update snakebids dependency

.github/workflows/python-testing.yml

@@ -148,10 +148,10 @@ jobs:
         poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
     - name: Test cropseg bids, with path override
       run: |
-        poetry run hippunfold - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+        poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
     - name: Test cropseg bids, with path override, left hemi
       run: | 
-        poetry run hippunfold - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
+        poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
     - name: Test T2w with T1w template registration
       run: |
         poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template

docs/tutorials/specializedScans.md

@@ -41,7 +41,7 @@ Here is an example of what the input directory might look like:
 
 This can be unfolded with the command:
 
-    hippunfold - PATH_TO_OUTPUT_DIR participant --modality cropseg \
+    hippunfold . PATH_TO_OUTPUT_DIR participant --modality cropseg \
     --path_cropseg exvivo/sub-{subject}/sub-{subject}_hemi-{hemi}_desc-hippo_dseg.nii.gz \
     --hemi R --skip_inject_template_labels
 
@@ -87,7 +87,7 @@ hippocampus. Once done, we may have a directory like this:
 
 Note that only the last file is needed for unfolding:
 
-    hippunfold - PATH_TO_OUTPUT_DIR participant --output_spaces corobl --hemi R --no_reg_template \
+    hippunfold . PATH_TO_OUTPUT_DIR participant --output_spaces corobl --hemi R --no_reg_template \
     --path_T2w PATH_TO_EXVIVO_DIR/sub-001/sub-001_hemi-R_desc-exvivo_space-CITI168_T2w.nii.gz \
     --output_spaces corobl
 

docs/tutorials/standardBIDS.md

@@ -79,7 +79,7 @@ HippUnfold will not recognize them without the suffix `_T2w`. We can
 thus use the `--path_T2w` flag to specify exactly which of these file(s)
 to use as inputs:
 
-    hippunfold - PATH_TO_OUTPUT_DIR participant \
+    hippunfold . PATH_TO_OUTPUT_DIR participant \
     --path_T1w PATH_TO_nonBIDS_DIR/sub-001_T1w.nii.gz \
     --path_T2w PATH_TO_nonBIDS_DIR/sub-{subject}_T2SPACE.nii.gz
 

hippunfold/workflow/Snakefile

@@ -79,6 +79,7 @@ config.update(
         participant_label=config["participant_label"],
         exclude_participant_label=config["exclude_participant_label"],
         limit_to=list(limit_to_list),
+        use_bids_inputs=False,
     )
 )
 

pyproject.toml

@@ -7,7 +7,7 @@ authors = ["Jordan DeKraker & Ali Khan <alik@robarts.ca>"]
 [tool.poetry.dependencies]
 python = ">=3.7.1,<3.10"
 snakemake = ">=6.0.0"
-snakebids = ">0.4.0"
+snakebids = ">=0.5.1"
 batchgenerators = "0.21"
 nnunet-inference-on-cpu-and-gpu = "1.6.6"
 numpy = "1.21.2"