Merge pull request #249 from h-mayorquin/black_test

Black format tests

.pre-commit-config.yaml

@@ -9,4 +9,4 @@ repos:
     rev: 24.1.1
     hooks:
     -   id: black
-        files: ^src/
+        files: ^src/|^tests/

pyproject.toml

@@ -45,7 +45,7 @@ test = [
     "scipy",
     "pandas",
     "h5py",
-]
+    ]
 
 docs = [
     "pillow",

tests/test_generator.py

@@ -1,6 +1,11 @@
-from probeinterface import (generate_dummy_probe, generate_dummy_probe_group,
-        generate_tetrode, generate_linear_probe, generate_multi_columns_probe,
-        generate_multi_shank)
+from probeinterface import (
+    generate_dummy_probe,
+    generate_dummy_probe_group,
+    generate_tetrode,
+    generate_linear_probe,
+    generate_multi_columns_probe,
+    generate_multi_shank,
+)
 
 
 from pathlib import Path
@@ -15,20 +20,19 @@ def test_generate():
 
     tetrode = generate_tetrode()
 
-    multi_columns = generate_multi_columns_probe(num_columns=3,
-                num_contact_per_column=[10, 12, 10],
-                xpitch=22, ypitch=20,
-                y_shift_per_column=[0, -10, 0])
+    multi_columns = generate_multi_columns_probe(
+        num_columns=3, num_contact_per_column=[10, 12, 10], xpitch=22, ypitch=20, y_shift_per_column=[0, -10, 0]
+    )
 
-    linear = generate_linear_probe(num_elec=16,  ypitch=20,
-                    contact_shapes='square', contact_shape_params={'width': 15})
+    linear = generate_linear_probe(num_elec=16, ypitch=20, contact_shapes="square", contact_shape_params={"width": 15})
 
     multi_shank = generate_multi_shank()
 
-    #~ from probeinterface.plotting import plot_probe_group, plot_probe
-    #~ import matplotlib.pyplot as plt
-    #~ plot_probe(multi_shank, with_contact_id=True,)
-    #~ plt.show()
+    # ~ from probeinterface.plotting import plot_probe_group, plot_probe
+    # ~ import matplotlib.pyplot as plt
+    # ~ plot_probe(multi_shank, with_contact_id=True,)
+    # ~ plt.show()
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     test_generate()

tests/test_io/test_io.py

@@ -43,6 +43,7 @@ def test_probeinterface_format(tmp_path):
     # ~ plot_probe_group(probegroup2, with_contact_id=True, same_axes=False)
     # ~ plt.show()
 
+
 def test_writeprobeinterface(tmp_path):
     probe = generate_dummy_probe()
     file_path = tmp_path / "test.prb"
@@ -61,7 +62,6 @@ def test_writeprobeinterface_raises_error_with_bad_input(tmp_path):
         write_probeinterface(file_path, probe)
 
 
-
 def test_BIDS_format(tmp_path):
     folder_path = tmp_path / "test_BIDS"
     folder_path.mkdir()
@@ -77,9 +77,7 @@ def test_BIDS_format(tmp_path):
     # with BIDS specifications
     n_els = sum([p.get_contact_count() for p in probegroup.probes])
     # using np.random.choice to ensure uniqueness of contact ids
-    el_ids = np.random.choice(
-        np.arange(1e4, 1e5, dtype="int"), replace=False, size=n_els
-    ).astype(str)
+    el_ids = np.random.choice(np.arange(1e4, 1e5, dtype="int"), replace=False, size=n_els).astype(str)
     for probe in probegroup.probes:
         probe_el_ids, el_ids = np.split(el_ids, [probe.get_contact_count()])
         probe.set_contact_ids(probe_el_ids)
@@ -102,12 +100,7 @@ def test_BIDS_format(tmp_path):
         assert all(np.isin(probe_orig.contact_ids, probe_read.contact_ids))
 
