Refactor test modules

README.md

@@ -30,6 +30,8 @@ Python package for brain decoding analysis
 - `fig` module
     - matplotlib
     - Pillow
+- `bdpy.ml` module
+    - tqdm
 - `mri` module
     - nipy
     - nibabel
@@ -38,6 +40,9 @@ Python package for brain decoding analysis
     - PyTorch
     - Pillow
 
+### Optional requirements for testing
+- fastl2lir
+
 ## Installation
 
 Latest stable release:

bdpy/preproc/preprocessor.py

@@ -11,6 +11,9 @@
 
 import numpy as np
 from numpy.matlib import repmat
+# NOTE: PendingDeprecationWarning: Importing from numpy.matlib is deprecated since 1.19.0.
+# repmat(a, m, n) is equivalent to tile(a, (m, n)). Use tile instead.
+# c.f. https://numpy.org/doc/stable/user/numpy-for-matlab-users.html
 
 
 ## Abstract preprocessor #######################################################

test/test_bdata.py → test/bdata/test_bdata.py

@@ -1,17 +1,15 @@
-'''Tests for bdpy.bdata'''
+'''Tests for bdpy.bdata.bdata.'''
 
 
-from unittest import TestCase, TestLoader, TextTestRunner
-
-import copy
+import unittest
 
 import numpy as np
 from numpy.testing import assert_array_equal
 
-import bdpy
+from bdpy.bdata.bdata import BData
 
 
-class TestBdata(TestCase):
+class TestBdata(unittest.TestCase):
     '''Tests of 'bdata' module'''
 
     def __init__(self, *args, **kwargs):
@@ -23,7 +21,7 @@ def test_add_get(self):
         data_y = np.random.rand(5, 8)
         data_z = np.random.rand(5, 20)
 
-        b = bdpy.BData()
+        b = BData()
 
         b.add(data_x, 'Data_X')
         b.add(data_y, 'Data_Y')
@@ -55,7 +53,7 @@ def test_metadata_add_get(self):
         metadata_a = np.random.rand(n_col)
         metadata_b = np.random.rand(n_col)
 
-        b = bdpy.BData()
+        b = BData()
 
         b.add(data_x, 'Data_X')
         b.add(data_y, 'Data_Y')
@@ -77,7 +75,7 @@ def test_metadata_add_get_where(self):
         metadata_a = np.random.rand(10)
         metadata_b = np.random.rand(8)
 
-        b = bdpy.BData()
+        b = BData()
 
         b.add(data_x, 'Data_X')
         b.add(data_y, 'Data_Y')
@@ -99,7 +97,7 @@ def test_set_metadatadescription_1(self):
         metadata_a = np.random.rand(10)
         metadata_b = np.random.rand(8)
 
-        b = bdpy.BData()
+        b = BData()
         b.add(data_x, 'Data_X')
         b.add(data_y, 'Data_Y')
         b.add_metadata('Metadata_A', metadata_a, where='Data_X')
@@ -117,7 +115,7 @@ def test_select(self):
         data_x = np.random.rand(5, 10)
         data_y = np.random.rand(5, 5)
 
-        b = bdpy.BData()
+        b = BData()
         b.add(data_x, 'Data_X')
         b.add(data_y, 'Data_Y')
 
@@ -142,7 +140,7 @@ def test_select(self):
 
     # Tests for vmap
     def test_vmap_add_get(self):
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(4, 3), 'MainData')
         bdata.add(np.arange(4) + 1, 'Label')
 
@@ -159,7 +157,7 @@ def test_vmap_add_get(self):
         np.testing.assert_array_equal(bdata.get_label('Label'), label)
 
     def test_vmap_add_same_map(self):
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(4, 3), 'MainData')
         bdata.add(np.arange(4) + 1, 'Label')
 
@@ -179,7 +177,7 @@ def test_vmap_add_same_map(self):
     def test_vmap_errorcases(self):
         n_sample = 4
 
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(n_sample, 3), 'MainData')
         bdata.add(np.arange(n_sample) + 1, 'Label')
 
