[MRG] Parallelize pytests where applicable (#932)

* feat: add marks and change pytest runs for pll

* Improve mark name, duplicate test cmds into Make

* chore: update pytest custom marker metadata

.github/workflows/unix_unit_tests.yml

@@ -39,14 +39,14 @@
           uses: actions/setup-python@v5
           with:
               python-version: ${{ matrix.python-version }}
-        
+
         - name: Install Python  dependencies
           shell: bash -el {0}
           run: |
             if [ ${{ matrix.os }} == 'macos-latest' ]; then
               python -m pip install --upgrade pip
               conda install --yes -c conda-forge mpi4py openmpi
-            elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then 
+            elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
               python -m pip install --upgrade pip
               python -m pip install mpi4py
             fi
@@ -58,11 +58,15 @@
           shell: bash -el {0}
           run: |
             flake8 --count hnn_core
-        - name: Test with pytest
+        - name: Test non-MPI, embarrassingly parallel tests with pytest
+          shell: bash -el {0}
+          run: |
+            python -m pytest ./hnn_core/tests/ -m "not uses_mpi" -n auto --cov=hnn_core --cov-report=xml
+        - name: Test MPI-using parallel tests with pytest
           shell: bash -el {0}
           run: |
-            python -m pytest ./hnn_core/tests/  --cov=hnn_core --cov-report=xml
+            python -m pytest ./hnn_core/tests/ -m "uses_mpi" --cov=hnn_core --cov-report=xml --cov-append
         - name:  Upload coverage to Codecov
           shell: bash -el {0}
           run: |
-            bash <(curl -s https://codecov.io/bash) -f ./coverage.xml
+            bash <(curl -s https://codecov.io/bash) -f ./coverage.xml

Makefile

@@ -17,7 +17,8 @@ check-manifest:
 	check-manifest
 
 test: flake
-	pytest .
+	pytest ./hnn_core/tests/ -m "not uses_mpi" -n auto
+	pytest ./hnn_core/tests/ -m "uses_mpi"
 
 flake:
 	@if command -v flake8 > /dev/null; then \

hnn_core/tests/test_dipole.py

@@ -213,6 +213,7 @@ def test_dipole_simulation():
 
 @requires_mpi4py
 @requires_psutil
+@pytest.mark.uses_mpi
 def test_cell_response_backends(run_hnn_core_fixture):
     """Test cell_response outputs across backends."""
 

hnn_core/tests/test_extracellular.py

@@ -170,6 +170,7 @@ def test_transfer_resistance():
 
 @requires_mpi4py
 @requires_psutil
+@pytest.mark.uses_mpi
 def test_extracellular_backends(run_hnn_core_fixture):
     """Test extracellular outputs across backends."""
     # calculation of CSD requires >=4 electrode contacts

hnn_core/tests/test_gui.py

@@ -368,6 +368,7 @@ def test_gui_init_network(setup_gui):
 
 @requires_mpi4py
 @requires_psutil
+@pytest.mark.uses_mpi
 def test_gui_run_simulation_mpi():
     """Test if run button triggers simulation with MPIBackend."""
     gui = HNNGUI()

hnn_core/tests/test_parallel_backends.py

@@ -77,6 +77,7 @@ def test_gid_assignment():
 
 
 @pytest.mark.incremental
+@pytest.mark.uses_mpi
 class TestParallelBackends():
     dpls_reduced_mpi = None
     dpls_reduced_default = None
@@ -241,6 +242,7 @@ def test_compare_hnn_core(self, run_hnn_core_fixture, backend, n_jobs=1):
 # class marked incremental
 @requires_mpi4py
 @requires_psutil
+@pytest.mark.uses_mpi
 def test_mpi_failure(run_hnn_core_fixture):
     """Test that an MPI failure is handled and messages are printed"""
     # this MPI parameter will cause a MPI job to fail

pytest.ini

@@ -1,3 +1,5 @@
 [pytest]
 markers =
+    uses_mpi: tests which should NOT be run in an embarrassingly-parallel fashion
     incremental: run tests with prerequisites in incremental order
+

setup.py

@@ -77,7 +77,7 @@ def run(self):
     extras = {
         'opt': ['scikit-learn'],
         'parallel': ['joblib', 'psutil'],
-        'test': ['flake8', 'pytest', 'pytest-cov', ],
+        'test': ['flake8', 'pytest', 'pytest-cov', 'pytest-xdist'],
         'docs': ['mne', 'nibabel', 'pooch', 'tdqm',
                  'sphinx', 'sphinx-gallery',
                  'sphinx_bootstrap_theme', 'sphinx-copybutton',