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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

pytest doesn't seem to be finding the tests?

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bjodah avatar bjodah commented on July 17, 2024

I think the last 3 lines in setup.py:

[pytest]
python_files = test_*.py
python_functions=test_*

usually go into setup.cfg (and I think the "new" header is [tool:pytest]).
But I think those globs are the default. My typical setup.cfg looks like this:

[tool:pytest]
norecursedirs = .* scripts build dist conda-recipe 

# https://github.com/pytest-dev/pytest/issues/1445
[easy_install]
zip_ok = 0

In setup.py, I would also change:

packages=['diffeqpy'],

into

packages=['diffeqpy', 'diffeqpy.tests'],

and add an empty file diffeqpy/tests/__init__.py.
That would include tests in the source distribution and one would then be able to execute e.g. python3.5 -m pytest --pyargs diffeqpy from anywhere on a machine with diffeqpy installed.

It should also work if it is a "development" installation (I would recommend installing via python3.5 -m pip install --user -e . or python3.5 setup.py develop --user). Alternatively one can set PYTHONPATH=/path/to/diffeqpy and run pytest from the package root.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

I think I made the changes @bjodah described but tests are still coming up blank. I pushed everything to master so you can see what the current setup it (I believe it matches what you were saying there).

crackauc@crackauc2 diffeqpy]$ python3.6 -m pip install --user -e .
Obtaining file:///home/crackauc/.julia/diffeqpy
Requirement already satisfied: julia in /usr/lib/python3.6/site-packages (from diffeqpy==0.2) (0.1.5)
Installing collected packages: diffeqpy
  Found existing installation: diffeqpy 0.2
    Uninstalling diffeqpy-0.2:
      Successfully uninstalled diffeqpy-0.2
  Running setup.py develop for diffeqpy
Successfully installed diffeqpy
[crackauc@crackauc2 diffeqpy]$ python3.6 -m pytest --pyargs diffeqpy
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/crackauc/.julia/diffeqpy, inifile: setup.cfg
collecting 0 items

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bjodah avatar bjodah commented on July 17, 2024

Hmmm.. maybe try:

$ PYTHONPATH=$(pwd) python3.6 -m pytest

or:

$ cd / && python3.6 -m pytest --pyargs diffeqpy  # shot in the dark...

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Looks like versions are mixed for some reason:

crackauc@crackauc2 diffeqpy]$ cd / && python3.6 -m pytest --pyargs diffeqpy
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /, inifile:
collecting 0 items                                                                                                                                                           [crackauc@crackauc2 /]$ PYTHONPATH=$(pwd) python3.6 -m pytest
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /, inifile:
collected 0 items / 1 errors                                                                                                                                                 

=================================================================================== ERRORS ===================================================================================
_____________________________________________________________________________ ERROR collecting  ______________________________________________________________________________
usr/lib/python3.6/site-packages/py/_error.py:66: in checked_call
    return func(*args, **kwargs)
E   PermissionError: [Errno 13] Permission denied: '//boot/grub2'

During handling of the above exception, another exception occurred:
usr/lib/python3.6/site-packages/py/_path/common.py:377: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
usr/lib/python3.6/site-packages/py/_path/common.py:429: in gen
    for p in self.gen(subdir):
usr/lib/python3.6/site-packages/py/_path/common.py:429: in gen
    for p in self.gen(subdir):
usr/lib/python3.6/site-packages/py/_path/common.py:414: in gen
    entries = path.listdir()
usr/lib/python3.6/site-packages/py/_path/local.py:387: in listdir
    names = py.error.checked_call(os.listdir, self.strpath)
usr/lib/python3.6/site-packages/py/_error.py:86: in checked_call
    raise cls("%s%r" % (func.__name__, args))
E   py.error.EACCES: [Permission denied]: listdir('//boot/grub2',)
============================================================================== warnings summary ==============================================================================
None
  could not create cache path /.pytest_cache/v/cache/nodeids
  could not create cache path /.pytest_cache/v/cache/lastfailed

