danforthcenter/plantcv: PlantCV v3.0.dev2

PlantCV v3.0.dev2 is an early release in the v3 release cycle. A full v3 will be released at a later date. While this is an early release, it should be considered essentially production-ready. Note that this release breaks previous syntax/functionality with the goal of making things easier. Updating existing code to the new styles should be fairly straightforward.

Overview of changes:

• The input and output device has been eliminated for all functions. The step counter still exists in the background.
• The input debug has been eliminated for all functions. It can now be set globally with the class Params: https://plantcv.readthedocs.io/en/latest/params/.
• The output location of images printed in debug mode can now be set using the plantcv.params.debug_outdir global setting: https://plantcv.readthedocs.io/en/latest/params/
• Some function arguments were refactored. Many were changed to make it more explicit what type of input image is required. The new vocabulary is generally: img = all image types, rgb_img = RGB images only, gray_img = Grayscale images only, bin_img or mask = Binary images only. Some other inputs were renamed for consistency and/or PEP8 formatting guidelines. All function call changes are summarized here: https://plantcv.readthedocs.io/en/latest/updating/#updating-to-v3.
• Several functions were removed and replaced with updated versions.
  • define_roi: replaced with the functions in the subpackage roi.
  • analyze_bound: replaced with the functions analyze_bound_horizontal and analyze_bound_vertical.
  • rotate_img: replaced with the function rotate.
  • The threshold functions binary_threshold, adaptive_threshold, otsu_auto_threshold, and triangle_auto_threshold were moved to a new subpackage and are now: plantcv.threshold.binary, plantcv.threshold.gaussian, plantcv.threshold.mean, plantcv.threshold.otsu, plantcv.threshold.triangle.
  • These changes are also summarized here: https://plantcv.readthedocs.io/en/latest/updating/#updating-to-v3.
• Testing coverage was increased to 94%.
• Some additional general documentation and docstring reformatting for consistency.
• The FAQ was updated.