Remove cache folder (#2927)

Remove pytest.global_test_folder in favor of create_cache_folder module fixture

Authored by: Paul Riganese
Co-authored-by: Alessio Buccino, Joe Ziminski

conftest.py

@@ -14,16 +14,10 @@
               "widgets", "exporters", "sortingcomponents", "generation"]
 
 
-# define global test folder
-def pytest_sessionstart(session):
-    # setup_stuff
-    pytest.global_test_folder = Path(__file__).parent / "test_folder"
-    if pytest.global_test_folder.is_dir():
-        shutil.rmtree(pytest.global_test_folder)
-    pytest.global_test_folder.mkdir()
-
-    for mark_name in mark_names:
-        (pytest.global_test_folder / mark_name).mkdir()
+@pytest.fixture(scope="module")
+def create_cache_folder(tmp_path_factory):
+    cache_folder = tmp_path_factory.mktemp("cache_folder")
+    return cache_folder
 
 def pytest_collection_modifyitems(config, items):
     """
@@ -45,12 +39,3 @@ def pytest_collection_modifyitems(config, items):
                 item.add_marker("sorters")
         else:
             item.add_marker(module)
-
-
-
-def pytest_sessionfinish(session, exitstatus):
-    # teardown_stuff only if tests passed
-    # We don't delete the test folder in the CI because it was causing problems with the code coverage.
-    if exitstatus == 0:
-        if pytest.global_test_folder.is_dir() and not ON_GITHUB:
-            shutil.rmtree(pytest.global_test_folder)

src/spikeinterface/comparison/tests/test_groundtruthstudy.py

@@ -7,19 +7,13 @@
 from spikeinterface.comparison import GroundTruthStudy
 
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "comparison"
-else:
-    cache_folder = Path("cache_folder") / "comparison"
-    cache_folder.mkdir(exist_ok=True, parents=True)
-
-study_folder = cache_folder / "test_groundtruthstudy/"
-
-
-def setup_module():
+@pytest.fixture(scope="module")
+def setup_module(tmp_path_factory):
+    study_folder = tmp_path_factory.mktemp("study_folder")
     if study_folder.is_dir():
         shutil.rmtree(study_folder)
     create_a_study(study_folder)
+    return study_folder
 
 
 def simple_preprocess(rec):
@@ -74,7 +68,8 @@ def create_a_study(study_folder):
     # print(study)
 
 
-def test_GroundTruthStudy():
+def test_GroundTruthStudy(setup_module):
+    study_folder = setup_module
     study = GroundTruthStudy(study_folder)
     print(study)
 

src/spikeinterface/comparison/tests/test_hybrid.py

@@ -11,13 +11,9 @@
 from spikeinterface.preprocessing import bandpass_filter
 
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "comparison" / "hybrid"
-else:
-    cache_folder = Path("cache_folder") / "comparison" / "hybrid"
-
-
-def setup_module():
+@pytest.fixture(scope="module")
+def setup_module(tmp_path_factory):
+    cache_folder = tmp_path_factory.mktemp("cache_folder")
     if cache_folder.is_dir():
         shutil.rmtree(cache_folder)
     cache_folder.mkdir(parents=True, exist_ok=True)
@@ -31,9 +27,11 @@ def setup_module():
     wvf_extractor = extract_waveforms(
         recording, sorting, folder=cache_folder / "wvf_extractor", ms_before=10.0, ms_after=10.0
     )
+    return cache_folder
 
 
-def test_hybrid_units_recording():
+def test_hybrid_units_recording(setup_module):
+    cache_folder = setup_module
     wvf_extractor = load_waveforms(cache_folder / "wvf_extractor")
     print(wvf_extractor)
     print(wvf_extractor.sorting_analyzer)
@@ -63,7 +61,8 @@ def test_hybrid_units_recording():
     check_recordings_equal(hybrid_units_recording, saved_2job, return_scaled=False)
 
 
-def test_hybrid_spikes_recording():
+def test_hybrid_spikes_recording(setup_module):
+    cache_folder = setup_module
     wvf_extractor = load_waveforms(cache_folder / "wvf_extractor")
     recording = wvf_extractor.recording
     sorting = wvf_extractor.sorting

src/spikeinterface/comparison/tests/test_multisortingcomparison.py

@@ -1,6 +1,4 @@
 import shutil
-import pytest
-from pathlib import Path
 
 import pytest
 import numpy as np
@@ -9,18 +7,14 @@
 from spikeinterface.extractors import NumpySorting
 from spikeinterface.comparison import compare_multiple_sorters, MultiSortingComparison
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "comparison"
-else:
-    cache_folder = Path("cache_folder") / "comparison"
-
-
-multicomparison_folder = cache_folder / "saved_multisorting_comparison"
-
 
