Test codes depend on external files

[ganow]

Here is the result of the test codes. Maybe it would be great if we isolate test cases from external files. We can use mock datasets, for example, https://pypi.org/project/pytest-mock/

$ pytest .
============================= test session starts ==============================
platform linux -- Python 3.8.16, pytest-7.2.2, pluggy-1.0.0
rootdir: /workspaces/bdpy
plugins: anyio-3.6.2
collected 98 items

test/test_bdata.py ...........                                           [ 11%]
test/test_bdata_metadata.py ........                                     [ 19%]
test/test_bdata_utils.py ............                                    [ 31%]
test/test_cv.py ..                                                       [ 33%]
test/test_dataform_sparse.py F..                                         [ 36%]
test/test_distcomp.py ..                                                 [ 38%]
test/test_evals.py FF..                                                  [ 42%]
test/test_feature.py ..                                                  [ 44%]
test/test_featureselector.py ........                                    [ 53%]
test/test_ml.py FFFFFF....                                               [ 63%]
test/test_ml_utils.py ......                                             [ 69%]
test/test_mri.py EEE                                                     [ 72%]
test/test_preproc.py ........                                            [ 80%]
test/test_stats.py ...........                                           [ 91%]
test/test_util.py ......                                                 [ 97%]
test/test_util_math.py ..                                                [100%]

==================================== ERRORS ====================================
_____________ ERROR at setup of TestMri.test_add_load_epi_pass0001 _____________

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
>           return open(file_like, mode), True
E           FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:39: FileNotFoundError

During handling of the above exception, another exception occurred:

self = <test_mri.TestMri testMethod=test_add_load_epi_pass0001>
args = ('test_add_load_epi_pass0001',), kwargs = {}

    def __init__(self, *args, **kwargs):

        super(TestMri, self).__init__(*args, **kwargs)

        self.data_dir = './data/mri'
        self.test_files = ['epi0001.img', 'epi0002.img', 'epi0003.img',
                           'epi0004.img', 'epi0005.img']
        self.exp_file = 'epi.mat'

        # Get exptected data
>       self.exp_dat = sio.loadmat(os.path.join(self.data_dir, self.exp_file))

test/test_mri.py:26: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:225: in loadmat
    with _open_file_context(file_name, appendmat) as f:
/usr/local/lib/python3.8/contextlib.py:113: in __enter__
    return next(self.gen)
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:17: in _open_file_context
    f, opened = _open_file(file_like, appendmat, mode)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
            return open(file_like, mode), True
        except OSError as e:
            # Probably "not found"
            if isinstance(file_like, str):
                if appendmat and not file_like.endswith('.mat'):
                    file_like += '.mat'
>               return open(file_like, mode), True
E               FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:45: FileNotFoundError
_____________ ERROR at setup of TestMri.test_get_roiflag_pass0001 ______________

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
>           return open(file_like, mode), True
E           FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:39: FileNotFoundError

During handling of the above exception, another exception occurred:

self = <test_mri.TestMri testMethod=test_get_roiflag_pass0001>
args = ('test_get_roiflag_pass0001',), kwargs = {}

    def __init__(self, *args, **kwargs):

        super(TestMri, self).__init__(*args, **kwargs)

        self.data_dir = './data/mri'
        self.test_files = ['epi0001.img', 'epi0002.img', 'epi0003.img',
                           'epi0004.img', 'epi0005.img']
        self.exp_file = 'epi.mat'

        # Get exptected data
>       self.exp_dat = sio.loadmat(os.path.join(self.data_dir, self.exp_file))

test/test_mri.py:26: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:225: in loadmat
    with _open_file_context(file_name, appendmat) as f:
/usr/local/lib/python3.8/contextlib.py:113: in __enter__
    return next(self.gen)
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:17: in _open_file_context
    f, opened = _open_file(file_like, appendmat, mode)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
            return open(file_like, mode), True
        except OSError as e:
            # Probably "not found"
            if isinstance(file_like, str):
                if appendmat and not file_like.endswith('.mat'):
                    file_like += '.mat'
>               return open(file_like, mode), True
E               FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:45: FileNotFoundError
_____________ ERROR at setup of TestMri.test_get_roiflag_pass0002 ______________

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
>           return open(file_like, mode), True
E           FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:39: FileNotFoundError

