updates to keep pace with changes in simpeg/discretize#134

• from pr #770
• commits from @kalen-sj
• review from: @fourndo, @lheagy

A complicated pattern that was copy/pasted several times in the code was able to be replaced with a simple np.where. An example:

actv = np.asarray([inds for inds, elem in enumerate(actv, 1) if elem], dtype=int) - 1 is now actv = np.where(actv)[0]

Also, a few spelling mistakes and corrections in the examples. A couple of cases where variables were defined twice before use are now just done once.

• commits from: @thast, @fourndo
• review from: @fourndo

This PR addresses issue #761 and follows PR #758 and PR #757 .

There was a naming discrepancy in the PF module and that causes me some trouble. In the Gravity module, there are two aliases for rhoMap: mapping and mapPair. In the Magnetics module, there is one alias for chiMap: modelMap.

This PR settle for modelMap as only alias, consistent with the definition of the LinearProblem class in Problem.py

Additional: Fix mapping name in LinearProblem (from mapping (depreciated) to modelMap)

• from pr #757
• commits from: @thast
• review from: @fourndo

This formulation takes into account the regularization mapping into the preconditioner and remove the need to check for a specific wiresmap.

• from pr: #758

• commits from: @lheagy

• review from: @thast

• soft removal of python 2.7: we don't explicitly break compatibility as in #731, but it is no longer tested on Python 2.7

• added a note in the docs saying we will not be working to ensure compatibility with python 2.7 anymore

DC Fields Derivatives

• from pr #724
• commits from: @lheagy
• review from: @sgkang

DC Resistivity

• add fields derivatives with respect to the electric field (in case you want to invert e-field data)
• add e-field receivers to DC problem
• see for example: https://github.com/simpeg-research/heagy-2018-injection-inversions

TDEM

• add charge and charge density to j-fields
• bug fix in calculation of db/dt in the j-fields object
• add grounded source that solves the mmr problem in the H-J formulation for permeable targets

Directives

• add option to save output to a directory, the default is the current working directory

numpy matlib imports

• from pr #755
• commits from: @lheagy
• review from: @thast

import matlib explicitly as in numpy 1.16, it isn't imported in the numpy namespace be default

• from pr: #670
• commits from: @fourndo, @thast
• review from: @thast , @lheagy

A couple of improvements or fix for Potential Fields:

• Fix reading functions for UBC file format (in case of line break)
• add ModelMap property
• Change survey.nD definition so it is independent of Problem
• Use reg.deriv2 instead of reg.W for computing the preconditioner in Directives.updatePreconditioner
• general PEP8 improvements (powered by AutoFormat)
• naming convention: readUBCgravObs becomes readGravityObservations (for consistency between Grav and Mag names conventions.)
• Combine all Mag problems (susc, amp, MVI) under Magnetics.MagneticIntegral
• Change coordinate system from legacy x, y, z(down) to convention x, y, z (up)
• Add test+example for MVI-S on TreeMesh
• Add test+example for Amplitude inversion (CSM algo)

• from pr #749
• commits from @lheagy
• review from @thast

update plot2Ddata

• update logic in plot2Ddata so that two vmin, vmax values cannot be provided to contourf (e.g. it was previously possible that an explicit vmin, vmax was provided by the user and that a vmin, vmax was chosen based on the colorbar)
• ensure that if both clim and vmin, vmax provided to contourOpts that they are identical

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 forSimPEG.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