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Commit c3d6b7a9 authored by Tyler Collins's avatar Tyler Collins
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Merge branch 'master' of https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context

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CHANGELOG deleted 100644 → 0
View file @ 7f196573
2018-01-31 Mike Cichonski <mike.cichonski@gmail.com>
* VERSION: 1.0.7
* batch/misc_func/key_strswap.m: Fixed bug that crashed script at job
submission if the preInd string didn't appear in the [batch_dfn]
2017-08-14 Brad Kennedy <bk@co60.ca>
* VERSION: 1.0.6
* mfile_name_gen: moved out of private/
* batch/pop_func/pop_runhtb.m: Fixed bug with long passwords, library
that we are using for the password prompt has a limit of 8 characters
which is really stupid
2017-08-14 Brad Kennedy <bk@co60.ca>
* VERSION: 1.0.5
* batch/exec_func/ef_current_base.m: Fixed reference to logging_log
* batch/exec_func/rsub_sys.m: Fixed reference to logging_log
2017-08-09 Mike Cichonski <mike.cichonski@gmail.com>
* VERSION: 1.0.4
* batch/pop_func/pop_batch_edit.m: fixed error message when cancelling
'Save As' popup window
2017-08-09 Mike Cichonski <mike.cichonski@gmail.com>
* VERSION: 1.0.3
* batch/pop_func/pop_batch_edit.m: fixed error messages from clear/new and
clear/load
* batch/exec_func/private/mfile_name_gen.m: enabled default mfile name if
both mfile_name and job_name are empty
2017-08-02 Mike Cichonski <mike.cichonski@gmail.com>
* VERSION: 1.0.2
* batch/exec_func/ef_gen_m.m: added string swap for scheduler
* batch/misc_func/batch_strswap.m: same as above
2017-08-01 Brad Kennedy <bk@co60.ca>
* VERSION: 1.0.1
* batch/exec_func/@ef_base_driver/submit_line.m: changed mfile name handling
* batch/exec_func/@ef_sbatch_driver/format_scheduler.m: bug fix with order
of sprintf values
* batch/exec_func/ef_exec_str.m: code-cleanup, mfile_name default string
swap added
* batch/exec_func/ef_gen_m.m: same as above
* batch/exec_func/octave_exit_wrapper.m: added sqsub to octave exit wrapper
jobid printers
2017-07-25 Brad Kennedy <bk@co60.ca>
* CHANGELOG: Change changelog format to actually contain changes
ensure you follow the format and put newer changes above this one
* eegplugin_batch_context.m: Added version such that it generates it
from the VERSION file in this directory
README.md
View file @ c3d6b7a9
# Batch Context
## Wiki / Documentation
All documentation is stored on [the Wiki](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home)
## Summary
The batch_context extension for EEGLAB provides and interface for generating data
processing pipelines and executing them on multiple data files either locally or
on remote compute clusters. This extension also provides the tools needed to manages
remote server addresses and facilitates working with a remote environments.
## Attribution
## Documentation
All documentation is stored on the [Wiki](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home).
## Attribution
Code initially designed and written by James A. Desjardins (SHARCNET) with contributions from Andrew Lofts, Allan Campopiano, Brad Kennedy and Mike Cichonski supported by NSERC to Sidney J. Segalowitz at the Jack and Nora Walker Centre for Lifespan Development Research (Brock University), Brain Canada funding to Alan C. Evans at the Montreal Neurological Institute and Hospital (McGill University), and a Dedicated Programming award from SHARCNET, Compute Ontario.
......
batch/exec_func/@ef_base_driver/make_job_dir.m
View file @ c3d6b7a9
% make_job_dir() - Helper function for creating the required state of a job folder.
%
% Usage:
% >> make_job_dir(driver,job_struct);
%
% Inputs:
% drive - Reference to object which specifies cluster configurations.
% job - Specific submission information. See job_struct usage in pop_runhtb.
%
% Outputs:
% An updated job_struct object with pathing information on each subject.
%
% See also:
% pop_runhtb()
%
% Copyright (C) 2017 Brock University Cognitive and Affective Neuroscience Lab
%
% Code written by James A. Desjardins, Allan Campopiano, Andrew Lofts,
% and Brad Kennedy
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program (LICENSE.txt file in the root directory); if not,
% write to the Free Software Foundation, Inc., 59 Temple Place,
% Suite 330, Boston, MA 02111-1307 USA
function job = make_job_dir(drive, job)
if nargin < 2
......
batch/exec_func/retry-fails.sh
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#!/bin/bash
# ------------------------------------------------------
# retry-fails.sh
#
# The purpose of this script is to combat the problem of
# a scheduler becoming too busy to handle a high demand of
# job submission. As such, this script will detect this failure
# and attempt to resubmit the job with the same terms for a
# given number of tries.
#
# See Batch Context Wiki and documentation for more details.
# ------------------------------------------------------
set -eu
if [ $# -lt 1 ] ; then
......
batch/misc_func/file_strswap.m
View file @ c3d6b7a9
% file_strswap() - Execute a string swap on a given file based on passed varargs.
% Functions as a find and replace in a given file.
% Usage:
% >> newstr = file_strswap(fname, varargin)
%
% Required Inputs:
% fname = File name to execute swaps on. This function opens the file
% internally.
%
% Optional Inputs:
% Any given pair of strings to swap. See Batch Context documentation for
% proper syntactical usage.
%
% Outputs:
% swapstr = Updated output in which instances of key strings have
% been swapped with their respective val strings.
%
% See also: pop_runhtb(), key_strswap()
% Copyright (C) 2017 Brock University Cognitive and Affective Neuroscience Lab
%
% Code written by James A. Desjardins, Allan Campopiano, and Andrew Lofts
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program (LICENSE.txt file in the root directory); if not,
% write to the Free Software Foundation, Inc., 59 Temple Place,
% Suite 330, Boston, MA 02111-1307 USA
function swapstr=file_strswap(fname,varargin)
for i=1:length(varargin)
......
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