Trouble with pytest - Githubissues

aringh commented 5 years ago

I am having trouble running the test in odl. I just installed a new conda environment, but still the troubles prevail. When I run pytest in the root directory, it starts showing images (examples?) and then crashes with a large error message. Here is the first few lines:

============================= test session starts ==============================
platform linux -- Python 3.6.2, pytest-3.2.1, py-1.4.34, pluggy-0.4.0
rootdir: [...]/git/odl, inifile: setup.cfg
plugins: pep8-1.0.6
collected 0 items / 304 errors                                                  

==================================== ERRORS ====================================
_______________________ ERROR collecting odl/__init__.py _______________________
odl/__init__.py:75: in <module>
    from . import tomo
odl/tomo/__init__.py:19: in <module>
    from .operators import *
odl/tomo/operators/__init__.py:14: in <module>
    from .ray_trafo import *
odl/tomo/operators/ray_trafo.py:21: in <module>
    from odl.tomo.backends import (
odl/tomo/backends/__init__.py:21: in <module>
    from .astra_cuda import *
odl/tomo/backends/astra_cuda.py:17: in <module>
    from packaging.version import parse as parse_version
E   ModuleNotFoundError: No module named 'packaging'
___________________ ERROR collecting odl/contrib/__init__.py ___________________
../../miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/py/_path/local.py:662: in pyimport
    __import__(modname)
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
______________ ERROR collecting odl/contrib/datasets/__init__.py _______________
../../miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/py/_path/local.py:662: in pyimport
    __import__(modname)
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
________________ ERROR collecting odl/contrib/datasets/util.py _________________
../../miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/py/_path/local.py:662: in pyimport
    __import__(modname)
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
_____________ ERROR collecting odl/contrib/datasets/ct/__init__.py _____________
../../miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/py/_path/local.py:662: in pyimport
    __import__(modname)
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
_______________ ERROR collecting odl/contrib/datasets/ct/fips.py _______________
odl/contrib/datasets/ct/fips.py:21: in <module>
    from odl.tomo import FanBeamGeometry
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
_______________ ERROR collecting odl/contrib/datasets/ct/mayo.py _______________
odl/contrib/datasets/ct/mayo.py:22: in <module>
    import dicom
E   ModuleNotFoundError: No module named 'dicom'
_________ ERROR collecting odl/contrib/datasets/ct/mayo_dicom_dict.py __________
../../miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/py/_path/local.py:662: in pyimport
    __import__(modname)
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
____ ERROR collecting odl/contrib/datasets/ct/examples/fips_reconstruct.py _____
odl/contrib/datasets/ct/examples/fips_reconstruct.py:3: in <module>
    import odl
odl/__init__.py:57: in <module>
    __all__ += set.__all__
E   AttributeError: type object 'set' has no attribute '__all__'
____ ERROR collecting odl/contrib/datasets/ct/examples/mayo_reconstruct.py _____

When I try to run python -c "import odl; odl.test()":

when run from a directory that is not the odl root directory I get the error

Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: module 'odl' has no attribute 'test'

when run from the root directory I get

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "[...]/git/odl/odl/__init__.py", line 75, in <module>
    from . import tomo
  File "[...]/git/odl/odl/tomo/__init__.py", line 19, in <module>
    from .operators import *
  File "[...]/git/odl/odl/tomo/operators/__init__.py", line 14, in <module>
    from .ray_trafo import *
  File "[...]/git/odl/odl/tomo/operators/ray_trafo.py", line 21, in <module>
    from odl.tomo.backends import (
  File "[...]/git/odl/odl/tomo/backends/__init__.py", line 21, in <module>
    from .astra_cuda import *
  File "[...]/git/odl/odl/tomo/backends/astra_cuda.py", line 17, in <module>
    from packaging.version import parse as parse_version
ModuleNotFoundError: No module named 'packaging'

List of packages installed in the conda environemt:

