Make CLI commands available as cubids <command> (#268)

* Add linting job. * Run black and isort. * Keep working on formatting. * Forgot to install the linters... * Wrong code path. * Address style issues in cubids. * Address style issues in validator. * Update metadata_merge.py * Make cubids a command-line interface. * Add deprecation warnings. * Improve messages. * Fix help strings. * Further refactor the CLI workflows. * Work on failing test. * Update the CLIs. * Update config.yml * Move test data files.
PennLINC · Jan 17, 2024 · 8e90140 · 8e90140
1 parent 068e319
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -68,7 +68,7 @@ jobs:
 
   deploy_pypi:
     machine:
-      image: circleci/classic:201711-01
+      image: ubuntu-2004:202201-02
     working_directory: /tmp/src/CuBIDS
     steps:
       - checkout:

diff --git a/BIDS_Dataset/README b/BIDS_Dataset/README
diff --git a/BIDS_Dataset/dataset_description.json b/BIDS_Dataset/dataset_description.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json b/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json
diff --git a/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz b/BIDS_Dataset/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz