add AreTomo2 compatibility

[alisterburt]

this PR adds changes for AreTomo2 compatibility and some useful debug output gated behind WARP_DEBUG=1

The AreTomo2 API is ~identical to AreTomo but when run on a stack called TS_11.st we end up with results called TS_11_st.xf in the TS_11_Imod folder

I also changed the way combinations of directories/filenames are generated so that you can easily specify a single tilt series directory in ts_import_alignments to only update a specific tilt series

closes #46

[alisterburt]

@jmdobbs @ThomasHoffmann77 this should be working but I've only been able to test alignment and import separately as I'm unable to get AreTomo2 built and running in the same environment as Warp right now - could you test and see if this solves your issues with alignment import at #41 ?

[jmdobbs]

can confirm it's working :)

there is an (extremely) slight formatting error in the output in the command line, 0/1 is in the same line as Importing 2D transforms ....

Running AreTomo with final average tilt axis angle:
0/1Importing 2D transforms from /struct/mahamid/jdobbs/warp2_testing/data_gseries/processing/tiltstack/gTS_003/gTS_003_Imod/gTS_003_st.xf
1/1, 00:00 remaining

[alisterburt]

Awesome - thanks for running the test! I'll have to wait until we can run it in our infrastructure before merging 🙂

[alisterburt]

confirmed working on our infra, thanks again @jmdobbs !

[alisterburt]

fyi @dtegunov compatible AreTomo2 is now available under the 'aretomo2' module in our module system