Merge branch 'main' into brchg/submit_array

Author: tien-tong

babs/babs.py

@@ -1239,7 +1239,6 @@ def babs_submit(self, count=1, df_job_specified=None):
                     # save updated df:
                     df_job_updated.to_csv(self.job_status_path_abs, index=False)
                     df_job_submit_updated.to_csv(self.job_submit_path_abs, index=False)
-
                 # here, the job status was not checked, so message from `report_job_status()`
                 #   based on current df is not trustable:
                 # # Report the job status:

babs/utils.py

@@ -76,8 +76,8 @@ How to install ``datalad-osf``::
     # Install datalad-osf:
     pip install datalad-osf
 
-    # Provide your OSF credentials (token) - this step is very important!
-    datalad osf-credentials
+    # Provide your OSF credentials  - this step is very important!
+    datalad osf-credentials --method userpassword
 
 
 Installation reference

docs/source/installation.rst

@@ -286,8 +286,8 @@ Below is an example YAML file for toy BIDS App:
 
 As you can see, there are several sections in this YAML file.
 
-Here, in section ``singularity_run``,
-both ``--dummy`` and ``-v`` are dummy arguments to this toy BIDS Apps:
+Here, in section ``singularity_run``, ``$SUBJECT_SELECTION_FLAG`` designates the flag used for selecting participants in the BIDS app.
+. Additionally, both ``--dummy`` and ``-v`` are dummy arguments to this toy BIDS Apps:
 argument ``--dummy`` can take any value afterwards, whereas argument ``-v`` does not take values.
 Here we use these arguments to show examples of:
 

docs/source/walkthrough.rst

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-20-2-3_anatonly.yaml

@@ -18,6 +18,7 @@
 #     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
 #     --input freesurfer <path/to/cloned_freesurfer_output_ria>    # 2nd input dataset \
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
     --n_cpus: '1'

notebooks/eg_fmriprep-20-2-3_ingressed-fs.yaml

@@ -12,6 +12,7 @@
 
 # Arguments when executing the BIDS App using `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-20-2-3_regular.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: "1"
     --stop-on-first-crash: ""

notebooks/eg_fmriprep-23-1-3_anatonly.yaml

@@ -18,6 +18,7 @@
 #     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
 #     --input fmriprep_anat <path/to/cloned_fmriprep_anat_output_ria>    # 2nd input dataset \
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'

notebooks/eg_fmriprep-23-1-3_ingressed-fs.yaml

@@ -12,6 +12,7 @@
 
 # Arguments in `singularity run`:
 singularity_run:
+    $SUBJECT_SELECTION_FLAG: "--participant-label"
     -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
     --n_cpus: '1'
     --stop-on-first-crash: ""