PennLINC babs issues - Githubissues

PennLINC / babs

BIDS App Bootstrap (BABS)

https://pennlinc-babs.readthedocs.io

MIT License

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issues

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Support SLURM array jobs in `babs-submit`

#175 tsalo opened 3 days ago
2
Allow `babs-init` to create the container dataset

#174 tsalo opened 3 days ago
0
Consolidate `--where-project` and `--project-name` in `babs-init`

#173 tsalo opened 3 days ago
0
Convert `--project-root` parameter in CLIs to positional argument

#172 tsalo opened 3 days ago
0
[ENH] Add workflow for processing and adding new subjects to BABS results

#171 mattcieslak opened 4 months ago
0
Make e2e testing run on PRs as well as e.g. weekly

#170 yarikoptic opened 4 months ago
0
Introducing e2e slurm tests

#169 asmacdo closed 4 months ago
2
Deprecation warning from pandas during `babs-status`

#168 asmacdo closed 5 months ago
3
Add user-configurable environment variable passthrough

#167 asmacdo opened 5 months ago
0
All templated bash scripts should be "robust" and shellcheck-clean

#166 yarikoptic opened 6 months ago
0
add backoff strategy for job polling

#165 asmacdo closed 6 months ago
0
[DOCS] minor changes in eg walkthrough: explain when Step 0 is optional

#164 zhao-cy closed 6 months ago
0
[DOCS] update paper citation

#163 zhao-cy opened 6 months ago
0
[DOCS] update contact email and add BABS paper

#162 zhao-cy closed 6 months ago
1
Make "Will check the test job's status every" smarter

#161 yarikoptic closed 6 months ago
0
Make parsing of output more robust

#160 yarikoptic opened 6 months ago
0
Step 0 does not affect the end result

#159 asmacdo closed 6 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 4 months ago
6
[FIX] fix `git commit --amend` error during `babs-init`

#157 zhao-cy closed 7 months ago
1
[FIX] `git commit --amend`error when `babs-init`: need to add `--allow-empty`?

#156 zhao-cy opened 7 months ago
2
Don't hardcode python interpreter in scripts

#155 asmacdo closed 8 months ago
1
[DOCS] docs enhancements from Austin

#154 zhao-cy opened 8 months ago
2
[DOCS] update example walkthrough: to use `$TMP"` for CUBIC cluster

#153 zhao-cy opened 8 months ago
0
[DOCS] ask Taylor to review new NMIND check achievements

#152 zhao-cy closed 8 months ago
3
(silver) A statement of supported operating systems / environments (i.e., could be a container recipe)

#151 zhao-cy closed 8 months ago
0
(silver) Any alternative usage that is advertised is thoroughly documented

#150 zhao-cy closed 8 months ago
0
(silver) Background/significance of program

#149 zhao-cy closed 8 months ago
0
[DOCS] achieve checks in NMIND docs domain at silver level

#148 zhao-cy closed 8 months ago
0
(silver) Issue template(s) available (i.e., information requested by developers)

#147 zhao-cy closed 8 months ago
0
[DOCS] update docs during paper revision

#146 zhao-cy closed 8 months ago
1
[ENH] `babs-status`: parse keywords of "Error" and "Warning" automatically without pre-definition from the user

#145 zhao-cy closed 8 months ago
1
[DOCS] add to `babs-check-setup` CLI doc: what if it fails / not desired setup

#144 zhao-cy closed 8 months ago
0
[FIX] Fix validator for unzipped input datasets: considering folders not in patterns of `sub-*`

#143 zhao-cy closed 9 months ago
1
babs-init raises exception when there is no ses- folders in a non sub- folder.

#142 Michael-Sun closed 9 months ago
4
Change permissions on NFS4 ACL filesystems in order to remove git annex files

#141 Michael-Sun opened 9 months ago
1
FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas.

#140 Michael-Sun opened 9 months ago
4
UnicodeEncodeError: 'latin-1' codec can't encode character '\u2713' in position 0: ordinal not in range(256)

#139 Michael-Sun opened 9 months ago
1
[FIX] path generated by BABS is too long for freesurfer to function/run properly

#138 yibeichan opened 10 months ago
15
errors encountered during fmriprep via babs

#137 yibeichan closed 9 months ago
5
[FIX] no 'analysis/code/babs_proj_config.yaml' file from `babs-check-setup`

#136 yibeichan closed 10 months ago
18
[DOCS] minor fix in docs

#135 zhao-cy closed 11 months ago
0
[FIX] add a function for deciding the command for job cancellation based on cluster system

#134 zhao-cy closed 11 months ago
1
[FIX] resubmitting jobs that are in queue: use `scancel` to delete the job in queue on Slurm clusters

#133 zhao-cy closed 11 months ago
4
[DOCS] clean example YAML files

#132 zhao-cy closed 11 months ago
0
[DOCS] minor changes in example walkthrough and docs for jobs

#131 zhao-cy closed 11 months ago
0
Add issue templates

#130 tsalo closed 8 months ago
2
[DOCS] add guide on how to test BABS

#129 zhao-cy closed 11 months ago
0
[DOCS] (NMIND bronze) Provide instructions for users to run tests that include instructions for evaluation for correct behavior

#128 zhao-cy closed 11 months ago
1
[DOCS] (NMIND gold) Continuous integration badges in README for coverage

#127 zhao-cy opened 11 months ago
1
[DOCS/TESTS] set up Codecov github workflow

#126 zhao-cy opened 11 months ago
0