On Sun, Oct 19, 2014 at 4:57 PM, Stefan Schwarzer <sschwar...@sschwarzer.net > wrote:
> > > According to > > http://www.ctcms.nist.gov/fipy/documentation/USAGE.html#running-under-python-3 > you should also run `2to3 --write --doctests_only`. Maybe > that makes the difference? :-) > Oh yeah. That works better. Thanks. > I gave it a try and installed Anaconda3. When running > `python setup.py install`, I still have/had some issues. > > For one, a few files have mixed indentation (mixed spaces > and tabs) which Python 3 doesn't like: > > Sorry: TabError: inconsistent use of tabs and spaces in indentation > (testBase.py, line 47) > Sorry: TabError: inconsistent use of tabs and spaces in indentation > (trilinosSolver.py, line 148) > Sorry: TabError: inconsistent use of tabs and spaces in indentation > (gistVectorViewer.py, line 70) > I've never seen that before when installing with Python 3 in Anaconda. Which version of FiPy are you using? > > After fixing the files, I got that far: > > The required module(s) ['pysparse'] cannot be loaded. > FiPy will not work properly until these modules are installed. > ------ > The optional module(s) ['gist', 'mayavi'] cannot be loaded. > FiPy will have improved capabilities if these modules are installed. > > It seems `pysparse` is only available for Python 2. Is this > correct? Is it indeed needed? > You don't need PySparse. It isn't available for Python 3 yet. The Scipy solvers are adequate to get started. None of the solvers are required packages, but you obviously need one of them. > > `gist` presumably is installed though: > > (diffusion)schwa@warpy:~/sd/python/diffusion/FiPy-3.1$ > ~/sd/anaconda3/bin/pip install gist > Requirement already satisfied (use --upgrade to upgrade): gist in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages > Requirement already satisfied (use --upgrade to upgrade): requests in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages (from gist) > Requirement already satisfied (use --upgrade to upgrade): argparse in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages (from gist) > Cleaning up... > (diffusion)schwa@warpy:~/sd/python/diffusion/FiPy-3.1$ > ~/sd/anaconda3/bin/pip install --upgrade gist > Requirement already up-to-date: gist in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages > Requirement already up-to-date: requests in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages (from gist) > Requirement already up-to-date: argparse in > /home/schwa/sd/anaconda3/lib/python3.4/site-packages (from gist) > Cleaning up... > > But I still get the message about the missing `gist` (see > above). > Gist is a very old package that we need to remove from the dependencies. It's a viewer. You don't actually need any of the viewers to use FiPy. However to see stuff interactively while the simulation is running, it is good to have one of them. I would suggest using Matplotlib to get started. Mayavi is just optional. > >>/site-packages/ez_setup.py", > >> line 116, in _build_egg > >> raise IOError('Could not build the egg.') > >> OSError: Could not build the egg. > > > > Could it be permission issues? Just speculation. > > Maybe. Also just speculation. ;-) But I don't get these > messages anymore with Anaconda. > Great. > > >> In [3]: len(dir(fipy)) > >> Out[3]: 144 > > > > If you're in the fipy directory then that's not surprising. > > Kind of. ;-) Still the import might have failed if some > things needed to be built but weren't. So it's not as > "natural" as one would expect. That said, you know more > about FiPy than me :-) ; is FiPy pure Python (apart from its > dependencies) and is supposed to run without any > installation other than copying the directory/file structure > one to one? > It is pure Python so an installation is exactly as you describe. > > >> When running `fipy.test()` from within the interpreter, the > >> summary output is > >> > >> Ran 343 tests in 9.262s > >> > >> FAILED (failures=7) > >> > >> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> Skipped 105 doctest examples because `gmsh` cannot be found on the > $PATH > >> Skipped 20 doctest examples because neither `lsmlib` nor `skfmm` can > be > >> found on the $PATH > >> Skipped 1 doctest examples because `skfmm` must be used to run some > tests > >> Skipped 83 doctest examples because the `tvtk` package cannot be > imported > >> > >> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> An exception has occurred, use %tb to see the full traceback. > > Now I get the same message (when running FiPy installed in > the environment, not from the unpacked FiPy directory). > I think things are working. (diffusion)schwa@warpy:~/sd/python/diffusion/FiPy-3.1$ python > examples/diffusion/variable.py > Traceback (most recent call last): > File "examples/diffusion/variable.py", line 86, in <module> > exec(fipy.tests.doctestPlus._getScript()) > File "<string>", line 8, in <module> > File > "/home/schwa/sd/anaconda3/envs/diffusion/lib/python3.4/site-packages/FiPy-3.1-py3.4.egg/fipy/viewers/__init__.py", > line 136, in Viewer > raise ImportError("Failed to import a viewer: %s" % str(errors)) > ImportError: Failed to import a viewer: ["gnuplot: __call__() missing 1 > required positional argument: 'func'", "gist: __call__() missing 1 required > positional argument: 'func'", "matplotlib: ufunc 'isfinite' not supported > for the input types, and the inputs could not be safely coerced to any > supported types according to the casting rule ''safe''", "mayavi: No module > named 'enthought'"] > > (diffusion)schwa@warpy:~/sd/python/diffusion/FiPy-3.1$ python > examples/diffusion/coupled.py > > /home/schwa/sd/anaconda3/envs/diffusion/lib/python3.4/site-packages/FiPy-3.1-py3.4.egg/fipy/viewers/matplotlibViewer/__init__.py:113: > UserWarning: Matplotlib1DViewer efficiency is improved by setting the > 'datamax' and 'datamin' keys > return Matplotlib1DViewer(vars=vars, title=title, axes=axes, > **kwlimits) > finished > > Again, no viewer opens here. > I'll have to look into those issues. At least the example is mostly working. > > By the way, when I execute the code from > > http://www.ctcms.nist.gov/fipy/fipy/generated/fipy.viewers.matplotlibViewer.html#matplotlibviewer-package > up to and including the `viewer1 = MatplotlibViewer(...)` > call and > > >>> viewer = MultiViewer(viewers=(viewer1,)) > >>> for kval in range(10): > ... k.setValue(kval) > ... viewer.plot() > > I get several diagram plotted in the top left figure. So it > seems that Matplotlib is working in this environment. Also > it seems to cooperate with FiPy. > That's good at least. There are certianly some rough edges with FiPy and Python 3 that we need to address. Good luck. -- Daniel Wheeler
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