subdirectories file

[aremazeilles]

We envision to launch the code through a docker image, and we need to have the process completely in batch (i.e no interaction with the user).

When I launch the command indicated (pepato_basic), there is an interaction hapening related to the interaction path:

For PEPATO to work correctly, please add "/data" and its subdirectories to your MATLAB path and restart the application. 
This needs to be done once, paths will be saved in .pepatopath file in the PEPATO home directory.
Add directory and save paths? [y/n] 

We would need to get rid of that for the eurobench automation. We can foresee three options:

• Create a default path file, like the pepato, store it in the repository (with a different name to maintain such functionality), and place it as .pepato file.
• Remove such interaction and add it automatically
• Take advantage of the launch script as we use in octave_csic to add these path (other issue to comment about this).

[aremazeilles]

Seems to be solved in octave branch. I would need to understand if you intent maintaining the octave branch, or want to merge it at a moment to master and or dev. Can you indicate the policy you would like to follow here?

[aremazeilles]

Could you confirm that we would focus on the octave-version branch to be the one prepared for Eurobench? Then I think we could close that issue

[dzhvansky]

Yes, I confirm, the branch octave-version will be entirely for Eurobench.

There are some changes in the last commits: 1) Modified calculation of two PI's (we will add information about this to the Excel). 2) The default NMF replication number was changed to 50 (this is for better approximation). This makes the calculation five times longer. To facilitate testing, you can change the parameter value in line 27 of run_pepato. 3) We also resolved the reproducibility issue. This was due to the initialization of the NMF algorithm. Now the results are the same from run to run.

[aremazeilles]

OK, I will check point 3, and get back to you

[aremazeilles]

With respect to 2, I would say that at the level of the code, I would need to have the proper configuration (as stated in the readme file) that enable to get the result that is to be also stored in the folder for consistency checking. We will talk back of this later, but for now, the main issue mentioned here is solved.