v4.2.1: Introducing an interactive dashboard web app for analyses

In this minor feature release we are including the first beta version of an interactive dashboard for analyses of cryoDRGN model outputs, now available using cryodrgn dashboard <outdir>!

This interface currently implements the following tools:

• Particle explorer — extends the interactive particle-picking functionality already implemented in cryodrgn filter to include a tool for viewing images and volumes from within a given particle selection
• Pair-plot generator — customizable visualizations for every pair of z-latent-space axes in one plot
• 3D visualizer — plots model and data covariates on an interactive 3D plot for easier elucidation of complex outputs
• Command builder — a helper tool for creating copy-and-pastable cryoDRGN reconstruction commands with any set of parameters and available option flags
• Trajectory creator — provides an interactive way of generating the trajectories made with direct_traversal and graph_traversal, and other types of trajectories too!

We have also made the following small improvements and changes to the codebase:

• default value for --num_workers when using --lazy is now 2 instead of 0 for more efficient use of hardware
• removing support for apex.amp, which has since been superseded by torch.amp (see e.g. this discussion)
• better log messages and code style in analysis_scripts/tsne.py
• replacing pickle.load(..., 'rb') and pickle.save(..., 'wb') with utils.load_pkl and utils.save_pkl throughout the codebase to avoid unclosed data streams
• avoiding import cryodrgn import statements in lieu of e.g. import cryodrgn.config for better maintainability