Description
============================= test session starts ==============================
platform linux2 -- Python 2.7.15, pytest-4.4.2, py-1.8.0, pluggy-0.11.0
rootdir: /home/nightwing
collected 266 items
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/test_cvode.py F [ 0%]
FFFFFFFFFFFFFFFFFFFxFFFFFFFFFFFF [ 12%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/test_gsl.py F [ 12%]
FFFFFFFFFFFFFF [ 18%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/test_odeint.py F [ 18%]
FFFFFFFFFFx [ 22%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_core.py F [ 22%]
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFsssF [ 35%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_plotting.py F [ 36%]
F [ 36%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_results.py F [ 36%]
FF [ 37%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_robertson.py F [ 37%]
FFFFFFFFF [ 41%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_symbolic.py . [ 41%]
F.FFFFFFF.FFFFFF..FF....FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF [ 68%]
FFFFFFFFFFFFFFFF.FFFFFF..FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.. [ 95%]
ssFF..FFF [ 99%]
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/tests/test_util.py F [ 99%]
. [100%]
=================================== FAILURES ===================================
________________________________ test_NativeSys ________________________________
(PS: too long to be put here.....)
== 241 failed, 18 passed, 5 skipped, 2 xfailed, 17 warnings in 75.23 seconds ===
Activity
bjodah commentedon May 13, 2019
Hi @WuShichao, thank you for reporting this.
What's the output of
pytest --pyargs pyodesys -x
?Also for Python 2 I would probably recommend
python2 -m pip install 'pyodesys<=0.12'
You can also look at https://github.com/bjodah/pyodesys/blob/master/scripts/environment/Dockerfile for an example of an environment which should pass all tests.
WuShichao commentedon May 13, 2019
@bjodah So should I install sundials-2.7.0.tar.gz and boost_1_65_0.tar.bz2 first, and then 'python2 -m pip install 'pyodesys<=0.12'?
WuShichao commentedon May 13, 2019
@bjodah the output of
pytest --pyargs pyodesys -x
============================= test session starts ==============================
platform linux2 -- Python 2.7.15, pytest-4.4.2, py-1.8.0, pluggy-0.11.0
rootdir: /home/nightwing
collected 266 items
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/test_cvode.py F [ 0%]
=================================== FAILURES ===================================
________________________________ test_NativeSys ________________________________
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/test_cvode.py:27:
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/native/tests/_tests.py:21: in _test_NativeSys
native = NativeSys.from_callback(vdp_f, 2, 1)
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/symbolic.py:443: in from_callback
exprs = _ensure_4args(rhs)(x, _y, _p, be)
func = <function vdp_f at 0x7fdba7807f50>
E AttributeError: 'module' object has no attribute 'getfullargspec'
anaconda3/envs/pyodesys/lib/python2.7/site-packages/pyodesys/util.py:139: AttributeError
=========================== 1 failed in 4.75 seconds ===========================
bjodah commentedon May 13, 2019
You can install sundials-3.2.1 if you're compiling from source. 2.7.0 should also work. (this is for
pycvodes
). Any recent boost version should do, again, if you're compiling from source I would go with latest (1.70.0). For GSL any recent version should do (say >2).For python2 I would then recommend:
If you're using Python 3.5+ you should be able to install latest versions of everything.
WuShichao commentedon May 13, 2019
@bjodah Thanks, so you mean if I don't install sundials/boost from source or apt-repo, pyodesys will not work?
bjodah commentedon May 13, 2019
pyodesys will work (with scipy backend), but the
pyodesys.native
subpackage require one or more of pycvodes/pygslodeiv2/pyodeint (each requiring sundials/GSL/boost respectively).The
pyodesys.native
subpackage generates C++ code and compiles on the fly for fast integration of systems of modest size (say <100 variables).