Quality (actions, pre-commit) and tests #31
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- Added opionated yaml linter to pre-commit hook and github action - Requires shell command to filter and exclude snakemake and snakebids files - Run yamlfix on all other yaml files
- Add gitignore - Add bids_dir - Adds necessary derivatives - dwi is doubled to perform two different tests (one for dwi_dir flag) - freesurfer directories / files
- ensure paths passed through are absolute (exception for testing) - fix workflow issues
- add poe task for testing --responsemean_dir flag - fixed responsemean call (expansion over subjects)
- Created check_dir_path function to check if user passed directories are absolute paths. Throw an error otherwise - Replace existing checks in freesurfer and mrtpipelines with function.
- Added dwi_flag for preprocessed data - Added check to make sure absolute path is passed - Added test data within prepdwi directory for testing purposes
kaitj
added
the
maintenance
4 tasks
- Added tpl and updated names for MNI152NLin6Asym - Renamed MNI2009b -> MNI152NLin2009bAsym - Removed unnecessary files - Update config
- Update config to include tsv for subcortical labels
- Update freesurfer tsv to match bids spec - Update file name of Freesurfer dseg tsv
- Add inputs to rule all for copying freesurfer and zona tsv files to appropriate location
- Still need to fix piping of workflow, update entities, and filenames
- Adds in rule for labelmerge (needs updating with container and proper command) - Update resources with correct names and paths - Add tsv to rule all for copying from resource to bids folders for labelmerge - Simplify rule all
tkkuehn
approved these changes
Dec 5, 2022
|
Will merge once we get #30 merged into |
Labelmerge
tkkuehn
requested changes
Dec 5, 2022
tkkuehn
approved these changes
Dec 5, 2022
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Proposed changes
This PR consolidates the changes first introduced in #18, adding quality actions and tasks. Additionally, adds dry-run testing for different flag options, namely to ensure the additional directory flags do not cause any issues for the workflow.
Note that this PR only ensure the dry-runs can pass without issues.
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