-- Docs: http://doc.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
==================================================================== 2 warnings, 1 error in 0.49 seconds =====================================================================
[crackauc@crackauc2 /]$ sudo PYTHONPATH=$(pwd) python3.6 -m pytest
[sudo] password for crackauc: 
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /, inifile:

collected 0 items / 1 errors                                                                                                                                                 

=================================================================================== ERRORS ===================================================================================
_____________________________________________________________________________ ERROR collecting  ______________________________________________________________________________
usr/lib/python3.6/site-packages/_pytest/config.py:334: in _getconftestmodules
    return self._path2confmods[path]
E   KeyError: local('//lib64/python2.7/site-packages/numpy')

During handling of the above exception, another exception occurred:
usr/lib/python3.6/site-packages/_pytest/config.py:365: in _importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError: local('//lib64/python2.7/site-packages/numpy/conftest.py')

During handling of the above exception, another exception occurred:
//lib64/python2.7/site-packages/numpy/core/__init__.py:16: in <module>
    from . import multiarray
E   ImportError: //lib64/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: _Py_ZeroStruct

During handling of the above exception, another exception occurred:
usr/lib/python3.6/site-packages/_pytest/config.py:371: in _importconftest
    mod = conftestpath.pyimport()
usr/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
//lib64/python2.7/site-packages/numpy/__init__.py:142: in <module>
    from . import add_newdocs
//lib64/python2.7/site-packages/numpy/add_newdocs.py:13: in <module>
    from numpy.lib import add_newdoc
//lib64/python2.7/site-packages/numpy/lib/__init__.py:8: in <module>
    from .type_check import *
//lib64/python2.7/site-packages/numpy/lib/type_check.py:11: in <module>
    import numpy.core.numeric as _nx
//lib64/python2.7/site-packages/numpy/core/__init__.py:26: in <module>
    raise ImportError(msg)
E   ImportError: 
E   Importing the multiarray numpy extension module failed.  Most
E   likely you are trying to import a failed build of numpy.
E   If you're working with a numpy git repo, try `git clean -xdf` (removes all
E   files not under version control).  Otherwise reinstall numpy.
E   
E   Original error was: //lib64/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: _Py_ZeroStruct

During handling of the above exception, another exception occurred:
usr/lib/python3.6/site-packages/py/_path/common.py:377: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
usr/lib/python3.6/site-packages/py/_path/common.py:429: in gen
    for p in self.gen(subdir):
usr/lib/python3.6/site-packages/py/_path/common.py:429: in gen
    for p in self.gen(subdir):
usr/lib/python3.6/site-packages/py/_path/common.py:429: in gen
    for p in self.gen(subdir):
usr/lib/python3.6/site-packages/py/_path/common.py:418: in gen
    dirs = self.optsort([p for p in entries
usr/lib/python3.6/site-packages/py/_path/common.py:419: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
usr/lib/python3.6/site-packages/_pytest/main.py:434: in _recurse
    ihook = self.gethookproxy(path)
usr/lib/python3.6/site-packages/_pytest/main.py:338: in gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
usr/lib/python3.6/site-packages/_pytest/config.py:348: in _getconftestmodules
    mod = self._importconftest(conftestpath)
usr/lib/python3.6/site-packages/_pytest/config.py:376: in _importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure: ImportError("\nImporting the multiarray numpy extension module failed.  Most\nlikely you are trying to import a failed build of numpy.\nIf you're working with a numpy git repo, try `git clean -xdf` (removes all\nfiles not under version control).  Otherwise reinstall numpy.\n\nOriginal error was: //lib64/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: _Py_ZeroStruct\n",)
E     File "//lib64/python2.7/site-packages/numpy/__init__.py", line 142, in <module>
E       from . import add_newdocs
E     File "//lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
E       from numpy.lib import add_newdoc
E     File "//lib64/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
E       from .type_check import *
E     File "//lib64/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
E       import numpy.core.numeric as _nx
E     File "//lib64/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module>
E       raise ImportError(msg)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================== 1 error in 67.62 seconds ==========================================================================

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bjodah avatar bjodah commented on July 17, 2024

Weird, for me I can run pytest from outside the root without errors:

~/vc$ python3 -m pytest --pyargs diffeqpy
=============================================================================================== test session starts ================================================================================================
platform linux -- Python 3.5.2, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/bjorn/vc/diffeqpy, inifile: setup.cfg
plugins: pep8-1.0.6, flakes-2.0.0
collected 2 items                                                                                                                                                                                                  

diffeqpy/diffeqpy/tests/test_ode.py ..                                                                                                                                                                       [100%]

============================================================================================ 2 passed in 79.28 seconds =============================================================================================

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Is there some package installation step that has to be done?