# packages in environment at [...]/miniconda3/envs/odl-py36_tmp:
#
_libgcc_mutex             0.1                        free  
alabaster                 0.7.10                   py36_0  
astroid                   1.5.3                    py36_0  
babel                     2.5.0                    py36_0  
blas                      1.0                    openblas  
bleach                    1.5.0                    py36_0  
certifi                   2016.2.28                py36_0  
chardet                   3.0.4                    py36_0  
cycler                    0.10.0                   py36_0  
dbus                      1.10.20                       0  
decorator                 4.1.2                    py36_0  
docutils                  0.14                     py36_0  
entrypoints               0.2.3                    py36_0  
execnet                   1.3.0                    py36_1  
expat                     2.1.0                         0  
fontconfig                2.12.1                        3  
freetype                  2.5.5                         2  
future                    0.16.0                   py36_1  
glib                      2.50.2                        1  
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
html5lib                  0.9999999                py36_0  
icu                       54.1                          0  
imagesize                 0.7.1                    py36_0  
ipykernel                 4.6.1                    py36_0  
ipython                   6.1.0                    py36_0  
ipython_genutils          0.2.0                    py36_0  
isort                     4.2.15                   py36_0  
jedi                      0.10.2                   py36_2  
jinja2                    2.9.6                    py36_0  
jpeg                      9b                            0  
jsonschema                2.6.0                    py36_0  
jupyter_client            5.1.0                    py36_0  
jupyter_core              4.3.0                    py36_0  
lazy-object-proxy         1.3.1                    py36_0  
libffi                    3.2.1                         1  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          0  
libpng                    1.6.30                        1  
libsodium                 1.0.10                        0  
libxcb                    1.12                          1  
libxml2                   2.9.4                         0  
markupsafe                1.0                      py36_0  
matplotlib                2.0.2               np113py36_0  
mistune                   0.7.4                    py36_0  
nbconvert                 5.2.1                    py36_0  
nbformat                  4.4.0                    py36_0  
nomkl                     3.0                           0  
numpy                     1.13.1             py36_nomkl_0  [nomkl]
numpydoc                  0.7.0                    py36_0  
openblas                  0.2.19                        0  
openssl                   1.0.2l                        0  
pandocfilters             1.4.2                    py36_0  
path.py                   10.3.1                   py36_0  
pcre                      8.39                          1  
pep8                      1.7.0                    py36_0  
pexpect                   4.2.1                    py36_0  
pickleshare               0.7.4                    py36_0  
pip                       9.0.1                    py36_1  
prompt_toolkit            1.0.15                   py36_0  
psutil                    5.2.2                    py36_0  
ptyprocess                0.5.2                    py36_0  
py                        1.4.34                   py36_0  
pycodestyle               2.3.1                    py36_0  
pyflakes                  1.6.0                    py36_0  
pygments                  2.2.0                    py36_0  
pylint                    1.7.2                    py36_0  
pyparsing                 2.2.0                    py36_0  
pyqt                      5.6.0                    py36_2  
pytest                    3.2.1                    py36_0  
pytest-cache              1.0                      py36_0  
pytest-pep8               1.0.6                    py36_0  
python                    3.6.2                         0  
python-dateutil           2.6.1                    py36_0  
pytz                      2017.2                   py36_0  
pyzmq                     16.0.2                   py36_0  
qt                        5.6.2                         5  
qtawesome                 0.4.4                    py36_0  
qtconsole                 4.3.1                    py36_0  
qtpy                      1.3.1                    py36_0  
readline                  6.2                           2  
requests                  2.14.2                   py36_0  
rope                      0.9.4                    py36_1  
scipy                     0.19.1          np113py36_nomkl_0  [nomkl]
setuptools                36.4.0                   py36_1  
simplegeneric             0.8.1                    py36_1  
singledispatch            3.4.0.3                  py36_0  
sip                       4.18                     py36_0  
six                       1.10.0                   py36_0  
snowballstemmer           1.2.1                    py36_0  
sphinx                    1.6.3                    py36_0  
sphinxcontrib             1.0                      py36_0  
sphinxcontrib-websupport  1.0.1                    py36_0  
spyder                    3.2.3                    py36_0  
sqlite                    3.13.0                        0  
testpath                  0.3.1                    py36_0  
tk                        8.5.18                        0  
tornado                   4.5.2                    py36_0  
traitlets                 4.3.2                    py36_0  
wcwidth                   0.1.7                    py36_0  
wheel                     0.29.0                   py36_0  
wrapt                     1.10.11                  py36_0  
xz                        5.2.3                         0  
zeromq                    4.1.5                         0  
zlib                      1.2.11                        0

Does anyone know what the problem could be?

aringh commented 5 years ago

Some soul searching later, I realize that the installation of odl might not have worked properly... When installing it using pip (following instructions here, i.e., running pip install --editable in the root directory of odl), I got the following error message

