Tests fail #36

yurivict · 2018-09-21T16:03:14Z

============================================================================ test session starts ============================================================================
platform freebsd11 -- Python 2.7.15, pytest-3.6.4, py-1.6.0, pluggy-0.6.0
rootdir: /usr/ports/math/py-pygslodeiv2/work-py27/pygslodeiv2-0.9.1, inifile: setup.cfg
collected 206 items / 3 errors                                                                                                                                              

================================================================================== ERRORS ===================================================================================
___________________________________________________________ ERROR collecting pyodesys/native/tests/test_cvode.py ____________________________________________________________
ImportError while importing test module '/usr/local/lib/python2.7/site-packages/pyodesys/native/tests/test_cvode.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python2.7/site-packages/pyodesys/native/__init__.py:14: in <module>
    from .cvode import NativeCvodeSys
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:18: in <module>
    class NativeCvodeCode(_NativeCodeBase):
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:22: in NativeCvodeCode
    _realtype = _config.env.get('REAL_TYPE', 'double')
/usr/local/lib/python2.7/site-packages/pyodesys/util.py:272: in __getattribute__
    raise self._exc  # ImportError("Failed to import %s" % self._modname)
E   ImportError: No module named pycvodes
____________________________________________________________ ERROR collecting pyodesys/native/tests/test_gsl.py _____________________________________________________________
ImportError while importing test module '/usr/local/lib/python2.7/site-packages/pyodesys/native/tests/test_gsl.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python2.7/site-packages/pyodesys/native/__init__.py:14: in <module>
    from .cvode import NativeCvodeSys
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:18: in <module>
    class NativeCvodeCode(_NativeCodeBase):
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:22: in NativeCvodeCode
    _realtype = _config.env.get('REAL_TYPE', 'double')
/usr/local/lib/python2.7/site-packages/pyodesys/util.py:272: in __getattribute__
    raise self._exc  # ImportError("Failed to import %s" % self._modname)
E   ImportError: No module named pycvodes
___________________________________________________________ ERROR collecting pyodesys/native/tests/test_odeint.py ___________________________________________________________
ImportError while importing test module '/usr/local/lib/python2.7/site-packages/pyodesys/native/tests/test_odeint.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python2.7/site-packages/pyodesys/native/__init__.py:14: in <module>
    from .cvode import NativeCvodeSys
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:18: in <module>
    class NativeCvodeCode(_NativeCodeBase):
/usr/local/lib/python2.7/site-packages/pyodesys/native/cvode.py:22: in NativeCvodeCode
    _realtype = _config.env.get('REAL_TYPE', 'double')
/usr/local/lib/python2.7/site-packages/pyodesys/util.py:272: in __getattribute__
    raise self._exc  # ImportError("Failed to import %s" % self._modname)
E   ImportError: No module named pycvodes
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================== 3 error in 2.14 seconds ==========================================================================
*** Error code 2

OS: FreeBSD 11.2
Occurs in the FreeBSD port.

The text was updated successfully, but these errors were encountered:

bjodah · 2018-09-21T16:35:00Z

why are pyodesys and pycvodes referenced there? (non of those are reqs. of pygslodeiv2)

yurivict · 2018-09-21T16:48:48Z

Sorry, I pasted a wrong log. The correct log is:

============================================================================ test session starts ============================================================================
platform freebsd11 -- Python 3.6.6, pytest-3.6.4, py-1.6.0, pluggy-0.6.0
rootdir: /usr/ports/math/py-pygslodeiv2/work-py36/pygslodeiv2-0.9.1, inifile: setup.cfg
collected 0 items / 1 errors                                                                                                                                                

================================================================================== ERRORS ===================================================================================
___________________________________________________________ ERROR collecting pygslodeiv2/tests/test_gsl_odeiv2.py ___________________________________________________________
ImportError while importing test module '/usr/ports/math/py-pygslodeiv2/work-py36/pygslodeiv2-0.9.1/pygslodeiv2/tests/test_gsl_odeiv2.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygslodeiv2/__init__.py:10: in <module>
    from ._gsl_odeiv2 import adaptive, predefined, requires_jac, steppers, fpes
E   ModuleNotFoundError: No module named 'pygslodeiv2._gsl_odeiv2'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================== 1 error in 0.27 seconds ==========================================================================
*** Error code 2

bjodah · 2018-09-21T18:44:51Z

OK, thanks. I won't be able to debug this I'm afraid since I don't know how to reproduce it. Is there something analogous to docker for FreeBSD for a minimal reproducer?