[crackauc@crackauc2 /]$ python3.6 -m pytest --pyargs diffeqpy
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /, inifile:
collecting 0 items

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bjodah avatar bjodah commented on July 17, 2024

I have run:

$ python3 -m pip install --user -e .

in the repo root before-hand. Which created a link:

$ ls -l $(python3 -c "import site; print(site.USER_SITE)") | grep diffeq
-rw-rw-r--  1 bjorn bjorn      25 apr 23 00:58 diffeqpy.egg-link
$ cat $(python3 -c "import site; print(site.USER_SITE)")/diffeqpy.egg-link
/home/bjorn/vc/diffeqpy

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tkf avatar tkf commented on July 17, 2024

@ChrisRackauckas Why not use tox? You can avoid this kind of it-works-in-my-computer problem. It simplifies Travis setup as well.

I know tox does not work with conda and probably many DifferentialEquations.jl dependencies invoke conda... But for testing interface to simple pure-Julia code, it may be fine.

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tkf avatar tkf commented on July 17, 2024

OK. I had a look at the code. First of all, the way Python organize unit tests are different from Julia: the tests have to be wrapped it into a function or a class. There are only two such cases in diffeqpy/tests which are in test_ode.py.

Second, I think pytest's default behavior is to stop test collection once it encounter an import error. This may explain why pytest in @bjodah environment can find tests while @ChrisRackauckas's can't. Since test_ode.py has import numba, pytest won't find tests unless it has numba installed in the environment. My guess is that @bjodah had numba installed while @ChrisRackauckas didn't.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Why not use tox?

I have no idea what that is.

First of all, the way Python organize unit tests are different from Julia: the tests have to be wrapped it into a function or a class.

I didn't finish changing them because pytest won't run.

My guess is that @bjodah had numba installed while @ChrisRackauckas didn't.

The code works for me (I wrote the README).

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tkf avatar tkf commented on July 17, 2024

I think I've encounter LLVM incompatibility issue in Julia and Numba. Even python -c 'import diffeqpy.tests.test_ode' segfaults. Reading JuliaPy/PyCall.jl#220 (comment) it looks like I need to install the right version of llvmlite. But building old version of llvmlite (0.16.0) requires an old version of LLVM (3.9.x) which I don't have at the moment.

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tkf avatar tkf commented on July 17, 2024

The code works for me

But you are not providing a reproducible way to make it work elsewhere. tox helps for that, at least for running tests.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

But you are not providing a reproducible way to make it work elsewhere. tox helps for that, at least for running tests.

What do you mean by that? Just that we need the checkout? I want to just get that fixed instead:

JuliaPy/PyCall.jl#496

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

I think I've encounter LLVM incompatibility issue in Julia and Numba. Even python -c 'import diffeqpy.tests.test_ode' segfaults. Reading JuliaPy/PyCall.jl#220 (comment) it looks like I need to install the right version of llvmlite. But building old version of llvmlite (0.16.0) requires an old version of LLVM (3.9.x) which I don't have at the moment.

That issue doesn't apply since we never PyCall numba. Instead, the user can optionally give an already JIT compiled Numba function, but Julia/PyCall shouldn't ever know that Numba was involved.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Update is that it now just stalls while testing:

[crackauc@crackauc2 ~]$ cd .julia/diffeqpy
[crackauc@crackauc2 diffeqpy]$ python3.6
Python 3.6.4 (default, Dec 19 2017, 14:48:12) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import diffeqpy
>>> de = diffeqpy.setup()
>>> def f(u,p,t):
...     return -u
... 
>>> u0 = 0.5
>>> tspan = (0., 1.)
>>> prob = de.ODEProblem(f, u0, tspan)
>>> sol = de.pysolve(prob)
>>> import matplotlib.pyplot as plt
>>> plt.plot(sol.t,sol.u)
[<matplotlib.lines.Line2D object at 0x7fdb915c75f8>]
>>> plt.show()
>>> exit()
[crackauc@crackauc2 diffeqpy]$ pytest
===================================================================== test session starts ======================================================================
platform linux -- Python 3.6.4, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/crackauc/.julia/diffeqpy, inifile: setup.cfg
collecting 0 items

Getting there.