(odl-py36_tmp) [...]/git/odl$ pip install --editable .
Obtaining file:///[...]/git/odl
Collecting setuptools>=39.2.0 (from odl===file-.odl-VERSION)
  Downloading https://files.pythonhosted.org/packages/d9/de/554b6310ac87c5b921bc45634b07b11394fe63bc4cb5176f5240addf18ab/setuptools-41.6.0-py2.py3-none-any.whl (582kB)
    100% |████████████████████████████████| 583kB 653kB/s 
Requirement already satisfied: future>=0.14 in [...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages (from odl===file-.odl-VERSION)
Collecting packaging>=15.0 (from odl===file-.odl-VERSION)
  Downloading https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl
Collecting numpy!=1.14.0,!=1.14.1,!=1.14.2,>=1.13.3 (from odl===file-.odl-VERSION)
  Downloading https://files.pythonhosted.org/packages/0e/46/ae6773894f7eacf53308086287897ec568eac9768918d913d5b9d366c5db/numpy-1.17.3-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
    100% |████████████████████████████████| 20.0MB 86kB/s 
Requirement already satisfied: scipy>=0.14 in [...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages (from odl===file-.odl-VERSION)
Requirement already satisfied: pyparsing>=2.0.2 in [...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages (from packaging>=15.0->odl===file-.odl-VERSION)
Requirement already satisfied: six in [...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages (from packaging>=15.0->odl===file-.odl-VERSION)
Installing collected packages: setuptools, packaging, numpy, odl
  Found existing installation: setuptools 36.4.0
    Uninstalling setuptools-36.4.0:
      Successfully uninstalled setuptools-36.4.0
  Rolling back uninstall of setuptools
Exception:
Traceback (most recent call last):
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/req/req_install.py", line 851, in install
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files
    isolated=self.isolated,
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/wheel.py", line 247, in move_wheel_files
    prefix=prefix,
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/pip/locations.py", line 141, in distutils_scheme
    d.parse_config_files()
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/setuptools/dist.py", line 437, in parse_config_files
    parse_configuration(self, self.command_options)
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/setuptools/config.py", line 110, in parse_configuration
    options.parse()
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/setuptools/config.py", line 382, in parse
    section_parser_method(section_options)
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/setuptools/config.py", line 520, in parse_section_entry_points
    self['entry_points'] = parsed
  File "[...]/miniconda3/envs/odl-py36_tmp/lib/python3.6/site-packages/setuptools/config.py", line 163, in __setitem__
    raise KeyError(option_name)
KeyError: 'entry_points'

In the send, I seem to end up with no installation of packaging, and setuptools version 36.4.0 and not 39.2.0 as required in according to setup.cfg. However, I do not seem to be ablo to get a later version than 36.4.0 in conda, and installing packaging (16.8.0) does not solve the problem. But it does alter the error; when running pytest the first lines now look like

=========================================================================================== test session starts ============================================================================================
platform linux -- Python 3.6.2, pytest-3.2.1, py-1.4.34, pluggy-0.4.0
rootdir: [...]/git/odl, inifile: setup.cfg
plugins: pep8-1.0.6
collected 3773 items / 56 errors                                                                                                                                                                            