         # the transformation of contact order between the two probes
-        t = np.array(
-            [
-                list(probe_read.contact_ids).index(elid)
-                for elid in probe_orig.contact_ids
-            ]
-        )
+        t = np.array([list(probe_read.contact_ids).index(elid) for elid in probe_orig.contact_ids])
 
         assert all(probe_orig.contact_ids == probe_read.contact_ids[t])
         assert all(probe_orig.shank_ids == probe_read.shank_ids[t])
@@ -116,21 +109,14 @@ def test_BIDS_format(tmp_path):
         assert probe_orig.si_units == probe_read.si_units
 
         for i in range(len(probe_orig.probe_planar_contour)):
-            assert all(
-                probe_orig.probe_planar_contour[i] == probe_read.probe_planar_contour[i]
-            )
+            assert all(probe_orig.probe_planar_contour[i] == probe_read.probe_planar_contour[i])
         for sid, shape_params in enumerate(probe_orig.contact_shape_params):
             assert shape_params == probe_read.contact_shape_params[t][sid]
         for i in range(len(probe_orig.contact_positions)):
-            assert all(
-                probe_orig.contact_positions[i] == probe_read.contact_positions[t][i]
-            )
+            assert all(probe_orig.contact_positions[i] == probe_read.contact_positions[t][i])
         for i in range(len(probe.contact_plane_axes)):
             for dim in range(len(probe.contact_plane_axes[i])):
-                assert all(
-                    probe_orig.contact_plane_axes[i][dim]
-                    == probe_read.contact_plane_axes[t][i][dim]
-                )
+                assert all(probe_orig.contact_plane_axes[i][dim] == probe_read.contact_plane_axes[t][i][dim])
 
 
 def test_BIDS_format_empty(tmp_path):
@@ -218,6 +204,7 @@ def test_prb(tmp_path):
     # plot_probe(probe)
     # plt.show()
 
+
 if __name__ == "__main__":
     # test_probeinterface_format()
     # test_BIDS_format()

tests/test_io/test_openephys.py

@@ -61,20 +61,15 @@ def test_NP_Ultra():
     assert len(np.unique(probeD.contact_positions[:, 0])) == 1
 
 
-
 def test_NP1_subset():
     # NP1 - 200 channels selected by recording_state in Record Node
-    probe_ap = read_openephys(
-        data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-AP"
-    )
+    probe_ap = read_openephys(data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-AP")
 
     assert probe_ap.get_shank_count() == 1
     assert "1.0" in probe_ap.model_name
     assert probe_ap.get_contact_count() == 200
 
-    probe_lf = read_openephys(
-        data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-LFP"
-    )
+    probe_lf = read_openephys(data_path / "OE_Neuropix-PXI-subset" / "settings.xml", stream_name="ProbeA-LFP")
 
     assert probe_lf.get_shank_count() == 1
     assert "1.0" in probe_lf.model_name
@@ -88,9 +83,7 @@ def test_NP1_subset():
 
 def test_multiple_probes():
     # multiple probes
-    probeA = read_openephys(
-        data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA"
-    )
+    probeA = read_openephys(data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA")
 
     assert probeA.get_shank_count() == 1
     assert "1.0" in probeA.model_name
@@ -109,9 +102,7 @@ def test_multiple_probes():
 
     assert probeC.get_shank_count() == 1
 
-    probeD = read_openephys(
-        data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeD"
-    )
+    probeD = read_openephys(data_path / "OE_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeD")
 
     assert probeD.get_shank_count() == 1
 
@@ -148,13 +139,10 @@ def test_np_opto_with_sync():
     assert probe.get_contact_count() == 384
 
 
-
 def test_older_than_06_format():
     ## Test with the open ephys < 0.6 format
 
-    probe = read_openephys(
-        data_path / "OE_5_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="100.0"
-    )
+    probe = read_openephys(data_path / "OE_5_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="100.0")
 
     assert probe.get_shank_count() == 4
     assert "2.0 - Four Shank" in probe.model_name

tests/test_io/test_spikeglx.py

@@ -11,6 +11,7 @@
 
 data_path = Path(__file__).absolute().parent.parent / "data" / "spikeglx"
 
+
 def test_parse_meta():
     for meta_file in [
         "doppio-checkerboard_t0.imec0.ap.meta",
@@ -19,19 +20,17 @@ def test_parse_meta():
     ]:
         meta = parse_spikeglx_meta(data_path / meta_file)
 
+
 def test_get_saved_channel_indices_from_spikeglx_meta():
     # all channel saved + 1 synchro
-    chan_inds = get_saved_channel_indices_from_spikeglx_meta(
-        data_path / "Noise_g0_t0.imec0.ap.meta"
-    )
+    chan_inds = get_saved_channel_indices_from_spikeglx_meta(data_path / "Noise_g0_t0.imec0.ap.meta")
     assert chan_inds.size == 385
 
