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AllenInstitute / mouse_connectivity_models

Python package providing mesoscale connectivity models for mouse.
http://mouse-connectivity-models.readthedocs.io/en/latest/
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can't import fn_temp_dir when running pytest mcmodels #38

Closed ChristianNitzsche closed 4 years ago

ChristianNitzsche commented 5 years ago

Hi,

I tried to install the package, which seemed fine in the first place. But when trying 'pytest mcmodels' i get the following error:

____ ERROR collecting mcmodels/core/tests/test_voxel_modelapi.py ____ ImportError while importing test module 'C:\Users\Christian\Desktop\Projekte\mouse_connectivity_models\mcmodels\core\tests\test_voxel_model_api.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: mcmodels\core\tests\test_voxel_model_api.py:9: in from allensdk.test_utilities.temp_dir import fn_temp_dir E ImportError: cannot import name 'fn_temp_dir' from 'allensdk.test_utilities.temp_dir' (C:\Users\Christian\Anaconda3\lib\site-packages\allensdk\test_utilities\temp_dir.py) _ ERROR collecting mcmodels/core/tests/test_voxel_model_cache.py __ ImportError while importing test module 'C:\Users\Christian\Desktop\Projekte\mouse_connectivity_models\mcmodels\core\tests\test_voxel_model_cache.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: mcmodels\core\tests\test_voxel_model_cache.py:11: in from allensdk.test_utilities.temp_dir import fn_temp_dir E ImportError: cannot import name 'fn_temp_dir' from 'allensdk.test_utilities.temp_dir' (C:\Users\Christian\Anaconda3\lib\site-packages\allensdk\test_utilities\temp_dir.py)

I am using:

Python 3.7.4 allensdk==0.16.3 mouse-connectivity-models==0.0.1

Is it possible, that the method fn_temp_dir was renamed into temp_dir in allensdk.test_utilities.temp_dir?

Thanks for your time Christian

kamdh commented 5 years ago

I just tried pytest, and it's working for me (on Linux). It's possible you may have a problem with your python configuration. I'd suggest working with an Anaconda environment specific for this. If you have access to a Linux machine, that would also be a good thing to try.

Perhaps the output of pytest that I ran can be helpful:

(py36) [kameron@fiddlehead mouse_connectivity_models]$ pytest mcmodels
============================= test session starts ==============================
platform linux -- Python 3.6.8, pytest-4.3.1, py-1.8.0, pluggy-0.9.0
rootdir: /home/kameron/src/mouse_connectivity_models, inifile:
plugins: remotedata-0.3.1, openfiles-0.3.2, doctestplus-0.3.0, arraydiff-0.3
collected 109 items                                                            

mcmodels/core/tests/test_base.py .....                                   [  4%]
mcmodels/core/tests/test_experiment.py .......                           [ 11%]
mcmodels/core/tests/test_masks.py ..........                             [ 20%]
mcmodels/core/tests/test_utils.py ..                                     [ 22%]
mcmodels/core/tests/test_voxel_model_api.py ........                     [ 29%]
mcmodels/core/tests/test_voxel_model_cache.py ...........                [ 39%]
mcmodels/models/homogeneous/tests/test_homogeneous_model.py ...          [ 42%]
mcmodels/models/homogeneous/tests/test_subset_selection.py ...           [ 44%]
mcmodels/models/voxel/tests/test_regionalized_model.py .......           [ 51%]
mcmodels/models/voxel/tests/test_voxel_connectivity_array.py ........... [ 61%]
......                                                                   [ 66%]
mcmodels/models/voxel/tests/test_voxel_model.py ....                     [ 70%]
mcmodels/regressors/nonnegative_linear/tests/test_base.py ....           [ 74%]
mcmodels/regressors/nonnegative_linear/tests/test_ridge.py ...           [ 77%]
mcmodels/regressors/nonparametric/tests/test_kernels.py .......          [ 83%]
mcmodels/regressors/nonparametric/tests/test_nadaraya_watson.py ........ [ 90%]
....                                                                     [ 94%]
mcmodels/tests/test_utils.py ......                                      [100%]

========================== 109 passed in 5.65 seconds ==========================
(py36) [kameron@fiddlehead mouse_connectivity_models]$
justuskebschull commented 4 years ago

Hey,

I am having the identical issue as Christian, both on Windows and Linux, inside a conda virtual environment.

$ pytest mcmodels
============================================================================== test session starts ===============================================================================
platform linux -- Python 3.7.4, pytest-5.2.1, py-1.8.0, pluggy-0.13.0
rootdir: /home/nomi/Documents/mouse_connectivity_models
collected 90 items / 2 errors / 88 selected                                                                                                                                      

===================================================================================== ERRORS =====================================================================================
__________________________________________________________ ERROR collecting mcmodels/core/tests/test_voxel_model_api.py __________________________________________________________
ImportError while importing test module '/home/nomi/Documents/mouse_connectivity_models/mcmodels/core/tests/test_voxel_model_api.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
mcmodels/core/tests/test_voxel_model_api.py:9: in <module>
    from allensdk.test_utilities.temp_dir import fn_temp_dir
E   ImportError: cannot import name 'fn_temp_dir' from 'allensdk.test_utilities.temp_dir' (/home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/allensdk/test_utilities/temp_dir.py)
_________________________________________________________ ERROR collecting mcmodels/core/tests/test_voxel_model_cache.py _________________________________________________________
ImportError while importing test module '/home/nomi/Documents/mouse_connectivity_models/mcmodels/core/tests/test_voxel_model_cache.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
mcmodels/core/tests/test_voxel_model_cache.py:11: in <module>
    from allensdk.test_utilities.temp_dir import fn_temp_dir
E   ImportError: cannot import name 'fn_temp_dir' from 'allensdk.test_utilities.temp_dir' (/home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/allensdk/test_utilities/temp_dir.py)
================================================================================ warnings summary ================================================================================
/home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/jinja2/utils.py:485
  /home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/jinja2/utils.py:485: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
    from collections import MutableMapping

/home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/jinja2/runtime.py:318
  /home/nomi/.linuxbrew/opt/python/lib/python3.7/site-packages/jinja2/runtime.py:318: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
    from collections import Mapping

-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================== 2 warnings, 2 error in 2.10s ==========================================================================
(allenenv) nomi@bio-h4tmkb2:~/Documents/mouse_connectivity_models$ ls
nbingo commented 4 years ago

@ChristianNitzsche Hey, I had the same error and I think I found the source of the error. Try changing the files 

/mcmodels/mouse_connectivity_models/mcmodels/core/tests/test_voxel_model_api.py
/mcmodels/mouse_connectivity_models/mcmodels/core/tests/test_voxel_model_cache.py

to the ones that I have attached here. I think the developers possibly have a different version of allenSDK and there are broken dependencies in the publicly available version.

Archive.zip

kamdh commented 4 years ago

Thanks @nbingo ... if you think the tests need to be updated, please submit a pull request and we can try integrating your fixes.

nbingo commented 4 years ago

@kharris Just created the PR!

DrJigsaw commented 4 years ago

Thank you @nbingo and @kharris! @ChristianNitzsche, @justuskebschull I'm going to leave this issue open for a few days in case the error is not corrected for you. Please let us know if the issue is not resolved.

kamdh commented 4 years ago

I started from a fresh clone of this module on python 3.7, newest version of allensdk, and it passes the tests.