Fix 0.11.0 region mask

[ctuguinay]

This PR addresses #134 #135 #136:

Major Changes

• regions2d.mask now produces a 3d mask using the regionmask mask_3d function
  • This now ensures that overlap error cannot arise in initial region mask creation.
  • Note: Overlap error can still occur in converting from 3D-2D if the 3D mask has overlap.
• Modification of 2D and 3D Mask Structure
  • Both 2D and 3D masks are now data arrays; previously, 3D mask was a dataset
  • 3D mask now stores region_id values in its dimensions and coordinates. Shape is now of the form (region_id, ping_time, depth) as opposed to storing region_id values/mask labels in a separate data array. Additionally, I felt it was confusing to give the user the ability to change the slice labels of the mask within regions2d.mask by passing in a list called mask_labels when this mask_labels list was index-dependent on the region IDs getting passed in, and those region IDs were now getting filtered out (based on depth) prior to the masking.

Minor Changes

• Modifications to align tests and mask converting functions (2d-3d and 3d-2d) with regions2d.mask changes
• region_id = None is now the default for masking
• Consistently using region_id as input for regions2d functions

[codecov[bot]]

Codecov Report

Merging #139 (732a279) into dev (b179117) will increase coverage by 2.59%. Report is 10 commits behind head on dev. The diff coverage is 92.59%.

:exclamation: Current head 732a279 differs from pull request most recent head 2276b11. Consider uploading reports for the commit 2276b11 to get more accurate results

@@            Coverage Diff             @@
##              dev     #139      +/-   ##
==========================================
+ Coverage   84.75%   87.35%   +2.59%     
==========================================
  Files          13       13              
  Lines         538      522      -16     
==========================================
  Hits          456      456              
+ Misses         82       66      -16     

Files	Coverage Δ
echoregions/core.py	100.00% <ø> (ø)
echoregions/regions2d/regions2d.py	85.45% <95.45%> (+1.50%)	:arrow_up:
echoregions/utils/api.py	92.59% <89.18%> (+16.20%)	:arrow_up:

... and 4 files with indirect coverage changes

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[ctuguinay]

@leewujung This PR is ready for a re-review. It addresses all the suggestions in the comment about and all the in-line comments.