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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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bab-init tries to datalad get a subject from input dataset that's NOT on subject list
#177
audreycluo
opened
2 weeks ago
0
babs requires all zips in original input dataset to be downloaded before doing babs-init
#176
audreycluo
opened
2 weeks ago
0
Support SLURM array jobs in `babs-submit`
#175
tsalo
opened
3 months ago
2
Allow `babs-init` to create the container dataset
#174
tsalo
opened
3 months ago
0
Consolidate `--where-project` and `--project-name` in `babs-init`
#173
tsalo
opened
3 months ago
0
Convert `--project-root` parameter in CLIs to positional argument
#172
tsalo
opened
3 months ago
0
[ENH] Add workflow for processing and adding new subjects to BABS results
#171
mattcieslak
opened
7 months ago
0
Make e2e testing run on PRs as well as e.g. weekly
#170
yarikoptic
opened
7 months ago
0
Introducing e2e slurm tests
#169
asmacdo
closed
7 months ago
2
Deprecation warning from pandas during `babs-status`
#168
asmacdo
closed
8 months ago
3
Add user-configurable environment variable passthrough
#167
asmacdo
opened
9 months ago
0
All templated bash scripts should be "robust" and shellcheck-clean
#166
yarikoptic
opened
9 months ago
0
add backoff strategy for job polling
#165
asmacdo
closed
9 months ago
0
[DOCS] minor changes in eg walkthrough: explain when Step 0 is optional
#164
zhao-cy
closed
9 months ago
0
[DOCS] update paper citation
#163
zhao-cy
opened
9 months ago
0
[DOCS] update contact email and add BABS paper
#162
zhao-cy
closed
9 months ago
1
Make "Will check the test job's status every" smarter
#161
yarikoptic
closed
9 months ago
0
Make parsing of output more robust
#160
yarikoptic
opened
10 months ago
0
Step 0 does not affect the end result
#159
asmacdo
closed
9 months ago
3
[FIX] `babs-init` creates a new branch `git-annex adjusted branch` at the end for `analysis` DataLad dataset
#158
zhao-cy
closed
7 months ago
6
[FIX] fix `git commit --amend` error during `babs-init`
#157
zhao-cy
closed
10 months ago
1
[FIX] `git commit --amend`error when `babs-init`: need to add `--allow-empty`?
#156
zhao-cy
opened
10 months ago
2
Don't hardcode python interpreter in scripts
#155
asmacdo
closed
11 months ago
1
[DOCS] docs enhancements from Austin
#154
zhao-cy
opened
11 months ago
2
[DOCS] update example walkthrough: to use `$TMP"` for CUBIC cluster
#153
zhao-cy
opened
11 months ago
0
[DOCS] ask Taylor to review new NMIND check achievements
#152
zhao-cy
closed
11 months ago
3
(silver) A statement of supported operating systems / environments (i.e., could be a container recipe)
#151
zhao-cy
closed
11 months ago
0
(silver) Any alternative usage that is advertised is thoroughly documented
#150
zhao-cy
closed
11 months ago
0
(silver) Background/significance of program
#149
zhao-cy
closed
11 months ago
0
[DOCS] achieve checks in NMIND docs domain at silver level
#148
zhao-cy
closed
11 months ago
0
(silver) Issue template(s) available (i.e., information requested by developers)
#147
zhao-cy
closed
11 months ago
0
[DOCS] update docs during paper revision
#146
zhao-cy
closed
11 months ago
1
[ENH] `babs-status`: parse keywords of "Error" and "Warning" automatically without pre-definition from the user
#145
zhao-cy
closed
11 months ago
1
[DOCS] add to `babs-check-setup` CLI doc: what if it fails / not desired setup
#144
zhao-cy
closed
11 months ago
0
[FIX] Fix validator for unzipped input datasets: considering folders not in patterns of `sub-*`
#143
zhao-cy
closed
1 year ago
1
babs-init raises exception when there is no ses- folders in a non sub- folder.
#142
Michael-Sun
closed
1 year ago
4
Change permissions on NFS4 ACL filesystems in order to remove git annex files
#141
Michael-Sun
opened
1 year ago
1
FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas.
#140
Michael-Sun
opened
1 year ago
4
UnicodeEncodeError: 'latin-1' codec can't encode character '\u2713' in position 0: ordinal not in range(256)
#139
Michael-Sun
opened
1 year ago
1
[FIX] path generated by BABS is too long for freesurfer to function/run properly
#138
yibeichan
opened
1 year ago
15
errors encountered during fmriprep via babs
#137
yibeichan
closed
1 year ago
5
[FIX] no 'analysis/code/babs_proj_config.yaml' file from `babs-check-setup`
#136
yibeichan
closed
1 year ago
18
[DOCS] minor fix in docs
#135
zhao-cy
closed
1 year ago
0
[FIX] add a function for deciding the command for job cancellation based on cluster system
#134
zhao-cy
closed
1 year ago
1
[FIX] resubmitting jobs that are in queue: use `scancel` to delete the job in queue on Slurm clusters
#133
zhao-cy
closed
1 year ago
4
[DOCS] clean example YAML files
#132
zhao-cy
closed
1 year ago
0
[DOCS] minor changes in example walkthrough and docs for jobs
#131
zhao-cy
closed
1 year ago
0
Add issue templates
#130
tsalo
closed
11 months ago
2
[DOCS] add guide on how to test BABS
#129
zhao-cy
closed
1 year ago
0
[DOCS] (NMIND bronze) Provide instructions for users to run tests that include instructions for evaluation for correct behavior
#128
zhao-cy
closed
1 year ago
1
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