During handling of the above exception, another exception occurred:

self = <test_mri.TestMri testMethod=test_get_roiflag_pass0002>
args = ('test_get_roiflag_pass0002',), kwargs = {}

    def __init__(self, *args, **kwargs):

        super(TestMri, self).__init__(*args, **kwargs)

        self.data_dir = './data/mri'
        self.test_files = ['epi0001.img', 'epi0002.img', 'epi0003.img',
                           'epi0004.img', 'epi0005.img']
        self.exp_file = 'epi.mat'

        # Get exptected data
>       self.exp_dat = sio.loadmat(os.path.join(self.data_dir, self.exp_file))

test/test_mri.py:26: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:225: in loadmat
    with _open_file_context(file_name, appendmat) as f:
/usr/local/lib/python3.8/contextlib.py:113: in __enter__
    return next(self.gen)
.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:17: in _open_file_context
    f, opened = _open_file(file_like, appendmat, mode)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

file_like = './data/mri/epi.mat', appendmat = True, mode = 'rb'

    def _open_file(file_like, appendmat, mode='rb'):
        """
        Open `file_like` and return as file-like object. First, check if object is
        already file-like; if so, return it as-is. Otherwise, try to pass it
        to open(). If that fails, and `file_like` is a string, and `appendmat` is true,
        append '.mat' and try again.
        """
        reqs = {'read'} if set(mode) & set('r+') else set()
        if set(mode) & set('wax+'):
            reqs.add('write')
        if reqs.issubset(dir(file_like)):
            return file_like, False

        try:
            return open(file_like, mode), True
        except OSError as e:
            # Probably "not found"
            if isinstance(file_like, str):
                if appendmat and not file_like.endswith('.mat'):
                    file_like += '.mat'
>               return open(file_like, mode), True
E               FileNotFoundError: [Errno 2] No such file or directory: './data/mri/epi.mat'

.venv/lib/python3.8/site-packages/scipy/io/matlab/_mio.py:45: FileNotFoundError
=================================== FAILURES ===================================
_________________________ TestUtil.test_load_array_jl __________________________

self = <test_dataform_sparse.TestUtil testMethod=test_load_array_jl>

    def test_load_array_jl(self):
        data = np.array([[1, 0, 0, 0],
                         [2, 2, 0, 0],
                         [3, 3, 3, 0]])

>       testdata = load_array('data/array_jl_dense_v1.mat', key='a')

test/test_dataform_sparse.py:70: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdpy/dataform/sparse.py:19: in load_array
    with h5py.File(fname, 'r') as f:
.venv/lib/python3.8/site-packages/h5py/_hl/files.py:567: in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
.venv/lib/python3.8/site-packages/h5py/_hl/files.py:231: in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
    ???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'data/array_jl_dense_v1.mat', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

h5py/h5f.pyx:106: FileNotFoundError
_______________________________ TestEval.test_2d _______________________________

self = <test_evals.TestEval testMethod=test_2d>

    def test_2d(self):
>       with open('data/testdata-2d.pkl.gz', 'rb') as f:
E       FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d.pkl.gz'

test/test_evals.py:72: FileNotFoundError
_____________________________ TestEval.test_2d_nan _____________________________

self = <test_evals.TestEval testMethod=test_2d_nan>

    def test_2d_nan(self):
>       with open('data/testdata-2d-nan.pkl.gz', 'rb') as f:
E       FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d-nan.pkl.gz'

test/test_evals.py:88: FileNotFoundError
_____________ TestUtil.test_ModelTest_fastl2lir_chunk_bd_modelpath _____________

self = <test_ml.TestUtil testMethod=test_ModelTest_fastl2lir_chunk_bd_modelpath>

    def test_ModelTest_fastl2lir_chunk_bd_modelpath(self):
        X = np.random.rand(30, 500)

        model = FastL2LiR()
        model_path = './test_models/fastl2lir-chunk-bd/model'

        test = ModelTest(model, X)
        test.model_path = model_path
        test.model_format = 'bdmodel'
        test.chunk_axis = 1
>       y_pred = test.run()

test/test_ml.py:205: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdpy.ml.learning.ModelTest object at 0xffff6a1ad3a0>

    def run(self):
        '''Run test.'''

        if self.dtype is not None:
            self.X = self.X.astype(self.dtype)

        if self.model_path is None:
            y_pred = self.model.predict(self.X, **self.model_parameters)
            return y_pred

        if self.model_format == 'pickle':
            if os.path.isfile(self.model_path):
                model_files = [self.model_path]
            elif os.path.isdir(self.model_path):
                model_files = sorted(glob.glob(os.path.join(self.model_path, '*.pkl')))
            else:
                raise ValueError('Invalid model path: %s' % self.model_path)
        elif self.model_format == 'bdmodel':
            if os.path.isfile(self.model_path):
                raise ValueError('BDmodel should be specified as a directory, not a file')

