Jmrt devel

[delarosatrevin]

Main changes:

• Allow to avoid appending the Conda activation; this might not be desired in some cases the cryolo environment is loaded in different ways (e.g., external conda, modules, etc.)
• Some refactoring in Cryolo picking, mainly to run the program from the batch folder, avoiding overwriting a folder that make it crash in parallel (2 or more GPUs)
• Added Cryolo with Tasks (using emtools Task, Pipeline and other helper classes). This version avoids writing the .txt done files, better continue and steps.sqlite.

[azazellochg]

thank you @delarosatrevin ! I'll have a look

[azazellochg]

All good, however the tasks protocol does not work:

00010:     File "/home/gsharov/soft/scipion-em-plugins/scipion-em-sphire/sphire/protocols/protocol_cryolo_picking_tasks.py", line 94, in <listcomp>
00011:       blacklist = [mic.clone() for mic in inputMics if mic.getObjId() in micIds]
00012:   NameError: free variable 'micIds' referenced before assignment in enclosing scope

[delarosatrevin]

I will have a look, maybe something no committed by mistake

[azazellochg]

Also I couldn't find where you create micrographs.json

On Sun, 28 Apr 2024, 00:35 Jose Miguel de la Rosa Trevin, < @.***> wrote:

I will have a look, maybe something no committed by mistake

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[delarosatrevin]

I fixed the mentioned issues