file cleanup, slurm scripts and timeout added to batchtools submit templates #831
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* batch tools subpackage * comm update * new search methods * fixed import issues * updates comm, search * search.py * wrapper tools search * update to batchtools * codebase moved to netpyne batchtools https://github.com/jchen6727/netpyne/tree/batch * update to comm.py, runners.py * update to search (kwargs) * config update (should delete two keys @ end?) * replace pubtk with batchtk for compatibility with pip * update the submit (zsh->sh) * update batchtools, submits * fixed socket functionality for submits.py * batchtools documentation * minor updates- search
cfg.progressBar = 2 will display all progress bars cfg.progressBar = 1 will call tqdm with progress bars w/ leave = 0 cfg.progressBar = 0 will disable the progress bar.
…tionary, fanova example started. batchtools.rst updated
update batch re: end user suggestion
can now initialize cfg with a dictionary:
``` Python
from netpyne.batchtools import specs
cfg = specs.SimConfig({'x': [None] * 4})
```
creates a new cfg such that it already has value x, e.g.
cfg.x = [None, None, None, None]
update to documentation with some minimal working examples (see https://github.com/suny-downstate-medical-center/netpyne/tree/batch/netpyne/batchtools/examples), esp. Rosenbrock w/ coupled parameters, nested parameters, etc.
fanova (large sample -- 625), running fanova analysis cfg.py of CA3 including additional cfg settings to avoid confusion
incorrect reference to old batchtk templates, now referencing appropriate templates in batchtools submits.
jchen6727
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* development: (49 commits) Extracellular stimulation via .mod small correction in plotter.py Conflict diversity and LFP Conflict between diversity and LFP for unit tests, rolled back to 3.12 so far test with python 3.9-3.13 drop python 3.7 for unit-tests plotCSD: time slicing on pre-loaded data (credit: Nikita Novikov) extracellular stimulation quick fix to `update` method that allows for working with lists. (#837) d/w expanse setup, moved {env} {res} {custom} (#834) hot fix (submits.py) (#833) code adjustments to internal sim.clearAll(), added sim.close() (#832) file cleanup, slurm scripts and timeout added to batchtools submit templates (#831) updated upload instructions to exclude downtime fixed sbi deprecation error. fixes in docs formatting minor correction to CHANGES.md VERSION 1.0.7 Revert "Exlude tests from discovery / installation" - due to issue that has emerged with spack installation (EBRAINS platform). Will re-visit later.. merge of batchtools into the development repository. (#829) ...
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see changes in netpyne.batchtools