nwbtest() fails in Matlab

[laurelrr]

From my nwb directory, I can generate the API with no issues but after running the test suite, a number of tests fail. They seem to relate to python files however so it is not clear if I should be worried by this.

MATLAB Version: 9.7.0.1737446 (R2019b) Update 9
Operating System: Microsoft Windows 11 Pro Insider Preview Version 10.0 (Build 22471)

addpath(genpath(pwd));
generateCore();
nwbtest()
....
================================================================================
Verification failed in tests.system.ElectricalSeriesIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.ElectricalSeriesIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
..

Verification failed in tests.system.ElectrodeGroupIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.ElectrodeGroupIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
..

Verification failed in tests.system.ImagingPlaneIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.ImagingPlaneIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
..

Verification failed in tests.system.NWBFileIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.NWBFileIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
...

Verification failed in tests.system.PhotonSeriesIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.PhotonSeriesIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
..

Verification failed in tests.system.TimeSeriesIOTest/testOutToPyNWB.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testOutToPyNWB) at 15

================================================================================
.

Assertion failed in tests.system.TimeSeriesIOTest/testInFromPyNWB and it did not run to completion.
----------------
Test Diagnostic:
----------------
E
======================================================================
ERROR: PyNWBIOTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: PyNWBIOTest
Traceback (most recent call last):
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\unittest\loader.py", line 154, in loadTestsFromName
module = import(module_name)
File "C:\Users\Laurel\Documents\MATLAB\nwb+tests+system\PyNWBIOTest.py", line 7, in
import h5py
ModuleNotFoundError: No module named 'h5py'

----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)

------------------
Stack Information:
------------------
In C:\Users\Laurel\Documents\MATLAB\nwb\+tests\+system\PyNWBIOTest.m (PyNWBIOTest.testInFromPyNWB) at 22

================================================================================
......... ......
Failure Summary:

 Name                                                 Failed  Incomplete  Reason(s)
==================================================================================================
 tests.system.ElectricalSeriesIOTest/testOutToPyNWB     X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.ElectricalSeriesIOTest/testInFromPyNWB    X         X       Failed by assertion.
--------------------------------------------------------------------------------------------------
 tests.system.ElectrodeGroupIOTest/testOutToPyNWB       X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.ElectrodeGroupIOTest/testInFromPyNWB      X         X       Failed by assertion.
--------------------------------------------------------------------------------------------------
 tests.system.ImagingPlaneIOTest/testOutToPyNWB         X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.ImagingPlaneIOTest/testInFromPyNWB        X         X       Failed by assertion.
--------------------------------------------------------------------------------------------------
 tests.system.NWBFileIOTest/testOutToPyNWB              X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.NWBFileIOTest/testInFromPyNWB             X         X       Failed by assertion.
--------------------------------------------------------------------------------------------------
 tests.system.PhotonSeriesIOTest/testOutToPyNWB         X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.PhotonSeriesIOTest/testInFromPyNWB        X         X       Failed by assertion.
--------------------------------------------------------------------------------------------------
 tests.system.TimeSeriesIOTest/testOutToPyNWB           X                 Failed by verification.
--------------------------------------------------------------------------------------------------
 tests.system.TimeSeriesIOTest/testInFromPyNWB          X         X       Failed by assertion.

results =

1×36 TestResult array with properties:

Name
Passed
Failed
Incomplete
Duration
Details

Totals:
24 Passed, 12 Failed (rerun), 6 Incomplete.
164.855 seconds testing time.

ans =

1×36 TestResult array with properties:

Name
Passed
Failed
Incomplete
Duration
Details

Totals:
24 Passed, 12 Failed (rerun), 6 Incomplete.
164.855 seconds testing time.

[oruebel]

It looks like h5py (and maybe PyNWB) may not be installed in your Python environment. MatNWB should not need those but they are required for round-trip-tests where MatNWB tests that it can read files from PyNWB and vice versa. Instructions for installing PyNWB are here https://pynwb.readthedocs.io/en/stable/getting_started.html#installation

[rly]

This latest error might be an incompatibility between the Windows Store version of Python and anaconda. I found this related issue. In your anaconda prompt, enter where python. The path to the version of Python that is bundled with Anaconda should come first. If the WindowsApps version comes before the Anaconda version, then I think you need to change your path environment variable to make your Anaconda Python path is before (left of) your Windows Python path.

[laurelrr]

No, it looks ok

(pynwb) C:\Users\Laurel\Documents\GitHub\pynwb>where python
C:\Users\Laurel\AppData\Local\Continuum\anaconda3\envs\pynwb\python.exe
C:\Users\Laurel\AppData\Local\Microsoft\WindowsApps\python.exe

[rly]

Did you happen to install Python from the Windows/Microsoft Store? In looking up this issue, I have found several reports of issues with that version. e.g., https://dev.to/naruaika/why-i-didn-t-install-python-from-the-microsoft-store-5cbd

If you did, then I would recommend uninstalling the version of Python that came from Windows/Microsoft. Then tox and anaconda will not get confused and try to use the one from Windows, which is what the path 'C:\Users\Laurel\AppData\Local\Microsoft\WindowsApps\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\python.exe' in the error message refers to. If you want to reinstall Python outside of Anaconda, I would recommend installing Python directly from the Python website.

[laurelrr]

I don't recall specifically installing python from the Microsoft store. I installed Anaconda when I first got the machine, around 3 years ago. Since then, I usually set up a conda environment for a specific python version. I also have WSL installed on this machine and that does have various python versions, which I installed through the command line in ubuntu, usually using miniconda.

[rly]

That's odd. Since you said that you are OK with this for the time being, do you want to continue troubleshooting? If so, then I think the next step would be to uninstall all non-Anaconda, non-WSL versions of Python on your machine: Go to Settings > Apps and Features > scroll down and select Python > click Uninstall. Then, in a conda environment with the developer dependencies installed, please try running tox again. If there is still an error, please report here your PATH environment variable.