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tkf avatar tkf commented on July 17, 2024

That issue doesn't apply since we never PyCall numba.

Indeed, it works:

https://travis-ci.org/JuliaDiffEq/diffeqpy/builds/369923283

It seems that the segfault is problem in my environment.

But you are not providing a reproducible way to make it work elsewhere. tox helps for that, at least for running tests.

What do you mean by that?

I mean, you are not providing a single entry point for running unit tests. For example, numba also has to be installed for the test. Manual installtion is not developer-friendly and doesn't scale if you need more packages. Also, ideally, it'd be better if it's isolated from user's environment. Julia needs to wait for Pkg3 for that, but Python already has it (virtualenv/venv) and a wrapper for testing (tox).

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Is there a way to use tox but not require it to precompile DiffEqPy each time? I guess that's just a test time problem but there must be a way to run it without rebuilding PyCall and recompiling the whole thing.

Do you know what's trying to use apt on Mac @tkf? https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935686#L28 I don't have any apt commands in the repo. If tox isn't compatible with Mac that's fine, but then we should at least change those tests to allow failure for now.

I mean, you are not providing a single entry point for running unit tests. For example, numba also has to be installed for the test. Manual installtion is not developer-friendly and doesn't scale if you need more packages. Also, ideally, it'd be better if it's isolated from user's environment. Julia needs to wait for Pkg3 for that, but Python already has it (virtualenv/venv) and a wrapper for testing (tox).

Yeah, part of the reason for doing this is to have an application for compiler/ecosystem folks to test and develop with. I hope that when the release of diffeqr and diffeqpy happen, that will then be a good incentive for Julia devs to care about the JuliaCall and pyjulia tools (we definitely will) along with the intersections of Pkg3 with static compilation and external calls, and so it'll start a nice feedback loop.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Is there a way to use tox but not require it to precompile DiffEqPy each time? I guess that's just a test time problem but there must be a way to run it without rebuilding PyCall and recompiling the whole thing.

Looks like that's just stalling when in the -py36 test. Happened to me locally, and happened on Travis:

https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935685

I am more than slightly puzzled by that.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

Locally having -py27 issues too.

[crackauc@crackauc2 diffeqpy]$ tox -e py27
GLOB sdist-make: /home/crackauc/.julia/diffeqpy/setup.py
py27 create: /home/crackauc/.julia/diffeqpy/.tox/py27
py27 installdeps: pytest, pytest-cov, numba
py27 inst: /home/crackauc/.julia/diffeqpy/.tox/dist/diffeqpy-0.2.zip
py27 installed: attrs==17.4.0,coverage==4.5.1,diffeqpy==0.2,enum34==1.1.6,funcsigs==1.0.2,julia==0.1.5,llvmlite==0.22.0,more-itertools==4.1.0,numba==0.37.0,numpy==1.14.2,pluggy==0.6.0,py==1.5.3,pytest==3.5.0,pytest-cov==2.5.1,singledispatch==3.4.0.3,six==1.11.0
py27 runtests: PYTHONHASHSEED='3824619191'
py27 runtests: commands[0] | julia --color=yes -e Pkg.add("DiffEqPy")
INFO: Package DiffEqPy is already installed
INFO: METADATA is out-of-date — you may not have the latest version of DiffEqPy
INFO: Use `Pkg.update()` to get the latest versions of your packages
py27 runtests: commands[1] | julia --color=yes -e Pkg.checkout("PyCall")
INFO: Checking out PyCall master...
INFO: Pulling PyCall latest master...
INFO: No packages to install, update or remove
py27 runtests: commands[2] | julia --color=yes -e Pkg.build("PyCall")
INFO: Building Conda
INFO: Building PyCall
Info: PyCall is using /home/crackauc/.julia/diffeqpy/.tox/py27/bin/python (Python 2.7.5) at /home/crackauc/.julia/diffeqpy/.tox/py27/bin/python, libpython = /usr/lib64/libpython2.7
Info: /home/crackauc/.julia/v0.6/PyCall/deps/deps.jl has been updated
Info: /home/crackauc/.julia/v0.6/PyCall/deps/PYTHON has been updated
py27 runtests: commands[3] | julia --color=yes -e using DiffEqPy
py27 runtests: commands[4] | python -c import diffeqpy.tests.test_ode
py27 runtests: commands[5] | py.test --pyargs diffeqpy
===================================================================== test session starts ======================================================================
platform linux2 -- Python 2.7.5, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/crackauc/.julia/diffeqpy, inifile: setup.cfg
plugins: cov-2.5.1
collecting 0 items                                                                                                                                             ERROR: InvocationError for command '/home/crackauc/.julia/diffeqpy/.tox/py27/bin/py.test --pyargs diffeqpy' (exited with code 1)
___________________________________________________________________________ summary ____________________________________________________________________________
ERROR:   py27: commands failed

