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