Simpeg

- commits from thast
- review from lheagy

Address issue 734

PR notes:
We have fixed the following bug:
- the `clim` argument was not used in the `SimPEG.Utils.plot2DData`. We added the functionality to modify the colorscale based on the `clim` argument.

Improvements of the `SimPEG.Utils.plot2DData` function:
- Levels of the `matplotlib.pyplot.contourf` function are defined by the function itself. This is done to give us complete control over the colorscale and colorbar.
- Before plotting, we check if any data are `NaN` or `infinite` to ensure reasonable colorscale. We also ensure positivity is `scale==log`
- colorbar limits choice through `clim` and `ncontours`: `ncontours` defines the number of contour inside the `clim` scale. If data lies outside that range on either side, an supplemental contour is added to regroup those data under a single color on either side (so two colors if on both side with of ncontour+2 contours).

- originally from pr 706
- commits from: lheagy
- review from: sgkang, rowanc1

Effective medium theory map
- extend the effective medium theory mapping to work for preferentially aligned ellipsoids so that anisotropic conductivities are estimated
- add a calculation of the Hashin-Shtrikman bounds

Anisotropic models
- allow the shape of models to include 2D arrays so that anisotropic models can be input into simulations

New Example
- add an example of the effective medium theory map from my thesis

Minor updates
- allow receiver orientation inputs to be upper or lowercase `z` or `Z` in the FDEM code

- from pr: 711
- commits from: dccowan, lheagy
- review from: prisae, lheagy

updates
- Add square loop receiver for VRM problem
- Create forward modeling and inversion example for VRM code
- Fully utilise properties class to auto generate API
- Edit VRM tests to include new OcTree refinement
- Fix Codacy errors
- Clean up and fix errors associated with autodoc creation. Includes fixing H5 error associated with Bookpurnong and adding any missing examples not found in toctrees.

Further fixes will be addressed in 714

- originally from 699
- commits from: lheagy
- review from: sgkang
- This pr depends on simpeg/discretize36 (3D cyl mesh and cell grad stencils being properties) and supersedes 683.

Changes across EM
- electric fields / fluxes and magnetic fields fluxes live on the same grid location (eg. in problem_e, `e`, `j` are on edges, `b`, `h` are on faces

TDEM improvements
- fill out the fields objects (addresses issue 633)
- added a raw vec grounded source for HJ forumlation

DC
- a few typo fixes `Dirichlet` (some places it was `Dirchlet`)
- a couple updates in the order of error checks to have the DC operate on the 3D cyl mesh

geoana dependence for sources
- rely on geoana for vector potentials in the sources
- add geoana to the dev requirements

General Cleanup
- import derivative tests from discretize
- only have dev requirements in the `requirements_dev.txt` rather than also including core dependencies which should be installed through the setup.py

Use of sparse inversion for non-linear inverse problems (DC, TDEM, FDEM),
where sensitivity matrix is changing in the inversion iterations.

This can be quite expensive when sparse inversion is used, because
we need a number of iterations to make sparse inversion converged;
requires a number of call for computing sensitivity matrix.

We are doing a simple cheat here. Sparse inversion starts when Smooth inversion finishes.
So, we assume that our inversion is close to the solution, and hence sensitivity matrix does not
change that much after while updating for sparse inversion.

By passing `fix_Jmatrix=True` to `Update_IRLS`, you can fix sensitivity matrix, that is we are using the same sensitivity matrix for all sparse inversion iterations.

- review from: fourndo and lheagy
- commits from: sgkang

- from pr 691
- commits from lheagy
- review from sgkang

Updates
- work on simplifying the storage of the inner product matrix derivatives
- implement storage of the mu matrix derivatives