================================================================================================== ERRORS ==================================================================================================
_____________________________________________________________________________ ERROR collecting odl/contrib/datasets/ct/mayo.py _____________________________________________________________________________
odl/contrib/datasets/ct/mayo.py:22: in <module>
    import dicom
E   ModuleNotFoundError: No module named 'dicom'
__________________________________________________________________ ERROR collecting odl/contrib/datasets/ct/examples/fips_reconstruct.py ___________________________________________________________________
odl/contrib/datasets/ct/examples/fips_reconstruct.py:10: in <module>
    ray_transform = odl.tomo.RayTransform(space, geometry)
odl/tomo/operators/ray_trafo.py:397: in __init__
    variant='forward', **kwargs)
odl/tomo/operators/ray_trafo.py:117: in __init__
    raise RuntimeError('no ray transform back-end available; '
E   RuntimeError: no ray transform back-end available; this requires 3rd party packages, please check the install docs
__________________________________________________________________ ERROR collecting odl/contrib/datasets/ct/examples/mayo_reconstruct.py ___________________________________________________________________
odl/contrib/datasets/ct/examples/mayo_reconstruct.py:11: in <module>
    from odl.contrib.datasets.ct import mayo
odl/contrib/datasets/ct/mayo.py:22: in <module>
    import dicom
E   ModuleNotFoundError: No module named 'dicom'
_________________________________________________________________________ ERROR collecting odl/contrib/datasets/images/__init__.py _________________________________________________________________________
odl/contrib/datasets/images/__init__.py:15: in <module>
    from .cambridge import *
odl/contrib/datasets/images/cambridge.py:21: in <module>
    import skimage.transform
E   ModuleNotFoundError: No module named 'skimage'
________________________________________________________________________ ERROR collecting odl/contrib/datasets/images/cambridge.py _________________________________________________________________________
odl/contrib/datasets/images/cambridge.py:21: in <module>
    import skimage.transform
E   ModuleNotFoundError: No module named 'skimage'
________________________________________________________________ ERROR collecting odl/contrib/datasets/images/examples/cambridge_images.py _________________________________________________________________
odl/contrib/datasets/images/examples/cambridge_images.py:3: in <module>
    import odl.contrib.datasets.images as images
odl/contrib/datasets/images/__init__.py:15: in <module>
    from .cambridge import *
odl/contrib/datasets/images/cambridge.py:21: in <module>
    import skimage.transform
E   ModuleNotFoundError: No module named 'skimage'
____________________________________________________________________ ERROR collecting odl/contrib/fom/examples/noise_power_spectrum.py _____________________________________________________________________
odl/contrib/fom/examples/noise_power_spectrum.py:18: in <module>
    odl.tomo.parallel_beam_geometry(space))
odl/tomo/operators/ray_trafo.py:397: in __init__
    variant='forward', **kwargs)
odl/tomo/operators/ray_trafo.py:117: in __init__
    raise RuntimeError('no ray transform back-end available; '
E   RuntimeError: no ray transform back-end available; this requires 3rd party packages, please check the install docs

aringh commented 5 years ago

Actually, looking at it I have a too old version of numpy as well... but I cannot upgrade that either in conda... :disappointed:

aringh commented 5 years ago

So... after updating my conda environment (conda update conda) I can install the later versions of dependencies, and things seem to work better. However, I still get errors on many skipif-parts, but I assume that is related to #1514.

kohr-h commented 5 years ago

So... after updating my conda environment (conda update conda) I can install the later versions of dependencies, and things seem to work better. However, I still get errors on many skipif-parts, but I assume that is related to #1514.

Those errors should be warnings though, or ignored, after applying the temporary fix in https://github.com/odlgroup/odl/commit/d1afcedaf61adb279fabd58e23b50abba2f583f2 Are you really getting errors? If yes, with variants to run the tests, i.e. pytest and odl.test()?

aringh commented 5 years ago

I use pytest, and those are really errors. And I think that this time I have all dependencies correct, with

# packages in environment at [...]/miniconda3/envs/odl-py36_new:
#
future                    0.18.2                    <pip>
numpy                     1.17.3                    <pip>
packaging                 19.2                       py_0
pytest                    5.0.1                    py36_0
scipy                     1.3.1                     <pip>
setuptools                41.6.0                   py36_0

This is the first and last parts of the (very long) output in the terminal

============================= test session starts ==============================
platform linux -- Python 3.6.9, pytest-5.0.1, py-1.8.0, pluggy-0.13.0
rootdir: [...]/git/odl, inifile: setup.cfg, testpaths: odl
plugins: pep8-1.0.6, odl-1.0.0.dev0
collected 5075 items                                                           