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tkf avatar tkf commented on July 17, 2024

Is there a way to use tox but not require it to precompile DiffEqPy each time? I guess that's just a test time problem but there must be a way to run it without rebuilding PyCall and recompiling the whole thing.

I don't know why PyCall needs rebuild each time so I don't know how to fix it.

If you just need to quickly run tests without invoking stuff inside tox.ini, you can just do

.tox/py36/bin/py.test --pyargs diffeqpy

Note that this runs tests installed in .tox/py36/lib. If you want this workflow, it's better to set usedevelop = true (http://tox.readthedocs.io/en/latest/config.html#confval-usedevelop=BOOL) so that the code in the git repository is used.

Do you know what's trying to use apt on Mac @tkf? https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935686#L28

Hmm... That's puzzling. But it looks like it had happened before my PR https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369880767#L28

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tkf avatar tkf commented on July 17, 2024

The issue in Travis is during using DiffEqPy https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935685#L980 and your local py27 failure is from py.test so I don't know if they are related.

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tkf avatar tkf commented on July 17, 2024

BTW, encouraging people to care about interoperability by releasing diffeqr and diffeqpy is really a great move!! Thank you!

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tkf avatar tkf commented on July 17, 2024

The issue in Travis is during using DiffEqPy https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935685#L980

Oops. I clicked the redo button in Travis to see if the problem is reproducible. But it turned out that Travis throws away old build. So the link https://travis-ci.org/JuliaDiffEq/diffeqpy/jobs/369935685#L980 above won't make sense anymore...

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tkf avatar tkf commented on July 17, 2024

Nevermind, it produces the same error.

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tkf avatar tkf commented on July 17, 2024

One thing I've forgotten was that Julia loads .juliarc.jl even for non-interactive session. Since I had ENV["PYTHON"] = ..., the setting in tox.ini was overwritten. If I empty .juliarc.jl then I can import diffeqpy.tests.test_ode but still the tests do not run.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

It seems I need to run

import julia
jul = julia.Julia()
import diffeqpy
de = diffeqpy.setup()

each time I switch Python versions. I wonder if that's some kind of race condition related to precompilation that needs to be reported to pyjulia.

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ChrisRackauckas avatar ChrisRackauckas commented on July 17, 2024

It looks like Travis is good now. AppVeyor is having a 32-bit vs 64-bit issue due to tox I think. @tkf can you check it out?

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tkf avatar tkf commented on July 17, 2024

It looks like the test itself choke sometimes randomly. It happens both locally and in Travis. It's probably that using DiffEqPy hangs. When it occurs, sudo strace -p <pid> shows something like

futex(0x7f507c45caa0, FUTEX_WAIT_PRIVATE, 2, NULL

I'm not sure it helps. Does it mean there is a deadlock somewhere in Julia-Python bridge?

Anyway, since it happens also locally, I guess Travis setup itself is fine.

I don't know what is happening in AppVeyor. tox should be using whatever installed in that system. So, as long as Python and Julia are compatible to the system, I think the rest should be handled by pip via tox without problem. But I'm not familiar with Windows...

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tkf avatar tkf commented on July 17, 2024

Oh, appveyor has many Python interpreters installed in one environment. I see... https://www.appveyor.com/docs/build-environment/#python

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