Run pre-commits

phys2bids/io.py

@@ -575,7 +575,7 @@ def load_smr(filename, chtrig=0):
         sonpy.lib.DataType.AdcMark: sonpy.lib.SonFile.ReadWaveMarks,
         sonpy.lib.DataType.RealMark: sonpy.lib.SonFile.ReadRealMarks,
         sonpy.lib.DataType.TextMark: sonpy.lib.SonFile.ReadTextMarks,
-        sonpy.lib.DataType.RealWave: sonpy.lib.SonFile.ReadFloats
+        sonpy.lib.DataType.RealWave: sonpy.lib.SonFile.ReadFloats,
     }
 
     smrfile = sonpy.lib.SonFile(filename, True)
@@ -601,8 +601,8 @@ def load_smr(filename, chtrig=0):
 
             n_samples = int(np.floor((max_n_tick) / divide))
             raw_signal = read_data[current_channel](
-                smrfile, chan=i, nMax=n_samples,
-                tFrom=0, tUpto=max_n_tick)
+                smrfile, chan=i, nMax=n_samples, tFrom=0, tUpto=max_n_tick
+            )
 
             signal = np.array(raw_signal) * gain + offset
 
@@ -618,8 +618,8 @@ def load_smr(filename, chtrig=0):
     time = np.arange(n_timepoints) * freq[idx_max]
 
     # prepend to the existing list
-    freq = [freq[idx_max], ] + freq
-    timeseries = [time, ] + timeseries
-    units = ['s', ] + units
-    names = ['time', ] + names
+    freq = [freq[idx_max]] + freq
+    timeseries = [time] + timeseries
+    units = ["s"] + units
+    names = ["time"] + names
     return BlueprintInput(timeseries, freq, names, units, chtrig)

phys2bids/tests/conftest.py

@@ -95,7 +95,6 @@ def multi_run_file(testpath):
     return fetch_file("gvy84", testpath, "Test2_samefreq_TWOscans.txt")
 
 
-
 @pytest.fixture
 def matlab_file_labchart(testpath):
     return fetch_file("2j43t", testpath, "test_2minRest.mat")
@@ -106,57 +105,46 @@ def matlab_file_acq(testpath):
     return fetch_file("mc96w", testpath, "Test_belt_pulse_multifreq.mat")
 
 
-
 @pytest.fixture
 def ge_one_gep_file(testpath):
     return fetch_file("wb84d", testpath, "PPGData_epiRT_0000000000_00_00_000.gep")
 
 
-
 @pytest.fixture
 def ge_two_gep_files_ppg(testpath):
     tmp = fetch_file("qawjv", testpath, "RESPData_epiRT_0000000000_00_00_000.gep")
     return fetch_file("wb84d", testpath, "PPGData_epiRT_0000000000_00_00_000.gep")
 
 
-
 @pytest.fixture
 def ge_two_gep_files_resp(testpath):
     tmp = fetch_file("wb84d", testpath, "PPGData_epiRT_0000000000_00_00_000.gep")
     return fetch_file("qawjv", testpath, "RESPData_epiRT_0000000000_00_00_000.gep")
 
 
-
 @pytest.fixture
 def ge_one_raw_file(testpath):
     return fetch_file("u9wsr", testpath, "PPGData_epiRT_0000000000_00_00_000")
 
 
-
 @pytest.fixture
 def ge_two_raw_files(testpath):
     tmp = fetch_file("49xpw", testpath, "RESPData_epiRT_0000000000_00_00_000")
     return fetch_file("u9wsr", testpath, "PPGData_epiRT_0000000000_00_00_000")
 
 
-
 @pytest.fixture
 def ge_badfiles(testpath):
-    tmp = fetch_file('tdmyn', testpath,
-                     'PPGData_epiRT_columnscsv_00_00_000')
-    tmp = fetch_file('b6skq', testpath,
-                     'PPGData_epiRT_columnstsv_00_00_000')
-    return fetch_file('8235b', testpath,
-                      'PPGData_epiRT_string0000_00_00_000')
+    tmp = fetch_file("tdmyn", testpath, "PPGData_epiRT_columnscsv_00_00_000")
+    tmp = fetch_file("b6skq", testpath, "PPGData_epiRT_columnstsv_00_00_000")
+    return fetch_file("8235b", testpath, "PPGData_epiRT_string0000_00_00_000")
 
 
 @pytest.fixture
 def spike2_smrx_file(testpath):
-    return fetch_file('7x5qw', testpath,
-                      'Test_ppg_pulse_spike2.smrx')
+    return fetch_file("7x5qw", testpath, "Test_ppg_pulse_spike2.smrx")
 
 
 @pytest.fixture
 def spike2_smr_file(testpath):
-    return fetch_file('zdpfr', testpath,
-                      'Test_ppg_pulse_spike2.smr')
+    return fetch_file("zdpfr", testpath, "Test_ppg_pulse_spike2.smr")

phys2bids/tests/test_io.py

@@ -219,33 +219,33 @@ def test_load_gep_two_files_resp(ge_two_gep_files_resp, testpath):
 
 @pytest.mark.skipif(
     sys.version_info < (3, 7) or sys.version_info > (3, 9),
-    reason="Requires python between 3.7 and 3.9"
+    reason="Requires python between 3.7 and 3.9",
 )
 @pytest.mark.xfail(reason="We need to fix sonpy install")
 def test_load_smr(spike2_smr_file, spike2_smrx_file):
     chtrig = 5
 
     # 32-bit file
     phys_obj = io.load_smr(spike2_smr_file, chtrig)
-    assert phys_obj.ch_name[0] == 'time'
+    assert phys_obj.ch_name[0] == "time"
     assert phys_obj.freq[0] == 1000.0
-    assert phys_obj.units[0] == 's'
+    assert phys_obj.units[0] == "s"
 
     # checks that the scanner strigger is in the right channel
     # the marker channels are stored as binary
-    assert phys_obj.ch_name[chtrig] == 'Scan Vol'
+    assert phys_obj.ch_name[chtrig] == "Scan Vol"
     assert phys_obj.freq[chtrig] == 200.0
-    assert phys_obj.units[chtrig] == ''
+    assert phys_obj.units[chtrig] == ""
     assert len(phys_obj.timeseries[chtrig]) == 60
 
     # 64-bit file should have the same
     phys_obj = io.load_smr(spike2_smrx_file, chtrig)
-    assert phys_obj.ch_name[0] == 'time'
+    assert phys_obj.ch_name[0] == "time"
     assert phys_obj.freq[0] == 1000.0
-    assert phys_obj.units[0] == 's'
+    assert phys_obj.units[0] == "s"
     # checks that the scanner trigger is in the right channel
     # the marker channels are stored as binary
-    assert phys_obj.ch_name[chtrig] == 'Scan Vol'
+    assert phys_obj.ch_name[chtrig] == "Scan Vol"
     assert phys_obj.freq[chtrig] == 200.0
-    assert phys_obj.units[chtrig] == ''
+    assert phys_obj.units[chtrig] == ""
     assert len(phys_obj.timeseries[chtrig]) == 60