MAINT: Simplify plotting module

[nawtrey]

Description

Refactor of the primary functions in plotting.py.

Details

• Refactor draw_diagrams and move redundant code into new functions

• Create new function _get_node_colors for handling diagram and cycle plotting function node colors

• Change all instances of save path logic to use os.path.join since this is much more stable

• Change all instances of save path such that input label parameter is effectively the filename for

• Move all instances of plt.close() such that the figures are only closed if the figure is saved

• Replace all instances of plt.axis("off") with ax.set_axis_off() so it is more explicit

• Create new function _plot_panel for handling cases where multiple subfigures need to be plotted together and use it to simplify draw_diagrams

• Add curved_arrows parameter to plotting functions so the curved arrows can be switched on/off with ease

• Change scope of flux_diagrams_4wl to "function"

• Change default behavior of plotting functions draw_diagrams() and draw_cycles() to plot a panel and fix the corresponding test cases to maintain current code coverage

• Add test test_plot_panel to cover automated position generation in _plot_panel()

• Small formatting changes for test_plotting.py

• Remove unnecessary plotting._contains_all_nodes()

• Abstract repeated code from _plot_panel() and draw_cycles() into new function plotting._get_panel_dimensions() to handle panel rows/cols/excess_plots acquisition

• Automate node list acquisition in _plot_single_diagram()

• Add node_colors parameter to _plot_single_diagram() and automate

• Set default of rows and cols parameters to None in _plot_panel()

• Add parameters rows, cols, and curved_arrows to draw_cycles()

• Refactor draw_cycles() to remove as much redundant code as possible. There is still more simplification available, but baby steps..

• Addresses some of the tasks in #34

• Fixes #38

[codecov[bot]]

Codecov Report

Merging #45 (7425fc6) into master (3511db2) will decrease coverage by 0.00%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #45      +/-   ##
==========================================
- Coverage   99.86%   99.86%   -0.01%     
==========================================
  Files           9        9              
  Lines         747      724      -23     
==========================================
- Hits          746      723      -23     
  Misses          1        1              

Impacted Files	Coverage Δ
kda/plotting.py	100.00% <100.00%> (ø)

[nawtrey]

The code coverage has dropped as a result of the code simplification, which is expected (and acceptable). There is still only 1 uncovered line across the code base, which is good.

[nawtrey]

Upon merging a few issues will have to be opened to address some remaining changes:

1. the documentation for the new and refactored functions needs to be updated
2. draw_cycles(panel=True) can likely be further simplified via _plot_panel()
3. A single function can probably be written to handle both cycles and diagrams. Since their structures are so similar, it shouldn't be too difficult to create a single function to handle either of those cases.
4. Add unit tests for each of the plotting helper functions
5. Change "label" parameter to "filename", and don't include the file extensions
6. Remove "single diagram/cycle" cases and change to enforcing an array or list as input since that code seems to be very redundant and largely unnecessary. It's nice to be able to input a single diagram, but the names draw_diagrams and draw_cycles are probably a bit misleading in the first place. Might be more appropriate to make a public function for plotting individual diagrams/cycles.

[nawtrey]

Overall these changes substantially improve the readability of the code, reduce many instances of repeated code, and still maintain the functionality of the code. The test suite also gets a makeover that allows much better error detection.

I've given the code a good look again, and tried all of the various plotting combinations out. Everything looks good to me, and CI is green, so merging.