ctboughter/AIMS: AIMS_0.9.4

This release is primarily focused on updates to the CLI to make it more useful in everyday applications. We have three new flags that can be added to the command-line call:

-co,--clustOnly,"Stop running the script after clustering? [T/F]",required=False,default=False,type=distutils.util.strtobool
-sf,--saveFmt,"Which format do you want figures saved as? [png or pdf]",required=False,default='pdf',type=str
-sac,--saveAllClusts,"Save the sequences for all clusters generated?[T/F]",required=False,default=False,type=distutils.util.strtobool

Changed the default CLI behavior when using DBSCAN clustering to have a user-defined minimum # samples per cluster (min_sample) rather than a user-defined cluster radius (eps). Also added some new updates to the ReadMe/ReadTheDocs (new publications added) and altered the pip install instructions to more properly match our install requirements.

Recommended python install is still 3.7 as the parallel processing issues are not yet fixed (numba has yet to be incorporated).

The primary install path is still via PyPI. Users can simply install AIMS using:

pip install aims-immune

You can launch the GUI, CLI, or Notebook using simple command line arguments "aims-gui", "aims-notebook", or "aims-cli".

Known Issues for v0.9.4: -Relatively inflexible dependencies. Specifically a requirement for python3.7. If this is a big problem, please open an "issue". -The CLI is unable to call parallelization scripts. A patch will come soon to switch from python multiprocessing to numba, which should fix the problem. -The GUI is still lagging behind the notebook, unable to do statistics. -The "aims-notebook" command can only be run once per directory. After users should call the more standard "jupyter lab" command. This is hopefully a minor issue.

NOTE: Users should be quick to complain about bugs! Use the issues tab, please. I'm just one person, and it is very difficult to track down all of these bugs myself.