip
+           python -m pip install mpi4py
+      - name: Install HNN-core
+        shell: bash -el {0}
+        run: |
+          python -m pip install --verbose '.[opt, parallel, test, gui]'
+      - name: Run MPI application
+        shell: bash -el {0}
+        run: |
+              mpiexec -np 2 python ./hnn_core/mpi_test.py
+      - name: Verify NEURON installation
+        shell: bash -el {0}
+        run: |
+            nrniv -python -nobanner -mpi python "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 python ./hnn_core/mpi_test.py
+
+      # - name: Lint with flake8
+      #   shell: bash -el {0}
+      #   run: |
+      #     flake8 --count hnn_core
+      - name: Freeze package versions
+        shell: bash -el {0}
+        run: |
+          python -m pip freeze
+
+      - name: Test with pytest
+        shell: bash -el {0}
+        run: |
+          python -m pytest ./hnn_core/tests/test_viz.py  --cov=hnn_core --cov-report=xml -s
+
+      # - name:  Upload coverage to Codecov
+      #   shell: bash -el {0}
+      #   run: |
+      #     bash <(curl -s https://codecov.io/bash) -f ./coverage.xml

.github/workflows/macos_unit_tests.yml

@@ -0,0 +1,45 @@
+name: Unit tests
+
+on:
+  push:
+    branches: ['**']
+  pull_request:
+    branches: ['**']
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest]
+        python-version: [3.8, 3.9, "3.10", 3.11]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+          fetch-depth: 2
+      - name: Install dependencies
+        shell: bash -el {0}
+        run: |
+          python -m pip install --upgrade pip
+          conda install --yes -c conda-forge mpi4py openmpi
+      # - name: Install HNN-core
+      #   shell: bash -el {0}
+      #   run: |
+      #     pip install --verbose '.[opt, parallel, test, gui]'
+      # - name: Lint with flake8
+      #   shell: bash -el {0}
+      #   run: |
+      #     flake8 --count hnn_core
+      # - name: Test with pytest
+      #   shell: bash -el {0}
+      #   run: |
+      #     python -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

.github/workflows/windows_unit_tests.yml

@@ -34,12 +34,12 @@ jobs:
           python -c "import neuron"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Install dependencies and HNN
-        shell: cmd
-        run: |
-          python -m pip install --upgrade pip
-          pip install --verbose .[opt,parallel,test,gui]
-      - name: Test with pytest
-        shell: cmd
-        run: |
-          python -m pytest ./hnn_core/tests/
+      # - name: Install dependencies and HNN
+      #   shell: cmd
+      #   run: |
+      #     python -m pip install --upgrade pip
+      #     pip install --verbose .[opt,parallel,test,gui]
+      # - name: Test with pytest
+      #   shell: cmd
+      #   run: |
+      #     python -m pytest ./hnn_core/tests/

hnn_core/gui/gui.py

@@ -24,8 +24,7 @@
 from hnn_core.gui._logging import logger
 from hnn_core.gui._viz_manager import _VizManager, _idx2figname
 from hnn_core.network import pick_connection
-from hnn_core.params import (_extract_drive_specs_from_hnn_params, _read_json,
-                             _read_legacy_params)
+from hnn_core.params import (_extract_drive_specs_from_hnn_params)
 from hnn_core.dipole import _read_dipole_txt
 
 import base64
@@ -1227,7 +1226,8 @@ def add_connectivity_tab(params, connectivity_out,
     return net
 
 
-def add_drive_tab(params, log_out, drives_out, drive_widgets, drive_boxes, tstop,
+def add_drive_tab(params, log_out, drives_out, drive_widgets,
+                  drive_boxes, tstop,
                   layout):
     net = jones_2009_model(params)
 
@@ -1275,9 +1275,11 @@ def load_drive_and_connectivity(params, log_out, drives_out,
     """Add drive and connectivity ipywidgets from params."""
     with log_out:
         # Add connectivity
-        add_connectivity_tab(params, connectivity_out, connectivity_textfields)
+        add_connectivity_tab(params, connectivity_out,
+                             connectivity_textfields)
         # Add drives
-        add_drive_tab(params, log_out, drives_out, drive_widgets, drive_boxes, tstop,
+        add_drive_tab(params, log_out, drives_out, drive_widgets,
+                      drive_boxes, tstop,
                       layout)
 
 
@@ -1339,7 +1341,8 @@ def on_upload_params_change(change, tstop, dt, log_out, drive_boxes,
         add_connectivity_tab(params, connectivity_out, connectivity_textfields)
     elif load_type == 'drives':
         with log_out:
-            add_drive_tab(params, log_out, drives_out, drive_widgets, drive_boxes, tstop,
+            add_drive_tab(params, log_out, drives_out,
+                          drive_widgets, drive_boxes, tstop,
                           layout)
     else:
         raise ValueError

hnn_core/mpi_test.py

@@ -0,0 +1,27 @@
+from mpi4py import MPI
+import logging
+from neuron import h
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger()
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
+
+logger.info(f"Process {rank} out of {size} processors")
+# Initialize NEURON with MPI support
+h('''
+objref pc
+pc = new ParallelContext()
+''')
+
+# Check if NEURON MPI is enabled
+is_mpi_enabled = int(h.pc.nhost() > 1)
+
+if is_mpi_enabled:
+    logger.info(f"NEURON MPI is enabled. Running on {int(h.pc.nhost())} processes")
+else:
+    logger.info("NEURON MPI is not enabled.")
+
+if rank == 0:
+    print("NEURON MPI test completed")

hnn_core/tests/test_parallel_backends.py

@@ -256,7 +256,9 @@ def test_mpi_failure(run_hnn_core_fixture):
     assert "MPI processes are unable to reach each other" in stdout
 
     expected_string = "Child process failed unexpectedly"
-    assert len(record) == 1
+    print(record[0].message.args[0])
     assert record[0].message.args[0] == expected_string
+    assert len(record) == 1
+
 
     del environ["OMPI_MCA_btl"]