From 85495235bf56eab19be576e39cc7f5b6b96b7ca5 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 11:57:16 -0500
Subject: [PATCH 01/12] Improvements for dev testing

- Use base Docker image directly instead of rebuilding for tests
  - Avoid double overlay/install
  - Avoid container rebuild for every change
- Remove docker build step from test scripts and CI
- Fix hardcoded paths to work from any checkout
- CI e2e job calls e2e_in_docker.sh directly
  - script was broken and untested

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .circleci/config.yml           | 29 +++++++----------------------
 Dockerfile_testing             |  6 ------
 docs/developer_how_to_test.rst | 21 +++++++++++++++++++--
 tests/e2e_in_docker.sh         | 19 +++++++------------
 tests/pytest_in_docker.sh      | 11 +++++------
 5 files changed, 38 insertions(+), 48 deletions(-)
 delete mode 100644 Dockerfile_testing

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 77deed95..12b7d3d0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -18,18 +18,15 @@ jobs:
           name: pytest of BABS
           no_output_timeout: 1h
           command: |
-            docker build \
-            -t pennlinc/slurm-docker-ci:unstable \
-            -f Dockerfile_testing .
-
-            # Make a directory that will hold the test artifacts
             mkdir -p ${HOME}/e2e-testing
             docker run -it \
-                -v ${PWD}:/tests \
+                -v ${PWD}:/babs \
                 -v ${HOME}/e2e-testing:/test-temp:rw \
+                -w /babs \
                 -h slurmctl --cap-add sys_admin \
                 --privileged \
-                pennlinc/slurm-docker-ci:unstable \
+                pennlinc/slurm-docker-ci:0.14 \
+                bash -c "pip install -e .[tests] && \
                 pytest -n 4 -sv \
                     --durations=0 \
                     --timeout=300 \
@@ -37,7 +34,7 @@ jobs:
                     --cov-report term-missing \
                     --cov-report xml:/test-temp/coverage.xml \
                     --cov=babs \
-                    /babs
+                    /babs/tests/"
 
       - store_test_results:
           path: /home/circleci/e2e-testing/junit.xml
@@ -54,22 +51,10 @@ jobs:
       - checkout:
           path: /home/circleci/src/babs
       - run:
-          name: pytest of BABS
+          name: e2e SLURM tests
           no_output_timeout: 1h
           command: |
-            docker build \
-            -t pennlinc/slurm-docker-ci:unstable \
-            -f Dockerfile_testing .
-
-            # Make a directory that will hold the test artifacts
-            mkdir -p ${HOME}/e2e-testing
-            docker run -it \
-                -v ${PWD}:/tests \
-                -v ${HOME}/e2e-testing:/test-temp:rw \
-                -h slurmctl --cap-add sys_admin \
-                --privileged \
-                pennlinc/slurm-docker-ci:unstable \
-                /tests/tests/e2e-slurm/container/walkthrough-tests.sh
+            E2E_DIR=${HOME}/e2e-testing bash tests/e2e_in_docker.sh
 
       - run:
           name: clean up test artifacts
diff --git a/Dockerfile_testing b/Dockerfile_testing
deleted file mode 100644
index 4b0cff97..00000000
--- a/Dockerfile_testing
+++ /dev/null
@@ -1,6 +0,0 @@
-FROM pennlinc/slurm-docker-ci:0.14
-
-# install BABS in development mode for proper coverage tracking
-COPY . /babs
-WORKDIR /babs
-RUN pip install -e .[tests]
diff --git a/docs/developer_how_to_test.rst b/docs/developer_how_to_test.rst
index a3292243..2cd0bf13 100644
--- a/docs/developer_how_to_test.rst
+++ b/docs/developer_how_to_test.rst
@@ -25,8 +25,25 @@ Manually run pytest
 
