Merge branch 'main' into fix-local-testing

Author: tien-tong

babs/bootstrap.py

@@ -3,6 +3,7 @@
 import os
 import os.path as op
 import subprocess
+import tempfile
 from pathlib import Path
 
 import datalad.api as dlapi
@@ -77,8 +78,11 @@ def babs_bootstrap(
                 f"The parent folder '{parent_dir}' does not exist! `babs init` won't proceed."
             )
 
-        # check if parent directory is writable:
-        if not os.access(parent_dir, os.W_OK):
+        # check if parent directory is writable (os.access unreliable on NFS/ACL):
+        try:
+            with tempfile.TemporaryFile(dir=parent_dir):
+                pass
+        except OSError:
             raise ValueError(
                 f"The parent folder '{parent_dir}' is not writable! `babs init` won't proceed."
             )

babs/templates/participant_job.sh.jinja2

@@ -164,6 +164,6 @@ datalad push --to output-storage
 echo '# Push the branch with provenance records:'
 # DSLOCKFILE set by sbatch --export= in container.py
 # shellcheck disable=SC2154
-flock "${DSLOCKFILE}" git push outputstore
+flock "${DSLOCKFILE}" git push outputstore "${BRANCH}"
 
 echo SUCCESS

babs/utils.py

@@ -648,10 +648,12 @@ def update_results_status(
         & ~updated_results_df['state'].isin(['PD', 'R'])
     )
 
-    # Drop the completion columns
-    updated_results_df = updated_results_df.drop(
-        columns=['job_id_completion', 'task_id_completion']
-    )
+    # Drop all completion columns (job_id, task_id, and any other overlapping
+    # columns like ses_id_completion when use_sesid was False in a prior run)
+    completion_suffix_columns = [
+        col for col in updated_results_df.columns if col.endswith('_completion')
+    ]
+    updated_results_df = updated_results_df.drop(columns=completion_suffix_columns)
 
     return updated_results_df
 

docs/walkthrough.rst

@@ -354,6 +354,13 @@ and results and provenance are saved. An example command of ``babs init`` is as
         --queue slurm \
         "${HOME}/babs_demo/my_BABS_project"
 
+Retrieve the container:
+
+..  code-block:: console
+
+    $ cd "${HOME}/babs_demo/my_BABS_project/analysis"
+    $ datalad get -r containers
+
 .. note::
     **Optional: Throttling array jobs**: If you have many jobs and want to limit how many
     run simultaneously, you can add ``--throttle <number>`` to the command above.