odl/deform/linearized.py ...                                             [  0%]
odl/diagnostics/examples.py .                                            [  0%]
odl/discr/diff_ops.py .....                                              [  0%]
odl/discr/discr_mappings.py ..                                           [  0%]
odl/discr/discr_ops.py ...                                               [  0%]
odl/discr/discretization.py ..                                           [  0%]
odl/discr/grid.py ...........................                            [  0%]
odl/discr/lp_discr.py ............                                       [  1%]
odl/discr/partition.py ...................                               [  1%]
odl/operator/default_ops.py ................................             [  2%]
odl/operator/operator.py ..................                              [  2%]
odl/operator/oputils.py ....                                             [  2%]
odl/operator/pspace_ops.py ..................                            [  2%]
odl/operator/tensor_ops.py ............                                  [  3%]
odl/phantom/geometric.py ...                                             [  3%]
odl/set/domain.py ................                                       [  3%]
odl/set/sets.py ................                                         [  3%]
odl/set/space.py ....                                                    [  3%]
odl/solvers/functional/default_functionals.py ..................         [  4%]
odl/solvers/functional/derivatives.py ...                                [  4%]
odl/solvers/functional/example_funcs.py .                                [  4%]
odl/solvers/functional/functional.py .....                               [  4%]
odl/solvers/util/callback.py ............                                [  4%]
odl/solvers/util/steplen.py ..                                           [  4%]
odl/space/base_tensors.py ..                                             [  4%]
odl/space/fspace.py .....                                                [  4%]
odl/space/npy_tensors.py .......................                         [  5%]
odl/space/pspace.py ................                                     [  5%]
odl/space/space_utils.py ....                                            [  5%]
odl/test/test_doc.py EEEEEEEEEEEEEEEEEEEE                                [  6%]
odl/test/test_examples.py EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [  6%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE                                       [  7%]
odl/test/deform/linearized_deform_test.py .................s....s....s.. [  8%]
..s..............s....s.........                                         [  8%]
odl/test/discr/diff_ops_test.py ........................................ [  9%]
........................................................................ [ 11%]
........................................................................ [ 12%]
...................................                                      [ 13%]
odl/test/discr/discr_mappings_test.py ........                           [ 13%]
odl/test/discr/discr_ops_test.py .................................       [ 13%]
odl/test/discr/grid_test.py ........................                     [ 14%]
odl/test/discr/lp_discr_test.py ........................................ [ 15%]
........................................................................ [ 16%]
...............................                                          [ 17%]
odl/test/discr/partition_test.py ...............                         [ 17%]
odl/test/largescale/solvers/nonsmooth/default_functionals_slow_test.py E [ 17%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 19%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 20%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 21%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 23%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 24%]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 26%]
EEEEEEEEEEEEEEEE                                                         [ 26%]
odl/test/largescale/space/tensor_space_slow_test.py EEEEEEEEEEEEEEEEEEEE [ 26%]
EEEEEEEEEEEEEEEE                                                         [ 27%]
odl/test/largescale/tomo/analytic_slow_test.py sssssssssssssssssssssssss [ 27%]
sssssssssssssssssssssss                                                  [ 28%]
odl/test/largescale/tomo/ray_transform_slow_test.py ssssssssssssssssssss [ 28%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 29%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 31%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 32%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 34%]
ssssssssssssssssssssssssssssssssssssssssssssssssssss                     [ 35%]
odl/test/largescale/trafos/fourier_slow_test.py EEssssEEssEEssEE         [ 35%]
odl/test/operator/operator_test.py ..................................... [ 36%]
................................                                         [ 36%]
odl/test/operator/oputils_test.py ..........                             [ 37%]
odl/test/operator/pspace_ops_test.py ......................              [ 37%]
odl/test/operator/tensor_ops_test.py ..........s....s.........s......... [ 38%]
.............                                                            [ 38%]
odl/test/set/domain_test.py .......................                      [ 38%]
odl/test/set/sets_test.py ......                                         [ 38%]
odl/test/set/space_test.py ............                                  [ 39%]
odl/test/solvers/functional/default_functionals_test.py ................ [ 39%]
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odl/test/solvers/functional/functional_test.py ......................... [ 42%]
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odl/test/solvers/iterative/iterative_test.py .................           [ 46%]
odl/test/solvers/nonsmooth/admm_test.py ..                               [ 46%]
odl/test/solvers/nonsmooth/alternating_dual_updates_test.py .            [ 46%]
odl/test/solvers/nonsmooth/difference_convex_test.py .                   [ 46%]
odl/test/solvers/nonsmooth/douglas_rachford_test.py ....                 [ 46%]
odl/test/solvers/nonsmooth/forward_backward_test.py .....                [ 46%]
odl/test/solvers/nonsmooth/primal_dual_hybrid_gradient_test.py ..        [ 46%]
odl/test/solvers/nonsmooth/proximal_operator_test.py ...............     [ 46%]
odl/test/solvers/nonsmooth/proximal_utils_test.py ...................... [ 47%]
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odl/test/solvers/smooth/smooth_test.py ................................. [ 48%]
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odl/test/solvers/util/steplen_test.py ...                                [ 49%]
odl/test/space/fspace_test.py .......................................... [ 50%]
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odl/test/space/pspace_test.py .......................................... [ 53%]
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odl/test/space/space_utils_test.py .                                     [ 54%]
odl/test/space/tensors_test.py ......................................... [ 55%]
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odl/test/system/import_test.py .                                         [ 74%]
odl/test/tomo/backends/astra_cpu_test.py ss                              [ 74%]
odl/test/tomo/backends/astra_cuda_test.py sssss                          [ 74%]
odl/test/tomo/backends/astra_setup_test.py ssssssssssss                  [ 74%]
odl/test/tomo/backends/skimage_test.py s                                 [ 74%]
odl/test/tomo/geometry/geometry_test.py ................................ [ 75%]
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odl/test/tomo/geometry/spect_geometry_test.py .                          [ 75%]
odl/test/tomo/operators/ray_trafo_test.py ssssssssssssssssssssssssssssss [ 76%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 77%]
ssssssssssssssssssss                                                     [ 78%]
odl/test/trafos/fourier_test.py ...................................sssss [ 79%]
ssssssssssss......ss......ss.s.............                              [ 79%]
odl/test/trafos/wavelet_test.py ssssssssssssssssssssssssssssssssssssssss [ 80%]
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odl/test/trafos/backends/pyfftw_bindings_test.py sssssssssssssssssssssss [ 86%]
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odl/test/trafos/backends/pywt_bindings_test.py ssssss                    [ 87%]
odl/test/trafos/util/ft_utils_test.py ..................                 [ 87%]
odl/test/util/normalize_test.py ........................................ [ 88%]
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odl/test/util/numerics_test.py ......................................... [ 89%]
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odl/test/util/utility_test.py ....                                       [ 94%]
odl/test/util/vectorization_test.py .........                            [ 94%]
odl/tomo/analytic/filtered_back_projection.py .                          [ 95%]
odl/tomo/geometry/conebeam.py ............                               [ 95%]
odl/tomo/geometry/detector.py ................                           [ 95%]
odl/tomo/geometry/geometry.py ..                                         [ 95%]
odl/tomo/geometry/parallel.py ..............                             [ 95%]
odl/tomo/util/utility.py ....                                            [ 95%]
odl/trafos/fourier.py ..                                                 [ 96%]
odl/ufunc_ops/ufunc_ops.py ............................................. [ 96%]
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odl/util/normalize.py ....                                               [ 99%]
odl/util/numerics.py ...                                                 [ 99%]
odl/util/testutils.py ....                                               [ 99%]
odl/util/utility.py ................                                     [ 99%]
odl/util/vectorization.py .                                              [100%]

