add ci tests

.github/workflows/test_containers_singularity.yml

@@ -0,0 +1,39 @@
+name: Test sorter images in singularity
+
+on:
+  pull_request:
+    branches: [main]
+    types: [synchronize, opened, reopened, ready_for_review]
+
+jobs:
+  build-and-test:
+    name: Test on (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # "macos-latest", "windows-latest"
+        os: ["ubuntu-latest", ]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          python-version: 3.8
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install git 
+
+          # get SI form master
+          git clone https://github.com/SpikeInterface/spikeinterface.git
+          cd spikeinterface
+          pip install .
+          pip install -r requirements_full.txt
+
+          cd ..
+          pip install spython pytest tridesclous
+      - name: Test singularity
+        run: |
+          pytest -v tests/test_singularity_containers.py

tests/test_singularity_containers.py

@@ -0,0 +1,70 @@
+import pytest
+
+import spikeinterface.sorters as ss
+from spikeinterface.core.testing_tools import generate_recording
+
+recording = generate_recording(
+    num_channels=32,
+    sampling_frequency=30000.0,  # in Hz
+    durations=[120],
+    set_probe=True,
+    ndim=2,
+)
+
+recording2 = recording.save(folder="test_recording")
+
+kwargs = dict(recording=recording2, verbose=True, singularity_image=True)
+
+
+@pytest.mark.xfail(reason="FAILING: investigate why")
+def test_spyking_circus():
+    ss.run_spykingcircus(output_folder="spyking_circus", **kwargs)
+
+
+@pytest.mark.xfail(reason="FAILING: investigate why")
+def test_mountainsort4():
+    ss.run_mountainsort4(output_folder="mountainsort4", **kwargs)
+
+
+def test_tridesclous():
+    ss.run_tridesclous(output_folder="tridesclous", **kwargs)
+
+
+def test_klusta():
+    ss.run_klusta(output_folder="klusta", **kwargs)
+
+
+def test_ironclust():
+    ss.run_ironclust(output_folder="ironclust", fGpu=False, **kwargs)
+
+
+def test_waveclus():
+    ss.run_waveclus(output_folder="waveclus", **kwargs)
+
+
+def test_hdsort():
+    ss.run_hdsort(output_folder="hdsort", **kwargs)
+
+
+def test_kilosort1():
+    ss.run_kilosort(output_folder="kilosort", useGPU=False, **kwargs)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort2():
+    ss.run_kilosort2(output_folder="kilosort2", **kwargs)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort2_5():
+    ss.run_kilosort2_5(output_folder="kilosort2_5", **kwargs)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort3():
+    ss.run_kilosort3(output_folder="kilosort3", **kwargs)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_pykilosort():
+    ss.run_pykilosort(output_folder="pykilosort", **kwargs)