plant traits save as scalars

[linwang9926]

• Update function get_base_length_ratio: return base_length_ratio results as scalar and return Nan if length=0
• convert the data in scalar column to the value without [].
• Modify stem width and base-related functions for rice traits (fixes Modify traits for monocots (rice) #38).
  • Modify function get_bases with an argument of 'lateral_only',
  • Modify functions get_base_xs, get_base_ys, get_base_ct_density, if no bases just return np.nan.
  • Modify function get_root_pair_widths_projections with an argument of 'lateral_only'.
  • Modify function get_traits_value_frame add the argument 'lateral_only' in trait_map dictionary.
• change the argument name of 'lateral_only' to 'monocots' in modules bases, graphpipeline, networklength, points, and scanline, as well as test modules test_graphpipeline, test_points, test_scanline, test_convhull, test_ellipse, and test_networklength. (fixes Modify traits for monocots (rice) #38 ).
• Added an if condition in function get_traits_value_plant_summary: not trait.isna().all() to filter out the all nan non-scalar traits. Those summarized traits are all nans (fixes get_traits_value_plant_summary takes length of float object #39 ).
• Add monocots=False for more base-related traits, so there won't be values calculated for rice (fixes get_traits_value_plant_summary takes length of float object #39).

[codecov]

Codecov Report

Merging #37 (052144f) into main (db93e0d) will decrease coverage by 2.01%.
The diff coverage is 83.50%.

@@            Coverage Diff             @@
##             main      #37      +/-   ##
==========================================
- Coverage   82.59%   80.59%   -2.01%     
==========================================
  Files          13       13              
  Lines         678      706      +28     
==========================================
+ Hits          560      569       +9     
- Misses        118      137      +19     

Impacted Files	Coverage Δ
sleap_roots/graphpipeline.py	87.41% <56.52%> (-7.98%)	⬇️
sleap_roots/bases.py	91.58% <90.90%> (-6.24%)	⬇️
sleap_roots/networklength.py	92.53% <100.00%> (ø)
sleap_roots/points.py	97.05% <100.00%> (ø)
sleap_roots/scanline.py	97.36% <100.00%> (ø)

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