New patching in dev branch not functional with setup.py installation

[muellerdo]

Newest version of scikit-image module does not have a pad() function under skimage.util:

Check out new CI checks:

• for requirement.txt: https://github.com/frankkramer-lab/MIScnn/actions/runs/1915561905
• for setup.py: https://github.com/frankkramer-lab/MIScnn/actions/runs/1915561911

Local pytest:

mudomini@misit004:~/projects/MIScnn$ pytest -v
=========================================================================================== test session starts ============================================================================================
platform linux -- Python 3.8.0, pytest-7.0.1, pluggy-1.0.0 -- /usr/bin/python
cachedir: .pytest_cache
rootdir: /home/mudomini/projects/MIScnn
plugins: typeguard-2.13.3
collected 0 items / 14 errors                                                                                                                                                                              

================================================================================================== ERRORS ==================================================================================================
_______________________________________________________________________________ ERROR collecting tests/test_architectures.py _______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_architectures.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_architectures.py:28: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
--------------------------------------------------------------------------------------------- Captured stderr ----------------------------------------------------------------------------------------------
2022-03-01 11:12:13.590077: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-03-01 11:12:13.590125: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
____________________________________________________________________________________ ERROR collecting tests/test_cli.py ____________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_cli.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_cli.py:20: in <module>
    import miscnn.cli.data_exploration as data_exp
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_____________________________________________________________________________ ERROR collecting tests/test_dataaugmentation.py ______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_dataaugmentation.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_dataaugmentation.py:29: in <module>
    from miscnn import Data_Augmentation
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_______________________________________________________________________________ ERROR collecting tests/test_datagenerator.py _______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_datagenerator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_datagenerator.py:29: in <module>
    from miscnn import Data_IO, Preprocessor, Data_Augmentation
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
__________________________________________________________________________________ ERROR collecting tests/test_dataio.py ___________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_dataio.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_dataio.py:28: in <module>
    from miscnn import Data_IO
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_____________________________________________________________________________ ERROR collecting tests/test_ensemblelearning.py ______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_ensemblelearning.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_ensemblelearning.py:28: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network, Data_Augmentation
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
________________________________________________________________________________ ERROR collecting tests/test_evaluations.py ________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_evaluations.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_evaluations.py:28: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_______________________________________________________________________________ ERROR collecting tests/test_iointerfaces.py ________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_iointerfaces.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_iointerfaces.py:31: in <module>
    import miscnn.data_loading.sample as MIScnn_sample
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
__________________________________________________________________________________ ERROR collecting tests/test_metrics.py __________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_metrics.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_metrics.py:28: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
________________________________________________________________________________ ERROR collecting tests/test_multimodel.py _________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_multimodel.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_multimodel.py:30: in <module>
    from miscnn.multi_model.model import Model as BaseModel
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_______________________________________________________________________________ ERROR collecting tests/test_neuralnetwork.py _______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_neuralnetwork.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_neuralnetwork.py:28: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network, Data_Augmentation
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
______________________________________________________________________________ ERROR collecting tests/test_patchoperations.py ______________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_patchoperations.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_patchoperations.py:28: in <module>
    from miscnn import Data_IO
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_______________________________________________________________________________ ERROR collecting tests/test_preprocessor.py ________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_preprocessor.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_preprocessor.py:29: in <module>
    from miscnn import Data_IO, Preprocessor
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)
_______________________________________________________________________________ ERROR collecting tests/test_subfunctions.py ________________________________________________________________________________
ImportError while importing test module '/home/mudomini/projects/MIScnn/tests/test_subfunctions.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_subfunctions.py:30: in <module>
    from miscnn import Data_IO, Preprocessor, Neural_Network
miscnn/__init__.py:21: in <module>
    from miscnn.processing.preprocessor import Preprocessor
miscnn/processing/preprocessor.py:35: in <module>
    from miscnn.processing.patching.partitioner import Partitioner
miscnn/processing/patching/partitioner.py:20: in <module>
    from miscnn.processing.patching.patch_operations import slice_matrix, concat_matrices, pad_patch, crop_patch
miscnn/processing/patching/patch_operations.py:24: in <module>
    from skimage.util import pad as ski_pad
E   ImportError: cannot import name 'pad' from 'skimage.util' (/usr/local/lib/python3.8/dist-packages/skimage/util/__init__.py)

[Deathlymad]

Seems i tested this with an old skimage version. It seems the pad function moved to numpy