Simpeg

fix std in DataMisfit and possible bug in PlotUtils

- from pr 745
- commits from thast
- review from micmitch, lheagy

Fix for Issue 746

- fixed `DataMisfit.std` that now take into consideration `survey.std`. So you are not forced to set `DataMisfit.W` manually anymore

- Fixed: `Survey.MakeSyntheticData`, if not given a `std`, was overwriting `survey.std` even if already set. Now it will use `survey.std` if not given a `std` argument.

Explanation:
`DataMisfit.std` was set to 5% by default, but to change it to `survey.std`, it expected a `None` value, thus it never gets updated...

- bonus: light improvement again of `Plot2DData` (reordering of `if` statement so specifying `contourOpts['vmin','vmax']` without a `clim` works.

- bonus: Somehow PR 725 did not make it to improve `plot_misfit_curves` so I put it back here. Mainly, more option to plot $\phi_m$ or $\phi_small$ and $\phi_smooth$ independently, plus more options to save the figure.


Code of conduct
- from pr 744
- commits from lheagy
- review from rowanc1

Add a code of conduct based on the contributor covenant to SimPEG

fixed possible issue for levels definition in `SimPEG.Utils.plot2DDdata`
- from pr: 738, closes 734
- commits from: thast

Description
- fixed possible issue for levels definition in `SimPEG.Utils.plot2DDdata`
- add mask functionality (already proposed as args but not implemented)
- choice of linear or nearest interpolation
- check if there is already a vmin, vmax in the contourOpts dict before adding them based on user-input clim
- improved example for`SimPEG.Utils.plot2DDdata`
- add an example for the IO.pseudosection function

Example output:


Installation docs
- from prs: 736, 737
- commits from: sdevriese, fourndo

Description
- Replace links to numpy example page with link to SimPEG examples
- update link for anaconda


Do not install tests in site-packages
- from pr: 740
- commits from: cgohlke

Description
- exclude tests from from SimPEG installation

- 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