 The easiest way to run pytest is to run the ``tests/pytest_in_docker.sh`` script
 from the root directory of BABS.
-This will build a docker container that has a running SLURM job scheduler system.
-It will also install the local copy of BABS and run the pytests in the container.
+This runs the tests inside a Docker container that has a running SLURM job scheduler system,
+and installs the local copy of BABS at runtime via volume mount.
+
+.. code-block:: bash
+
+   bash tests/pytest_in_docker.sh
+
+To run the end-to-end walkthrough tests (``babs init`` → ``submit`` → ``merge``):
+
+.. code-block:: bash
+
+   bash tests/e2e_in_docker.sh
+
+By default, e2e test artifacts go to a temporary directory under ``/tmp``.
+To specify a location (e.g., for inspection after the run):
+
+.. code-block:: bash
+
+   E2E_DIR=/path/to/output bash tests/e2e_in_docker.sh
 
 -----------------------------
 Automatic pytest via CircleCI
diff --git a/tests/e2e_in_docker.sh b/tests/e2e_in_docker.sh
index 9de3de14..a571a449 100755
--- a/tests/e2e_in_docker.sh
+++ b/tests/e2e_in_docker.sh
@@ -1,17 +1,12 @@
 #!/bin/bash
-mkdir -p "${HOME}"/projects/e2e-testing
-docker build --platform linux/amd64 \
-    -t pennlinc/slurm-docker-ci:unstable \
-    -f Dockerfile_testing .
+E2E_DIR="${E2E_DIR:-$(mktemp -d /tmp/babs-e2e-XXXXXX)}"
+mkdir -p "${E2E_DIR}"
+echo "E2E_DIR=${E2E_DIR}"
 docker run -it \
     --platform linux/amd64 \
-    -v "${HOME}"/projects/babs:/tests \
-    -v "${HOME}"/projects/e2e-testing:/test-temp:rw \
+    -v "$(pwd)":/tests \
+    -v "${E2E_DIR}":/test-temp:rw \
     -h slurmctl --cap-add sys_admin \
     --privileged \
-    pennlinc/slurm-docker-ci:unstable #\
-        #/babs/tests/e2e-slurm/container/walkthrough-tests.sh
-
-
-    #pytest -svx --pdb \
-    #/babs/tests
\ No newline at end of file
+    pennlinc/slurm-docker-ci:0.14 \
+        /tests/tests/e2e-slurm/container/walkthrough-tests.sh
diff --git a/tests/pytest_in_docker.sh b/tests/pytest_in_docker.sh
index c8646923..509c3252 100755
--- a/tests/pytest_in_docker.sh
+++ b/tests/pytest_in_docker.sh
@@ -1,15 +1,14 @@
 #!/bin/bash
-docker build --platform linux/amd64 -t pennlinc/slurm-docker-ci:unstable -f Dockerfile_testing .
 docker run -it \
     --platform linux/amd64 \
     -h slurmctl --cap-add sys_admin \
     --privileged \
-    -v "${HOME}"/projects/babs:/babs \
-    pennlinc/slurm-docker-ci:unstable \
-        pytest -svx \
+    -v "$(pwd)":/babs \
+    -w /babs \
+    pennlinc/slurm-docker-ci:0.14 \
+        bash -c "pip install -e .[tests] && pytest -svx \
         --cov-report=term-missing \
         --cov-report=xml \
         --cov=babs \
         --pdb \
-        /babs/tests/
-    
\ No newline at end of file
+        /babs/tests/"

From ef2b97ff14c9eb5691afaf4337a711384672b6ef Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 12:30:23 -0500
Subject: [PATCH 02/12] Write test artifacts to tmp_path instead of repo root

Tests were writing generated shell scripts to the working directory,
which left root-owned files in the checkout when run via Docker.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 tests/test_generate_bidsapp_runscript.py | 8 ++++----
 tests/test_generate_submit_script.py     | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/test_generate_bidsapp_runscript.py b/tests/test_generate_bidsapp_runscript.py
index 9c454475..19a34402 100644
--- a/tests/test_generate_bidsapp_runscript.py
+++ b/tests/test_generate_bidsapp_runscript.py
@@ -112,7 +112,7 @@ def test_get_input_unipping_cmds():
 