     # example by Pierre Yger NP1.0 with 384 but only 151 channels are saved + 1 synchro
-    chan_inds = get_saved_channel_indices_from_spikeglx_meta(
-        data_path / "NP1_saved_only_subset_of_channels.meta"
-    )
+    chan_inds = get_saved_channel_indices_from_spikeglx_meta(data_path / "NP1_saved_only_subset_of_channels.meta")
     assert chan_inds.size == 152
 
+
 def test_NP1():
     probe = read_spikeglx(data_path / "Noise_g0_t0.imec0.ap.meta")
     assert "1.0" in probe.model_name
@@ -187,6 +186,7 @@ def tes_NP1_384_channels():
     assert probe.get_contact_count() == 151
     assert 152 not in probe.contact_annotations["channel_ids"]
 
+
 def test_NPH_long_staggered():
     # Data provided by Nate Dolensek
     probe = read_spikeglx(data_path / "non_human_primate_long_staggered.imec0.ap.meta")
@@ -242,6 +242,7 @@ def test_NPH_long_staggered():
     assert np.allclose(references, 0)
     assert np.allclose(filters, 1)
 
+
 def test_NPH_short_linear_probe_type_0():
     # Data provided by Jonathan A Michaels
     probe = read_spikeglx(data_path / "non_human_primate_short_linear_probe_type_0.meta")
@@ -254,7 +255,6 @@ def test_NPH_short_linear_probe_type_0():
     assert probe.get_shank_count() == 1
     assert probe.get_contact_count() == 384
 
-
     # Test contact geometry
     x_pitch = 56.0
     y_pitch = 20.0
@@ -320,6 +320,7 @@ def test_ultra_probe():
     unique_y_values = np.unique(y)
     assert unique_y_values.size == expected_electode_rows
 
+
 def test_CatGT_NP1():
     probe = read_spikeglx(data_path / "catgt.meta")
     assert "1.0" in probe.model_name

tests/test_library.py

@@ -1,6 +1,5 @@
 from probeinterface import Probe
-from probeinterface.library import (download_probeinterface_file,
-        get_from_cache, get_probe)
+from probeinterface.library import download_probeinterface_file, get_from_cache, get_probe
 
 
 from pathlib import Path
@@ -9,19 +8,20 @@
 import pytest
 
 
-manufacturer = 'neuronexus'
-probe_name = 'A1x32-Poly3-10mm-50-177'
+manufacturer = "neuronexus"
+probe_name = "A1x32-Poly3-10mm-50-177"
 
 
 def test_download_probeinterface_file():
     download_probeinterface_file(manufacturer, probe_name)
 
+
 def test_get_from_cache():
     download_probeinterface_file(manufacturer, probe_name)
     probe = get_from_cache(manufacturer, probe_name)
     assert isinstance(probe, Probe)
 
-    probe = get_from_cache('yep', 'yop')
+    probe = get_from_cache("yep", "yop")
     assert probe is None
 
 
@@ -31,7 +31,7 @@ def test_get_probe():
     assert probe.get_contact_count() == 32
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     test_download_probeinterface_file()
     test_get_from_cache()
     test_get_probe()

tests/test_plotting.py

@@ -13,15 +13,15 @@ def test_plot_probe():
     plot_probe(probe)
     plot_probe(probe, with_contact_id=True)
     plot_probe(probe, with_device_index=True)
-    plot_probe(probe, text_on_contact=['abcde'[i%5] for i in range(probe.get_contact_count())])
+    plot_probe(probe, text_on_contact=["abcde"[i % 5] for i in range(probe.get_contact_count())])
 
     # with color
     n = probe.get_contact_count()
     contacts_colors = np.random.rand(n, 3)
     plot_probe(probe, contacts_colors=contacts_colors)
 
     # 3d
-    probe_3d = probe.to_3d(axes='xz')
+    probe_3d = probe.to_3d(axes="xz")
     plot_probe(probe_3d)
 
     # on click
@@ -43,7 +43,7 @@ def test_plot_probe_group():
     plot_probe_group(probegroup_3d, same_axes=True)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     test_plot_probe()
     # test_plot_probe_group()
     plt.show()