@@ -208,7 +206,7 @@ def test_vmap_errorcases(self):
             bdata.add_vmap('Label', label_map_inconsist)
 
     def test_vmap_add_unnecessary_vmap(self):
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(4, 3), 'MainData')
         bdata.add(np.arange(4) + 1, 'Label')
 
@@ -226,7 +224,7 @@ def test_vmap_add_unnecessary_vmap(self):
         assert bdata.get_vmap('Label') == label_map_ture
 
     def test_vmap_add_insufficient_vmap(self):
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(4, 3), 'MainData')
         bdata.add(np.arange(4) + 1, 'Label')
 
@@ -238,7 +236,7 @@ def test_vmap_add_insufficient_vmap(self):
             bdata.add_vmap('Label', label_map)
 
     def test_vmap_add_invalid_name_vmap(self):
-        bdata = bdpy.BData()
+        bdata = BData()
         bdata.add(np.random.rand(4, 3), 'MainData')
         bdata.add(np.arange(4) + 1, 'Label')
 
@@ -252,5 +250,4 @@ def test_vmap_add_invalid_name_vmap(self):
 
 
 if __name__ == "__main__":
-    test_suite = TestLoader().loadTestsFromTestCase(TestBdata)
-    TextTestRunner(verbosity=2).run(test_suite)
+    unittest.main()

test/test_bdata_metadata.py → test/bdata/test_metadata.py

@@ -1,23 +1,23 @@
 '''Tests for bdpy.bdata.metadata.'''
 
 
-from unittest import TestCase, TestLoader, TextTestRunner
+import unittest
 
 import numpy as np
 from numpy.testing import assert_array_equal
 
-import bdpy
+from bdpy.bdata import metadata
 
 
-class TestBdataMetadata(TestCase):
+class TestMetadata(unittest.TestCase):
     '''Tests for bdpy.bdata.metadata.'''
 
     def __init__(self, *args, **kwargs):
-        super(TestBdataMetadata, self).__init__(*args, **kwargs)
+        super(TestMetadata, self).__init__(*args, **kwargs)
 
     def test_set_get(self):
         '''Test for MetaData.set() and MetaData.get().'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
@@ -28,7 +28,7 @@ def test_set_get(self):
 
     def test_set_get_resize(self):
         '''Test for MetaData.set() and MetaData.get(); resizing values.'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
         md.set('MetaData_C', [0] * 15 + [1] * 3, 'Test metadata C')
@@ -42,7 +42,7 @@ def test_set_get_resize(self):
 
     def test_set_get_overwrite(self):
         '''Test for MetaData.set() and MetaData.get(); overwriting values.'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
@@ -55,7 +55,7 @@ def test_set_get_overwrite(self):
 
     def test_set_get_overwrite_resize(self):
         '''Test for MetaData.set() and MetaData.get(); overwriting and resizing values.'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1, 1, 1, 0, 0], 'Test metadata A')
         md.set('MetaData_B', [0, 0, 0, 1, 1], 'Test metadata B')
 
@@ -68,7 +68,7 @@ def test_set_get_overwrite_resize(self):
 
     def test_set_get_update(self):
         '''Test for MetaData.set() and MetaData.get(); updating values.'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
@@ -81,7 +81,7 @@ def test_set_get_update(self):
 
     def test_get_notfound(self):
         '''Test for MetaData.get(); key not found case.'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
@@ -90,21 +90,20 @@ def test_get_notfound(self):
 
     def test_get_value_len(self):
         '''Test for get_value_len().'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
         assert_array_equal(md.get_value_len(), 15)
 
     def test_keylist(self):
         '''Test for keylist().'''
-        md = bdpy.bdata.metadata.MetaData()
+        md = metadata.MetaData()
         md.set('MetaData_A', [1] * 10 + [0] * 5, 'Test metadata A')
         md.set('MetaData_B', [0] * 10 + [1] * 5, 'Test metadata B')
 
         assert_array_equal(md.keylist(), ['MetaData_A', 'MetaData_B'])
 
 
 if __name__ == '__main__':
-    test_suite = TestLoader().loadTestsFromTestCase(TestBdataMetadata)
-    TextTestRunner(verbosity=2).run(test_suite)
+    unittest.main()