-def setup_module():
+@pytest.fixture(scope="module")
+def setup_module(tmp_path_factory):
+    cache_folder = tmp_path_factory.mktemp("cache_folder")
+    multicomparison_folder = cache_folder / "saved_multisorting_comparison"
     if multicomparison_folder.is_dir():
         shutil.rmtree(multicomparison_folder)
+    return multicomparison_folder
 
 
 def make_sorting(times1, labels1, times2, labels2, times3, labels3):
@@ -34,7 +28,8 @@ def make_sorting(times1, labels1, times2, labels2, times3, labels3):
     return sorting1, sorting2, sorting3
 
 
-def test_compare_multiple_sorters():
+def test_compare_multiple_sorters(setup_module):
+    multicomparison_folder = setup_module
     # simple match
     sorting1, sorting2, sorting3 = make_sorting(
         [100, 200, 300, 400, 500, 600, 700, 800, 900],

src/spikeinterface/comparison/tests/test_templatecomparison.py

@@ -1,21 +1,11 @@
 import shutil
 import pytest
-from pathlib import Path
 import numpy as np
 
 from spikeinterface.core import create_sorting_analyzer, generate_ground_truth_recording
 from spikeinterface.comparison import compare_templates, compare_multiple_templates
 
 
-# if hasattr(pytest, "global_test_folder"):
-#     cache_folder = pytest.global_test_folder / "comparison"
-# else:
-#     cache_folder = Path("cache_folder") / "comparison"
-
-
-# test_dir = cache_folder / "temp_comp_test"
-
-
 # def setup_module():
 #     if test_dir.is_dir():
 #         shutil.rmtree(test_dir)

src/spikeinterface/core/tests/test_analyzer_extension_core.py

@@ -1,5 +1,4 @@
 import pytest
-from pathlib import Path
 
 import shutil
 
@@ -11,13 +10,8 @@
 
 import numpy as np
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
 
-
-def get_sorting_analyzer(format="memory", sparse=True):
+def get_sorting_analyzer(cache_folder, format="memory", sparse=True):
     recording, sorting = generate_ground_truth_recording(
         durations=[30.0],
         sampling_frequency=16000.0,
@@ -53,7 +47,7 @@ def get_sorting_analyzer(format="memory", sparse=True):
     return sorting_analyzer
 
 
-def _check_result_extension(sorting_analyzer, extension_name):
+def _check_result_extension(sorting_analyzer, extension_name, cache_folder):
     # select unit_ids to several format
     for format in ("memory", "binary_folder", "zarr"):
         # for format in ("memory", ):
@@ -83,39 +77,42 @@ def _check_result_extension(sorting_analyzer, extension_name):
         False,
     ],
 )
-def test_ComputeRandomSpikes(format, sparse):
-    sorting_analyzer = get_sorting_analyzer(format=format, sparse=sparse)
+def test_ComputeRandomSpikes(format, sparse, create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format=format, sparse=sparse)
 
     ext = sorting_analyzer.compute("random_spikes", max_spikes_per_unit=10, seed=2205)
     indices = ext.data["random_spikes_indices"]
     assert indices.size == 10 * sorting_analyzer.sorting.unit_ids.size
 
-    _check_result_extension(sorting_analyzer, "random_spikes")
+    _check_result_extension(sorting_analyzer, "random_spikes", cache_folder)
     sorting_analyzer.delete_extension("random_spikes")
 
     ext = sorting_analyzer.compute("random_spikes", method="all")
     indices = ext.data["random_spikes_indices"]
     assert indices.size == len(sorting_analyzer.sorting.to_spike_vector())
 
-    _check_result_extension(sorting_analyzer, "random_spikes")
+    _check_result_extension(sorting_analyzer, "random_spikes", cache_folder)
 
 
 @pytest.mark.parametrize("format", ["memory", "binary_folder", "zarr"])
 @pytest.mark.parametrize("sparse", [True, False])
-def test_ComputeWaveforms(format, sparse):
-    sorting_analyzer = get_sorting_analyzer(format=format, sparse=sparse)
+def test_ComputeWaveforms(format, sparse, create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format=format, sparse=sparse)
 
     job_kwargs = dict(n_jobs=2, chunk_duration="1s", progress_bar=True)
     sorting_analyzer.compute("random_spikes", max_spikes_per_unit=50, seed=2205)
     ext = sorting_analyzer.compute("waveforms", **job_kwargs)
     wfs = ext.data["waveforms"]
-    _check_result_extension(sorting_analyzer, "waveforms")
+    _check_result_extension(sorting_analyzer, "waveforms", cache_folder)
 
 
 @pytest.mark.parametrize("format", ["memory", "binary_folder", "zarr"])
 @pytest.mark.parametrize("sparse", [True, False])
-def test_ComputeTemplates(format, sparse):
-    sorting_analyzer = get_sorting_analyzer(format=format, sparse=sparse)
+def test_ComputeTemplates(format, sparse, create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format=format, sparse=sparse)
 
     sorting_analyzer.compute("random_spikes", max_spikes_per_unit=50, seed=2205)
 
