Merge pull request #2938 from RosettaCommons/JackMaguire/MultistageRosettaScripts
Small feature additions and bug fixes for multistage rosetta scripts:
Features:
- [x] Reverse script converter: convert a MRS script to a traditional rosetta script. Code is written but untested.
- [x] Added a more dynamic result-storing method in the NodeManager class. Not super useful now, but will be essential when (if) JD3 is able to submit jobs from node n+1 before node n is completely finished.
- [x] Added support for `<Checkpoint/>` tags to be intermixed with the `<Stage/>` tags. These do not currently do anything, but will save us time in the future.
Bug Fixes:
- [x] Each `<Add/>` call used to create a new mover/filter. This prevented us from being able to call the same mover twice (unfortunate for things like SaveAndRetrieveSidechains). Now, movers and filters can be called multiple times within the same MRSJob. I am taking this opportunity to remove the `job_bundle` Stage option because it is not that useful and really makes the code ugly.
~Upgrade the newick tree printing so that the values for the leaf nodes match the filenames created.~
- [x] Renumber the output files so that they match the newick tree