implement properties in discretize

Implement properties in discretize

• from pr #70
• commits from: @lheagy, reviews from: @rowanc1, @fwkoch

Use properties to define the properties of a class that are necessary to completely define the object. This allows us to serialize, save and load meshes (also copy!)

Related issues and discussion

• private properties: seequent/properties#191
• arrays with arbitrary shape: seequent/properties#192

Extract Core Mesh Util

originally from pr #67, with commits from @thast, @lheagy, review from @rowanc1

• port over fixes that were made in SimPEG extract core mesh
• add testing on the 1D and 2D extract core mesh util

cleanup imports

Clean up Tree Mesh imports

• pr #63. commits from @lheagy, review from @rowanc1

Try / except the import of TreeMesh in Tests. This should remove all dependence that the cython code be properly set up in order to import discretize (continues to be an issue on windows...)

numpy upgrades, IO for UBC meshes

IO: UBC meshes

contributions from: @thast, @micmitch, review from @lheagy
from pr #54

• discretize.TensorMesh.readUBC is now a wrapper for loading either 2D or 3D mesh
• discretize.TensorMesh.readUBC can take care of recognizing if the file is a 2D or 3D UBC mesh, or it can be an input given by the user (arg: meshdim)
• the original functions are now hidden class function under discretize.TensorMesh._readUBC_3DMesh and discretize.TensorMesh._readUBC_2DMesh
• comments in UBC files are assumed to be marked with "!" in front

utils.Zero: Numpy upgrades

contributions from: @lheagy, review and comments from @rowanc1, @jcapriot
from pr #61

• Updates to Identity() and Zero() so that they are consistent with numpy upgrades in numpy=1.13.0 (https://github.com/charris/numpy/blob/master/doc/source/reference/arrays.classes.rst)
• use scipy.sparse.dia_matrix for spzeros (closed #60)

Install Cleanup

Noteworthy Changes

• use a try / except pair when importing the TreeMesh in the main init
• have efficiency warnings state that the user should use python setup.py install if cython code is not there in the interp utils
• use a try / except in the setup.py when importing numpy to tell the user to install numpy if it fails.

Minor Changes

• add codacy, quantified code badges to docs
• pinning to sphinx==1.5.6 for sphinx gallery to build. This is stated in #57 and will be released when upstream changes are made

MeshIO, PyPi deploy, Cache averaging operators

Minor Updates

• bug fix in MeshIO for UBC mesh (and associated test)
• deploy to pypi from appveyor, travis on tag
• cache the averaging operator

Contributors

• @grosenkj
• @lheagy
• @rowanc1

Interpolation improvements

Interpolation Improvements

implementing the bisection algorithm without the GIL. Gets rid of a lot of python overhead for speed-ups. If using Cython, might as well use it to get down to C-like code.

All of the for loops are executed without any calls to the python interpreter, and the bisection algorithm is equivalent to the np.searchsorted without the python overhead. Also, since we know how big the inds and vals array will be, might as well pre-allocate them.

At least 2x-3x speed on decent sized arrays.

Should address #23

Ints

• bug fix to ensure we are using ints as indices and to create numpy arrays

Utils

• Zero and Identity have a transpose

pypi distribution

• include *.pyx files in the MANIFEST.in so they get included in the pypi distribution

Windows and Mesh View

• add down-sampling capability to _plot2DImage as per simpeg/simpeg#537
• Changes for windows compatibility:
  • long changed to long long
• Changes for appveyor testing:
  • needed to cd into a different directory to do the tests
• Setup.py changes:
  • Used numpy's distutils for package management
• This can now be built and installed without any special arguments to the setup.py file. For example, python setup.py build and python setup.py install
  both work.
• The setup.py files within each subpackage take care of cythonizing and attaching the extensions, making the main setup.py file a little cleaner.
• This version was able to be pip installed on my Windows machine, should consider building wheels for distribution without compilation.

Updates to testing and pypi

This should be slightly smoother to install on pypi, and is now tested on windows.