Merge branch 'add_ci_tests' into main

Author: chyumin

.github/workflows/test_containers_singularity.yml

@@ -0,0 +1,33 @@
+name: Test sorter images in singularity
+
+on:
+  workflow_dispatch:
+
+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 
+
+          pip install -r requirements_test.txt
+      - name: Test tridesclous image
+        run: |
+          pip install tridesclous
+          pytest -sv tests/test_singularity_containers.py::test_tridesclous
+      - name: Test spyking-circus image
+        run: pytest -sv tests/test_singularity_containers.py::test_spyking_circus

.gitignore

@@ -0,0 +1 @@
+__pycache__

requirements_test.txt

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+git+https://github.com/SpikeInterface/spikeinterface.git#egg=spikeinterface[full]
+spython==0.2.1
+pytest==7.1.2

tests/test_singularity_containers.py

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+import os
+import shutil
+
+import pytest
+
+import spikeinterface.extractors as se
+import spikeinterface.sorters as ss
+
+
+@pytest.fixture
+def work_dir(request, tmpdir_factory):
+    tmpdir = tmpdir_factory.mktemp("work_dir")
+    os.chdir(tmpdir)
+    yield
+    os.chdir(request.config.invocation_dir)
+    shutil.rmtree(str(tmpdir))
+
+
+@pytest.fixture
+def run_kwargs(work_dir):
+    test_recording, _ = se.toy_example(
+        duration=30,
+        seed=0,
+        num_channels=32,
+        num_segments=1
+    )
+    test_recording = test_recording.save(name='toy')
+    return dict(recording=test_recording, verbose=True, singularity_image=True)
+
+
+def test_spyking_circus(run_kwargs):
+    sorting = ss.run_spykingcircus(output_folder="spyking_circus", **run_kwargs)
+    print(sorting)
+
+
+@pytest.mark.xfail(reason="FAILING: investigate why")
+def test_mountainsort4(run_kwargs):
+    sorting = ss.run_mountainsort4(output_folder="mountainsort4", **run_kwargs)
+    print(sorting)
+
+
+def test_tridesclous(run_kwargs):
+    sorting = ss.run_tridesclous(output_folder="tridesclous", **run_kwargs)
+    print(sorting)
+
+
+def test_klusta(run_kwargs):
+    sorting = ss.run_klusta(output_folder="klusta", **run_kwargs)
+    print(sorting)
+
+
+def test_ironclust(run_kwargs):
+    sorting = ss.run_ironclust(output_folder="ironclust", fGpu=False, **run_kwargs)
+    print(sorting)
+
+
+def test_waveclus(run_kwargs):
+    sorting = ss.run_waveclus(output_folder="waveclus", **run_kwargs)
+    print(sorting)
+
+
+def test_hdsort(run_kwargs):
+    sorting = ss.run_hdsort(output_folder="hdsort", **run_kwargs)
+    print(sorting)
+
+
+def test_kilosort1(run_kwargs):
+    sorting = ss.run_kilosort(output_folder="kilosort", useGPU=False, **run_kwargs)
+    print(sorting)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort2(run_kwargs):
+    sorting = ss.run_kilosort2(output_folder="kilosort2", **run_kwargs)
+    print(sorting)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort2_5(run_kwargs):
+    sorting = ss.run_kilosort2_5(output_folder="kilosort2_5", **run_kwargs)
+    print(sorting)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_kilosort3(run_kwargs):
+    sorting = ss.run_kilosort3(output_folder="kilosort3", **run_kwargs)
+    print(sorting)
+
+
+@pytest.mark.skip(reason="GPU required")
+def test_pykilosort(run_kwargs):
+    sorting = ss.run_pykilosort(output_folder="pykilosort", **run_kwargs)
+    print(sorting)