            # W: shape = (n_voxels, shape_features)
            if os.path.isdir(os.path.join(self.model_path, 'W')):
                W_files = sorted(glob.glob(os.path.join(self.model_path, 'W', '*.mat')))
            elif os.path.isfile(os.path.join(self.model_path, 'W.mat')):
                W_files = [os.path.join(self.model_path, 'W.mat')]
            else:
>               raise RuntimeError('W not found.')
E               RuntimeError: W not found.

bdpy/ml/learning.py:507: RuntimeError
____________ TestUtil.test_ModelTest_fastl2lir_chunk_pkl_modelpath _____________

self = <test_ml.TestUtil testMethod=test_ModelTest_fastl2lir_chunk_pkl_modelpath>

    def test_ModelTest_fastl2lir_chunk_pkl_modelpath(self):
        X = np.random.rand(30, 500)

        model = FastL2LiR()
        model_path = './test_models/fastl2lir-chunk-pkl/model'

        test = ModelTest(model, X)
        test.model_path = model_path
        test.chunk_axis = 1
>       y_pred = test.run()

test/test_ml.py:180: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdpy.ml.learning.ModelTest object at 0xffff6a19a400>

    def run(self):
        '''Run test.'''

        if self.dtype is not None:
            self.X = self.X.astype(self.dtype)

        if self.model_path is None:
            y_pred = self.model.predict(self.X, **self.model_parameters)
            return y_pred

        if self.model_format == 'pickle':
            if os.path.isfile(self.model_path):
                model_files = [self.model_path]
            elif os.path.isdir(self.model_path):
                model_files = sorted(glob.glob(os.path.join(self.model_path, '*.pkl')))
            else:
>               raise ValueError('Invalid model path: %s' % self.model_path)
E               ValueError: Invalid model path: ./test_models/fastl2lir-chunk-pkl/model

bdpy/ml/learning.py:496: ValueError
____________ TestUtil.test_ModelTest_fastl2lir_nochunk_bd_modelpath ____________

self = <test_ml.TestUtil testMethod=test_ModelTest_fastl2lir_nochunk_bd_modelpath>

    def test_ModelTest_fastl2lir_nochunk_bd_modelpath(self):
        X = np.random.rand(30, 500)

        model = FastL2LiR()
        model_path = './test_models/fastl2lir-nochunk-bd/model'

        test = ModelTest(model, X)
        test.model_path = model_path
        test.model_format = 'bdmodel'
>       y_pred = test.run()

test/test_ml.py:192: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdpy.ml.learning.ModelTest object at 0xffff6a257e50>

    def run(self):
        '''Run test.'''

        if self.dtype is not None:
            self.X = self.X.astype(self.dtype)

        if self.model_path is None:
            y_pred = self.model.predict(self.X, **self.model_parameters)
            return y_pred

        if self.model_format == 'pickle':
            if os.path.isfile(self.model_path):
                model_files = [self.model_path]
            elif os.path.isdir(self.model_path):
                model_files = sorted(glob.glob(os.path.join(self.model_path, '*.pkl')))
            else:
                raise ValueError('Invalid model path: %s' % self.model_path)
        elif self.model_format == 'bdmodel':
            if os.path.isfile(self.model_path):
                raise ValueError('BDmodel should be specified as a directory, not a file')

            # W: shape = (n_voxels, shape_features)
            if os.path.isdir(os.path.join(self.model_path, 'W')):
                W_files = sorted(glob.glob(os.path.join(self.model_path, 'W', '*.mat')))
            elif os.path.isfile(os.path.join(self.model_path, 'W.mat')):
                W_files = [os.path.join(self.model_path, 'W.mat')]
            else:
>               raise RuntimeError('W not found.')
E               RuntimeError: W not found.

