Version 3.3.0: direct traversal, TestPyPI

[michal-g]

In this release we have added cryodrgn direct_traversal, a tool for interpolating a path in the latent conformation space connecting two points in a direct line.

We have also updated and improved the interfaces of cryodrgn graph_traversal and cryodrgn pc_traversal so that the arguments, argument formats, and help docstrings between all three traversal methods are as consistent and clear as possible:

• --ind in direct_traversal is replaced with --anchors as in graph_traversal; allowing both to take a list of integers as well as files containing lists of integers
• -o now also has a more verbose alias --outtxt in graph_traversal and direct_traversal; we updated its behavior in graph to save the latent space co-ordinates and updated --outind to save path indices; similarly verbose alias --outdir in pc_traversal
• -o now also has a default value that is used when the flag is given with no argument across all three traversal commands to mean that we want to save output but don't have a file name
• when -o is not given, all three commands now display a prettier log message to screen with traversal output

Finally, we have added the --datadir flag to cryodrgn abinit_homo, addressing an oversight that complicated using .star files with this command (#343), as well as fixed some bugs and other issues found in our demonstration Jupyter notebooks (#363) and tools such as eval_images.

With this release we are making cryodrgn available for installation using the TestPyPI distribution service: pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ 'cryodrgn==3.3.0a1.dev4' This will allow us to make both development and stable versions of the package available for easy download using pip, as opposed to having to use git clone for the former.