@@ -187,13 +184,14 @@ def test_ComputeTemplates(format, sparse):
     #     ax.legend()
     # plt.show()
 
-    _check_result_extension(sorting_analyzer, "templates")
+    _check_result_extension(sorting_analyzer, "templates", cache_folder)
 
 
 @pytest.mark.parametrize("format", ["memory", "binary_folder", "zarr"])
 @pytest.mark.parametrize("sparse", [True, False])
-def test_ComputeNoiseLevels(format, sparse):
-    sorting_analyzer = get_sorting_analyzer(format=format, sparse=sparse)
+def test_ComputeNoiseLevels(format, sparse, create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format=format, sparse=sparse)
 
     sorting_analyzer.compute("noise_levels")
     print(sorting_analyzer)
@@ -212,8 +210,9 @@ def test_get_children_dependencies():
     assert rs_children.index("waveforms") < rs_children.index("templates")
 
 
-def test_delete_on_recompute():
-    sorting_analyzer = get_sorting_analyzer(format="memory", sparse=False)
+def test_delete_on_recompute(create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format="memory", sparse=False)
     sorting_analyzer.compute("random_spikes")
     sorting_analyzer.compute("waveforms")
     sorting_analyzer.compute("templates")
@@ -224,8 +223,9 @@ def test_delete_on_recompute():
     assert sorting_analyzer.get_extension("waveforms") is None
 
 
-def test_compute_several():
-    sorting_analyzer = get_sorting_analyzer(format="memory", sparse=False)
+def test_compute_several(create_cache_folder):
+    cache_folder = create_cache_folder
+    sorting_analyzer = get_sorting_analyzer(cache_folder, format="memory", sparse=False)
 
     # should raise an error since waveforms depends on random_spikes, which isn't calculated
     with pytest.raises(AssertionError):

src/spikeinterface/core/tests/test_baserecording.py

@@ -18,14 +18,9 @@
 
 from spikeinterface.core import generate_recording
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
-    cache_folder.mkdir(exist_ok=True, parents=True)
 
-
-def test_BaseRecording():
+def test_BaseRecording(create_cache_folder):
+    cache_folder = create_cache_folder
     num_seg = 2
     num_chan = 3
     num_samples = 30

src/spikeinterface/core/tests/test_basesnippets.py

@@ -14,14 +14,9 @@
 from spikeinterface.core.npysnippetsextractor import NpySnippetsExtractor
 from spikeinterface.core.base import BaseExtractor
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
-    cache_folder.mkdir(exist_ok=True, parents=True)
 
-
-def test_BaseSnippets():
+def test_BaseSnippets(create_cache_folder):
+    cache_folder = create_cache_folder
     duration = [4, 3]
     num_channels = 3
     nbefore = 20

src/spikeinterface/core/tests/test_basesorting.py

@@ -25,13 +25,9 @@
 from spikeinterface.core.testing import check_sorted_arrays_equal, check_sortings_equal
 from spikeinterface.core.generate import generate_sorting
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
 
-
-def test_BaseSorting():
+def test_BaseSorting(create_cache_folder):
+    cache_folder = create_cache_folder
     num_seg = 2
     file_path = cache_folder / "test_BaseSorting.npz"
     file_path.parent.mkdir(exist_ok=True)

src/spikeinterface/core/tests/test_binaryfolder.py

@@ -9,13 +9,8 @@
 from spikeinterface.core import generate_recording
 
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
-
-
-def test_BinaryFolderRecording():
+def test_BinaryFolderRecording(create_cache_folder):
+    cache_folder = create_cache_folder
     rec = generate_recording(num_channels=10, durations=[2.0, 2.0])
     folder = cache_folder / "binary_folder_1"
 

src/spikeinterface/core/tests/test_binaryrecordingextractor.py

@@ -1,17 +1,12 @@
 import pytest
 import numpy as np
-from pathlib import Path
 
 from spikeinterface.core import BinaryRecordingExtractor
 from spikeinterface.core.numpyextractors import NumpyRecording
 
-if hasattr(pytest, "global_test_folder"):
-    cache_folder = pytest.global_test_folder / "core"
-else:
-    cache_folder = Path("cache_folder") / "core"
 
-
-def test_BinaryRecordingExtractor():
+def test_BinaryRecordingExtractor(create_cache_folder):
+    cache_folder = create_cache_folder
     num_seg = 2
     num_channels = 3
     num_samples = 30

src/spikeinterface/core/tests/test_channelslicerecording.py

@@ -10,11 +10,8 @@
 from spikeinterface.core.generate import generate_recording
 
 
-def test_ChannelSliceRecording():
-    if hasattr(pytest, "global_test_folder"):
-        cache_folder = pytest.global_test_folder / "core"
-    else:
-        cache_folder = Path("cache_folder") / "core"
+def test_ChannelSliceRecording(create_cache_folder):
+    cache_folder = create_cache_folder
 
     num_seg = 2
     num_chan = 3