Update conda package and compass to better support MPI

[xylar]

This merge makes two scripts into stubs so that the functionality from the scripts is fully available through functions within the mpas_tools package:

• The functionality of the paraview VTK extractor is now in mpas_tools.viz.paraview_extractor
• Creation of SCRIP files from MPAS meshes is now in mpas_tools.scrip.from_mpas
  The scripts for this functionality still exist but are just stubs that call the functions.

These changes allow VTK and SCRIP files to be created directly within python scripts, rather than through awkward subprocess calls that are causing trouble for conda environments with MPI support.

This merge also updates to the compass metapckage to 0.1.3:

• updates mpas_tools to 0.1.10 (not yet released)
• adds rasterio
• adds affine
• adds ipython
• adds jupyter

closes #305

[xylar]

Testing

I test-build the packages using these steps for building the packages and installing this version of mpas_tools and compass in a test environment:

source ~/miniconda3/etc/profile.d/conda.sh
conda activate base
# if needed:
conda install -y conda-build
conda update -y conda conda-build
rm -rf ~/miniconda3/conda-bld/
conda build --python=3.7 conda_package/recipe/
conda build compass/
conda create -y -n test_compass --use-local "compass=0.1.3=mpi_mpich*"
conda activate test_compass

Then, I ran the QU240wISC COMPASS test case from MPAS-Dev/MPAS-Model#480

[xylar]

The rasterio and affine packages are needed by MPAS-Dev/MPAS-Model#473, the work for making meshes with a signed-distance function.

[pwolfram]

Approved by visual inspection.

[mark-petersen]

This looks good. Thanks for the upkeep. @xylar I'm guessing you can merge this, and we can then merge MPAS-Dev/MPAS-Model#480 after that when we are ready?

[xylar]

@mark-petersen, I think considerably more testing of this COMPASS with MPI is needed before this is ready to merge. I have been waiting for us to get spun-up initial conditions for the EC60to30 configurations (and the changes related to those) before I start doing testing again. I should be able to start on that later today or tomorrow.

[xylar]

This version of the mpas_tools package and compass environment have been tested thoroughly as part of MPAS-Dev/MPAS-Model#480. Merging and releasing...