==================================== ERRORS ====================================
_ ERROR at setup of test_file[/home/axel/git/odl/doc/source/guide/vectorization_guide.rst] _
Error evaluating 'skipif' expression
    not pytest.config.getoption('--doctest-doc')
pytest.PytestDeprecationWarning: the `pytest.config` global is deprecated.  Please use `request.config` or `pytest_configure` (if you're a pytest plugin) instead.

[...]
[...]
[...]

_ ERROR at setup of test_fourier_trafo_forward_complex[ domain=uniform_discr([-2., -2., -2.], [ 2.,  2.,  2.], (200, 200, 200), dtype=complex) - impl=ParameterSet(values=('numpy',), marks=(), id=None) ] _
Error evaluating 'skipif' expression
    not pytest.config.getoption('--largescale')
pytest.PytestDeprecationWarning: the `pytest.config` global is deprecated.  Please use `request.config` or `pytest_configure` (if you're a pytest plugin) instead.

=============================== warnings summary ===============================
odl/operator/oputils.py::odl.operator.oputils.as_scipy_operator
  [...]/miniconda3/envs/odl-py36_new/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/iterative.py:2: DeprecationWarning: scipy.sparse.linalg.cg called without specifying `atol`. The default value will be changed in a future release. For compatibility, specify a value for `atol` explicitly, e.g., ``cg(..., atol=0)``, or to retain the old behavior ``cg(..., atol='legacy')``

odl/test/solvers/functional/default_functionals_test.py::test_kullback_leibler_cross_entorpy[ space=power_space_unif_discr - tspace_impl='numpy' ]
  [...]/git/odl/odl/space/npy_tensors.py:430: ComplexWarning: Casting complex values to real discards the imaginary part
    order=order)

