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PennLINC
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babs
BIDS App Bootstrap (BABS)
https://pennlinc-babs.readthedocs.io
MIT License
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[DOCS] (NMIND gold) Continuous integration badges in README for coverage
#127
zhao-cy
opened
1 year ago
1
[DOCS/TESTS] set up Codecov github workflow
#126
zhao-cy
opened
1 year ago
0
[DOCS] add DOI link to zenodo archive
#125
zhao-cy
closed
1 year ago
0
[DOCS] (NMIND bronze) Digital Object Identifier (DOI) points to latest version (e.g., Zenodo)
#124
zhao-cy
closed
1 year ago
2
Test out: XCP-D when FreeSurfer derivatives are needed (i.e., `–cifti` and `--warp-surfaces-native2std`)
#123
zhao-cy
opened
1 year ago
0
installation error on Hanke group local cluster
#122
zhao-cy
opened
1 year ago
0
[DOC] add guides in eg walkthrough: if there is no internet on compute nodes
#121
zhao-cy
closed
1 year ago
4
[DOCS] review: generated `singularity run` commands from example YAML files
#120
zhao-cy
closed
1 year ago
2
Update walkthrough.rst
#119
yibeichan
closed
1 year ago
0
[FIX]Batch job submission failed: Requested time limit is invalid (missing or exceeds some limit)
#118
yibeichan
closed
1 year ago
13
Update walkthrough.rst
#117
yibeichan
closed
1 year ago
2
[ENH] Add an option of creating a wrapper output folder of all derivatives
#116
zhao-cy
closed
1 year ago
2
[DOCS] minor enhancements in docs after Sydney's review
#115
zhao-cy
opened
1 year ago
0
[ENH] Add option of creating output folders to zip
#114
zhao-cy
closed
1 year ago
1
[tests] infrastructure for automatic pytest of `babs-submit` and `babs-status`
#113
zhao-cy
opened
1 year ago
0
[ENH] incorporating configs from `--call-fmt` when `babs-init`
#112
zhao-cy
opened
1 year ago
0
[DOCS] NMIND checklist: on roadmap
#111
zhao-cy
opened
1 year ago
0
[DOCS] NMIND checklist - targets that are easy to achieve
#110
zhao-cy
opened
1 year ago
0
Revisions in docs after testing on MIT slurm cluster
#109
djarecka
closed
1 year ago
5
[DOCS] add instructions on how to add partitions for slurm in example walkthrough
#108
zhao-cy
closed
1 year ago
1
[docs] Review updated example walkthrough
#107
zhao-cy
opened
1 year ago
0
[ENH] make sure no bug caused by `soft_memory_limit` on Slurm cluster
#106
zhao-cy
opened
1 year ago
1
[paper] go through NMIND checklist
#105
zhao-cy
closed
1 year ago
2
some refactoring to the unit tests, adding cases for slurm
#104
djarecka
opened
1 year ago
1
[DOCS/ENH] Documentation enhancement and review
#103
zhao-cy
closed
1 year ago
4
[ENH] make sure OSF link in example walkthrough works
#102
zhao-cy
closed
1 year ago
4
[ENH] improve printed messages from BABS functions
#101
zhao-cy
opened
1 year ago
0
[ENH] incorporate job status `Rr`, a subtype of running state
#100
zhao-cy
opened
1 year ago
0
[ENH] refactoring of babs_submit function and updator of job status table
#99
djarecka
closed
1 year ago
8
[FIX/ENH] Fix directives and job accounting; enhance example container config YAML filenames
#98
zhao-cy
closed
1 year ago
1
[FIX] get_existing_babs_proj() in `cli.py`: fix error message when wrong `--project-root`
#97
zhao-cy
opened
1 year ago
1
[ENH] test out BABS's Slurm version
#96
zhao-cy
closed
1 year ago
4
[ENH] test out BABS after Slurm version is added
#95
zhao-cy
opened
1 year ago
1
[FIX] directives for interpreting shell
#94
zhao-cy
closed
1 year ago
2
[ENH] sanity check that container config yaml file exists at the beginning of `babs-init`
#93
zhao-cy
opened
1 year ago
0
[ENH] adding slurm as a system type
#92
djarecka
closed
1 year ago
4
[ENH] add `--job-csv` option to `babs-submit`
#91
zhao-cy
opened
1 year ago
0
[ENH] update toy BIDS App version used for CircleCI testing
#90
zhao-cy
closed
1 year ago
1
[ENH] refactor: move some functions from `utils.py` to classes in `babs.py`
#89
zhao-cy
opened
1 year ago
0
[ENH] Improve section names in container config YAML file
#88
zhao-cy
closed
1 year ago
1
[ENH] example walkthrough: compatible with latest BABS version
#87
zhao-cy
closed
1 year ago
1
[ENH] save the `job_status.csv` even if the user kills `babs-submit` or `babs-status`
#86
zhao-cy
opened
1 year ago
0
[ENH] minor enhance in `babs-status` and `babs-submit`
#85
zhao-cy
closed
1 year ago
0
[ENH] create a folder within `<output_dir>` if needed for results zipping
#84
zhao-cy
closed
1 year ago
2
[ENH] `singularity run`: handle FreeSurfer license and Templateflow home
#83
zhao-cy
closed
1 year ago
1
[ENH] clean notebooks/ folder in BABS repo
#82
zhao-cy
closed
1 year ago
1
[docs] prepare example walkthrough
#81
zhao-cy
closed
1 year ago
4
[review] Review of container config YAML file
#80
zhao-cy
closed
1 year ago
3
[ENH] get ready to release BABS on pypi
#79
zhao-cy
closed
1 year ago
1
[FIX] metadata in setup.cfg regarding license
#78
zhao-cy
closed
1 year ago
0
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