…

On Fri, Sep 21, 2018, 18:48 ***@***.*** ***@***.***> wrote: Sorry, I pasted a wrong log. The correct log is: ============================================================================ test session starts ============================================================================ platform freebsd11 -- Python 3.6.6, pytest-3.6.4, py-1.6.0, pluggy-0.6.0 rootdir: /usr/ports/math/py-pygslodeiv2/work-py36/pygslodeiv2-0.9.1, inifile: setup.cfg collected 0 items / 1 errors ================================================================================== ERRORS =================================================================================== ___________________________________________________________ ERROR collecting pygslodeiv2/tests/test_gsl_odeiv2.py ___________________________________________________________ ImportError while importing test module '/usr/ports/math/py-pygslodeiv2/work-py36/pygslodeiv2-0.9.1/pygslodeiv2/tests/test_gsl_odeiv2.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygslodeiv2/__init__.py:10: in <module> from ._gsl_odeiv2 import adaptive, predefined, requires_jac, steppers, fpes E ModuleNotFoundError: No module named 'pygslodeiv2._gsl_odeiv2' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ========================================================================== 1 error in 0.27 seconds ========================================================================== *** Error code 2 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#36 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAdqMI_Gmz_OLYkzkZnI-Iz0rnxbleFOks5udRhwgaJpZM4W0cuv> .

yurivict · 2018-09-21T19:42:19Z

install FreeBSD ISO image into a VM: https://download.freebsd.org/ftp/releases/amd64/amd64/ISO-IMAGES/11.2/FreeBSD-11.2-RELEASE-amd64-disc1.iso
install prerequisites: pkg install py36-pygslodeiv2 subversion
check out the ports tree: cd /usr && svn checkout https://svn.FreeBSD.org/ports/head ports
build the port and run tests: cd /usr/ports/math/py-pygslodeiv2 && make test FLAVOR=py36
observe the failure

bjodah · 2018-09-22T17:49:39Z

Thanks, I could reproduce the test failure. However, I'm a bit lost:

# cd work-py36
#  find . -iname "*.so"             
./pygslodeiv2-0.9.1/build/lib.freebsd-11.2-STABLE-amd64-3.6/pygslodeiv2/_gsl_ode         iv2.so                                                                                   
./stage/usr/local/lib/python3.6/site-packages/pygslodeiv2/_gsl_odeiv2.so

So the shared library is getting built. If I cd into that site-packages folder and run:

# python3.6 -c "import pygslodeiv2"
# echo $?
0

which to me looks like things are working as expected. Up to the packaging(?) point?

EDIT:
also from site-packages:

        root@freebsd:/usr/ports/math/py-pygslodeiv2/work-py36/stage/usr/local/lib/python         
        3.6/site-packages # python3.6 -m pytest --pyargs pygslodeiv2                             
        ============================= test session starts ==============================         
        platform freebsd11 -- Python 3.6.6, pytest-3.6.4, py-1.6.0, pluggy-0.6.0                 
        rootdir: /usr/ports/math/py-pygslodeiv2/work-py36/stage/usr/local/lib/python3.6/         
        site-packages, inifile:                                                                  
        collected 21 items                                                                       
                                                                                                 
        pygslodeiv2/tests/test_gsl_odeiv2.py .....................               [100%]          
                                                                                                 
        ========================== 21 passed in 43.09 seconds ==========================         
        root@freebsd:/usr/ports/math/py-pygslodeiv2/work-py36/stage/usr/local/lib/python

bjodah · 2018-10-19T07:54:14Z

ok, so this is a packaging issue in FreeBSD/ports then?

yurivict · 2018-10-19T08:07:31Z

Packaging issue means that something is wrong with the package.
But what is wrong? It is packaged in a standard way, using distutils.

bjodah · 2018-10-19T08:23:47Z

is it picking up the package from the source directory instead of the build directory?
It seems to matter from where the command is issued. It works on multiple linux distributions and on macOS.

yurivict · 2018-10-19T08:32:19Z

It is trying to open the shared library in the source location:

 81247 python2.7 NAMI  "/usr/ports/math/py-pygslodeiv2/work-py27/pygslodeiv2-0.9.1/pygslodeiv2/_gsl_odeiv2.so"
 81247 python2.7 RET   open -1 errno 2 No such file or directory

when it only exists in the build directory:
work-py27/pygslodeiv2-0.9.1/build/lib.freebsd-11.2-STABLE-amd64-2.7/pygslodeiv2/_gsl_odeiv2.so

bjodah · 2018-10-19T08:36:56Z

I see. To me it sounds like the scripts in FreeBSD/ports need to be adapted to setuptools or vice versa. I'm not doing anything unusual in setup.py in that respect.

bjodah mentioned this issue Oct 19, 2018

Tests fail with version 0.7.3 with installed extras bjodah/chempy#111

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Tests fail #36

Tests fail #36

yurivict commented Sep 21, 2018 •

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Tests fail #36

Tests fail #36

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