odl/test/solvers/functional/default_functionals_test.py::test_kullback_leibler_cross_entorpy[ space=r10 - tspace_impl='numpy' ]
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: overflow encountered in exp
    res = ufunc(*inputs, **kwargs)

odl/test/solvers/functional/default_functionals_test.py::test_kullback_leibler_cross_entorpy[ space=r10 - tspace_impl='numpy' ]
  [...]/git/odl/odl/space/npy_tensors.py:1797: RuntimeWarning: invalid value encountered in multiply
    out.data[:] = a * x1.data + b * x2.data

odl/test/space/pspace_test.py::test_real_setter_product_space[ space=product_space - element=space ]
odl/test/space/pspace_test.py::test_imag_setter_product_space[ space=product_space - element=space ]
odl/test/space/pspace_test.py::test_real_setter_product_space[ space=power_space - element=space ]
odl/test/space/pspace_test.py::test_imag_setter_product_space[ space=power_space - element=space ]
  [...]/git/odl/odl/space/base_tensors.py:666: ComplexWarning: Casting complex values to real discards the imaginary part
    return self.asarray().astype(dtype, copy=False)

odl/test/trafos/util/ft_utils_test.py::test_reciprocal_grid_nd_axes
odl/test/trafos/util/ft_utils_test.py::test_reciprocal_grid_nd_axes
  [...]/git/odl/odl/util/testutils.py:114: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
    if iter1 == iter2:

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arccos_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in arccos
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arccosh_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in arccosh
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arcsin_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in arcsin
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arctanh_func
  [...]/git/odl/odl/ufunc_ops/ufunc_ops.py:334: RuntimeWarning: divide by zero encountered in arctanh
    return getattr(np, name)(x)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arctanh_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: divide by zero encountered in arctanh
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.arctanh_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in arctanh
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.log10_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in log10
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.log1p_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: divide by zero encountered in log1p
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.log2_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in log2
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.log_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in log
    res = ufunc(*inputs, **kwargs)

odl/ufunc_ops/ufunc_ops.py::odl.ufunc_ops.ufunc_ops.sqrt_op
  [...]/git/odl/odl/space/npy_tensors.py:1669: RuntimeWarning: invalid value encountered in sqrt
    res = ufunc(*inputs, **kwargs)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
====== 3508 passed, 974 skipped, 21 warnings, 593 error in 19.24 seconds =======

aringh commented 5 years ago

Looking at the output again, the errors are confined to the following files

odl/test/test_doc.py EEEEEEEEEEEEEEEEEEEE [ 6%]
odl/test/test_examples.py EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 6%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 7%]
odl/test/largescale/solvers/nonsmooth/default_functionals_slow_test.py E [ 17%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 19%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 20%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 21%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 23%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 24%] EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 26%] EEEEEEEEEEEEEEEE [ 26%]
odl/test/largescale/space/tensor_space_slow_test.py EEEEEEEEEEEEEEEEEEEE [ 26%] EEEEEEEEEEEEEEEE [ 27%]
odl/test/largescale/trafos/fourier_slow_test.py EEssssEEssEEssEE [ 35%]

So the errors are confined to the test folder itself, or slow tests that should not be run since I did not give the flag --largescale.

kohr-h commented 5 years ago

It's clearly #1514, but it shouldn't result in errors anyway...

One thing that strikes me is that it says inifile: setup.cfg at the top, and I realized that the fix

# Temporary fix for https://github.com/odlgroup/odl/issues/1514, works with pytest<5.1
filterwarnings =
    ignore::pytest.PytestDeprecationWarning

is only in odl/pytest.ini, not in setup.cfg. It seems like pytest will pick up the latter for configuration (since there is a [tool:pytest] section, unless run explicitly with pytest odl/test or so.

Could you try adding the above lines to the setup.cfg section?

I just tried a fresh installation of master and can't reproduce the errors. I'm on pytest 4.* though.

aringh commented 5 years ago

You seem to correctly have identified the problem :smile: When I run python -c "import odl; odl.test()" I do not get errors, but when I run pytest I do. And adding the above line in setup.cfg, under [tool:pytest], removes the errors. I will push the fix.

kohr-h commented 5 years ago

Great, thanks for investigating!

odlgroup / odl

Trouble with pytest #1532