bdpy/ml/learning.py:507: RuntimeError
___________ TestUtil.test_ModelTest_fastl2lir_nochunk_pkl_modelpath ____________

self = <test_ml.TestUtil testMethod=test_ModelTest_fastl2lir_nochunk_pkl_modelpath>

    def test_ModelTest_fastl2lir_nochunk_pkl_modelpath(self):
        X = np.random.rand(30, 500)

        model = FastL2LiR()
        model_path = './test_models/fastl2lir-nochunk-pkl/model.pkl'

        test = ModelTest(model, X)
        test.model_path = model_path
>       y_pred = test.run()

test/test_ml.py:168: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdpy.ml.learning.ModelTest object at 0xffff6a1c35b0>

    def run(self):
        '''Run test.'''

        if self.dtype is not None:
            self.X = self.X.astype(self.dtype)

        if self.model_path is None:
            y_pred = self.model.predict(self.X, **self.model_parameters)
            return y_pred

        if self.model_format == 'pickle':
            if os.path.isfile(self.model_path):
                model_files = [self.model_path]
            elif os.path.isdir(self.model_path):
                model_files = sorted(glob.glob(os.path.join(self.model_path, '*.pkl')))
            else:
>               raise ValueError('Invalid model path: %s' % self.model_path)
E               ValueError: Invalid model path: ./test_models/fastl2lir-nochunk-pkl/model.pkl

bdpy/ml/learning.py:496: ValueError
_________________ TestUtil.test_ModelTest_sklearn_nochunk_pkl __________________

self = <test_ml.TestUtil testMethod=test_ModelTest_sklearn_nochunk_pkl>

    def test_ModelTest_sklearn_nochunk_pkl(self):
        X = np.random.rand(30, 500)

        model_path = './test_models/lir-nochunk-pkl/model.pkl'
>       with open(model_path, 'rb') as f:
E       FileNotFoundError: [Errno 2] No such file or directory: './test_models/lir-nochunk-pkl/model.pkl'

test/test_ml.py:142: FileNotFoundError
____________ TestUtil.test_ModelTest_sklearn_nochunk_pkl_modelpath _____________

self = <test_ml.TestUtil testMethod=test_ModelTest_sklearn_nochunk_pkl_modelpath>

    def test_ModelTest_sklearn_nochunk_pkl_modelpath(self):
        X = np.random.rand(30, 500)

        model = LinearRegression()
        model_path = './test_models/lir-nochunk-pkl/model.pkl'

        test = ModelTest(model, X)
        test.model_path = model_path
>       y_pred = test.run()

test/test_ml.py:157: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <bdpy.ml.learning.ModelTest object at 0xffff8518f7c0>

    def run(self):
        '''Run test.'''

        if self.dtype is not None:
            self.X = self.X.astype(self.dtype)

        if self.model_path is None:
            y_pred = self.model.predict(self.X, **self.model_parameters)
            return y_pred

        if self.model_format == 'pickle':
            if os.path.isfile(self.model_path):
                model_files = [self.model_path]
            elif os.path.isdir(self.model_path):
                model_files = sorted(glob.glob(os.path.join(self.model_path, '*.pkl')))
            else:
>               raise ValueError('Invalid model path: %s' % self.model_path)
E               ValueError: Invalid model path: ./test_models/lir-nochunk-pkl/model.pkl

bdpy/ml/learning.py:496: ValueError
=============================== warnings summary ===============================
../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_bdata.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_bdata_metadata.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_bdata_utils.py)
    class TestLoader(object):

.venv/lib/python3.8/site-packages/fastl2lir/fastl2lir.py:10
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/fastl2lir/fastl2lir.py:10: PendingDeprecationWarning: Importing from numpy.matlib is deprecated since 1.19.0. The matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 
    from numpy.matlib import repmat

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_dataform_sparse.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_distcomp.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_feature.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_featureselector.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_ml_utils.py)
    class TestLoader(object):

.venv/lib/python3.8/site-packages/nibabel/quaternions.py:31
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nibabel/quaternions.py:31: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    MAX_FLOAT = np.maximum_sctype(np.float)

.venv/lib/python3.8/site-packages/nibabel/quaternions.py:32
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nibabel/quaternions.py:32: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    FLOAT_EPS = np.finfo(np.float).eps

.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:75
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:75: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype = np.dtype([('x', np.float),

.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:76
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:76: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    ('y', np.float),

.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:77
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:77: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    ('z', np.float)])

.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:82
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:82: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    def __init__(self, coord_names, name='', coord_dtype=np.float):

.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:423
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/nipy/core/reference/coordinate_system.py:423: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    def __init__(self, coord_names, name='', coord_dtype=np.float):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_mri.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_preproc.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_stats.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_util.py)
    class TestLoader(object):

