Python 3 Support

[capaulson]

Python 3 Support

[capaulson]

Hey @Jwely @mattharrigan, I've just started a new branch aimed at moving to Python3. There are likely to be a large number of bugs, but it seems that the basic functionality for at least 2D plotting is there.

See: https://github.com/capaulson/pyKriging/tree/Python3-Support

More coming shortly, I'll leave open until Python3 support is in master.

[capaulson]

It doesn't support Python3 now, but shouldn't be too difficult to port. It's on the todo list, but please feel free to start a Python3 branch!

[Jwely]

+1

Lack of python3 was a total showstopper for me. If a scikit-learn GaussianProcess implementation doesn't seem easier for my use case I may port this myself.

[capaulson]

To get this to work I needed to run the following in Ubuntu 16.04:

apt-get install python3-pip python3-numpy python3-matplotlib python3-scipy
pip3 install inspyred
apt-get install python3-cairocffi

I've attached a screen shot of the expected result.

[capaulson]

Also, to install the Python3 version, you would do:

git clone https://github.com/capaulson/pyKriging.git
(or git pull, if you've already cloned it)
git checkout Python3-Support
python3 setup.py install

edit: seems that the plotting library for 3D isocontour on my system isn't running. seems that you need vtk compiled with Python3 support. I'm trying to build vtk following these instructions: http://ghoshbishakh.github.io/blog/blogpost/2016/07/13/building-vtk-with-python3-wrappers.html

[takluyver]

I've done a bit more work on Py3 support in PR #16. Some tests would be good to check that things aren't breaking. ;-) I'm running the examples to check that they don't crash, but I'm not sure how to check if it's doing the right thing.

[capaulson]

@takluyver the quickest way to check is to plot a test function contour lines over the end result (scaled the same). The 2D_simple_train.py example shows how to do this. Simply pass the test function to the main Kriging call: 'testfunction=testfun'. This then plots black contours on the filled color plot that is predicted from PyKriging. That provides a quick visual check to make sure the code is working. I'll take a look at the PR this weekend. Have you tested in in Py2.7?

[capaulson]

Also, @takluyver thanks for the contributions on this code!!

[takluyver]

I've posted on #16 screenshots of running 2D_simple_train on Python 3 and 2; it appears to be working nicely. I assume the choice of sampling points in non-deterministic, so we wouldn't expect those to be the same.

[capaulson]

I've just merged Python3 support into the main branch. Closing this thread now

[Daniel-M]

In Debian Linux 4.13.0-1-amd64 #1 SMP Debian 4.13.4-2 (2017-10-15) x86_64 GNU/Linux,
with python 3.5.4, The package pykriging installed from the pip sources (using pip3, pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.5)) still produces the same issue,

# python3 -c "import pyKriging"
...
except Exception, err:
^
SyntaxError: invalid syntax

Fixed with,

git clone https://github.com/capaulson/pyKriging.git
cd pyKriging
python3 setup.py install # installed as root 

I'm not sure why, if the python3 support was merged months ago, the pip package had the same problems. That's why i'm posting at this issue.

[takluyver]

It will need a new version released on PyPI before you can pip install it with the Python 3 support.

https://pypi.python.org/pypi/pyKriging

[Daniel-M]

I see that the version on PyPI is the 0.1.0, though this repo is 0.2.0. Why the update isn't sent?

[takluyver]

Making a release is a separate thing from updating the repo - it's up to @capaulson when he wants to release.