../../usr/local/lib/python3.8/unittest/loader.py:66
  /usr/local/lib/python3.8/unittest/loader.py:66: PytestCollectionWarning: cannot collect test class 'TestLoader' because it has a __init__ constructor (from: test/test_util_math.py)
    class TestLoader(object):

test/test_ml.py: 20 warnings
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/fastl2lir/fastl2lir.py:243: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    def submean(a): return a - np.matrix(np.mean(a, axis=1)).T

test/test_ml.py: 10 warnings
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/fastl2lir/fastl2lir.py:246: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    np.dot(np.matrix(np.std(x, axis=1, ddof=1)).T,

test/test_ml.py: 10 warnings
  /workspaces/bdpy/.venv/lib/python3.8/site-packages/fastl2lir/fastl2lir.py:247: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    np.matrix(np.std(y, axis=1, ddof=1)))

test/test_preproc.py::TestPreprocessor::test_select_top_axisone
test/test_preproc.py::TestPreprocessor::test_select_top_default
  /workspaces/bdpy/bdpy/preproc/select_top.py:44: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    rank = np.zeros(num_elem, dtype=np.int)

test/test_preproc.py::TestPreprocessor::test_select_top_axisone
  /workspaces/bdpy/bdpy/preproc/select_top.py:54: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    selected_index = np.array(range(0, num_elem), dtype=np.int)[selected_index_bool]

test/test_preproc.py::TestPreprocessor::test_select_top_default
  /workspaces/bdpy/bdpy/preproc/select_top.py:51: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    selected_index = np.array(range(0, num_elem), dtype=np.int)[selected_index_bool]

test/test_stats.py::TestStats::test_corrmat_default
test/test_stats.py::TestStats::test_corrmat_default
test/test_stats.py::TestStats::test_corrmat_varcol
test/test_stats.py::TestStats::test_corrmat_varcol
  /workspaces/bdpy/bdpy/stats/corr.py:112: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    submean = lambda a: a - np.matrix(np.mean(a, axis=1)).T

test/test_stats.py::TestStats::test_corrmat_default
test/test_stats.py::TestStats::test_corrmat_default
test/test_stats.py::TestStats::test_corrmat_varcol
test/test_stats.py::TestStats::test_corrmat_varcol
  /workspaces/bdpy/bdpy/stats/corr.py:114: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    cmat = (np.dot(submean(x), submean(y).T) / (nobs - 1)) / np.dot(np.matrix(np.std(x, axis=1, ddof=1)).T, np.matrix(np.std(y, axis=1, ddof=1)))

test/test_util.py::TestUtil::test_divide_chunks
test/test_util.py::TestUtil::test_divide_chunks
  /workspaces/bdpy/bdpy/util/utils.py:93: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    n_chunk = np.int(np.ceil(len(input_list) / chunk_size))

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED test/test_dataform_sparse.py::TestUtil::test_load_array_jl - FileNotFo...
FAILED test/test_evals.py::TestEval::test_2d - FileNotFoundError: [Errno 2] N...
FAILED test/test_evals.py::TestEval::test_2d_nan - FileNotFoundError: [Errno ...
FAILED test/test_ml.py::TestUtil::test_ModelTest_fastl2lir_chunk_bd_modelpath
FAILED test/test_ml.py::TestUtil::test_ModelTest_fastl2lir_chunk_pkl_modelpath
FAILED test/test_ml.py::TestUtil::test_ModelTest_fastl2lir_nochunk_bd_modelpath
FAILED test/test_ml.py::TestUtil::test_ModelTest_fastl2lir_nochunk_pkl_modelpath
FAILED test/test_ml.py::TestUtil::test_ModelTest_sklearn_nochunk_pkl - FileNo...
FAILED test/test_ml.py::TestUtil::test_ModelTest_sklearn_nochunk_pkl_modelpath
ERROR test/test_mri.py::TestMri::test_add_load_epi_pass0001 - FileNotFoundErr...
ERROR test/test_mri.py::TestMri::test_get_roiflag_pass0001 - FileNotFoundErro...
ERROR test/test_mri.py::TestMri::test_get_roiflag_pass0002 - FileNotFoundErro...
============= 9 failed, 86 passed, 75 warnings, 3 errors in 2.95s ==============

[ganow]

I'm trying to resolve this issue in #66

[ganow]

Partly solved in #66. We have decided that we tentatively skip some part of the problem (test_metrics.py and test_mri.py)