 
 @pytest.mark.parametrize(('input_datasets', 'config_file', 'processing_level'), testing_pairs)
-def test_generate_bidsapp_runscript(input_datasets, config_file, processing_level):
+def test_generate_bidsapp_runscript(input_datasets, config_file, processing_level, tmp_path):
     """Test that the bidsapp runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / config_file
     container_name = config_file.split('_')[1]
@@ -130,7 +130,7 @@ def test_generate_bidsapp_runscript(input_datasets, config_file, processing_leve
         templateflow_home='/path/to/templateflow_home',
     )
 
-    out_fn = Path('.') / f'{config_path.name}_{processing_level}.sh'
+    out_fn = tmp_path / f'{config_path.name}_{processing_level}.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))
@@ -164,7 +164,7 @@ def run_shellcheck(script_path):
         return False, str(e)
 
 
-def test_generate_pipeline_runscript():
+def test_generate_pipeline_runscript(tmp_path):
     """Test that the pipeline runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / 'eg_nordic-fmriprep_pipeline.yaml'
     config = read_yaml(config_path)
@@ -180,7 +180,7 @@ def test_generate_pipeline_runscript():
         final_zip_foldernames=config.get('zip_foldernames', {}),
     )
 
-    out_fn = Path('.') / f'{config_path.name}_pipeline.sh'
+    out_fn = tmp_path / f'{config_path.name}_pipeline.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))
diff --git a/tests/test_generate_submit_script.py b/tests/test_generate_submit_script.py
index 6d0868a3..62184ef0 100644
--- a/tests/test_generate_submit_script.py
+++ b/tests/test_generate_submit_script.py
@@ -91,7 +91,7 @@
 
 
 @pytest.mark.parametrize(('input_datasets', 'config_file', 'processing_level'), testing_pairs)
-def test_generate_submit_script(input_datasets, config_file, processing_level):
+def test_generate_submit_script(input_datasets, config_file, processing_level, tmp_path):
     """Test that the bidsapp runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / config_file
     container_name = config_file.split('_')[1]
@@ -107,7 +107,7 @@ def test_generate_submit_script(input_datasets, config_file, processing_level):
         zip_foldernames=config['zip_foldernames'],
     )
 
-    out_fn = Path('.') / f'participant_job_{config_path.name}_{processing_level}.sh'
+    out_fn = tmp_path / f'participant_job_{config_path.name}_{processing_level}.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))

From c7a8ed54e2441694d84b6694714e9770c8f3c93e Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 12:33:42 -0500
Subject: [PATCH 03/12] Write coverage.xml to /tmp instead of repo root

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 tests/pytest_in_docker.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pytest_in_docker.sh b/tests/pytest_in_docker.sh
index 509c3252..4251d601 100755
--- a/tests/pytest_in_docker.sh
+++ b/tests/pytest_in_docker.sh
@@ -8,7 +8,7 @@ docker run -it \
     pennlinc/slurm-docker-ci:0.14 \
         bash -c "pip install -e .[tests] && pytest -svx \
         --cov-report=term-missing \
-        --cov-report=xml \
+        --cov-report=xml:/tmp/coverage.xml \
         --cov=babs \
         --pdb \
         /babs/tests/"

From 54aff89bee720afe5762a1936f5fa5fc9b73acca Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 14:40:22 -0500
Subject: [PATCH 04/12] Discover container image path via containers-list and
 register at analysis level

Instead of hardcoding the container path as
containers/.datalad/environments/{name}/image, use datalad
containers-list to discover it from the container dataset, then
register it at the analysis level via containers-add. This makes
babs work with any container dataset layout.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/bootstrap.py | 46 +++++++++++++++++++++++++++++++++++++++-------
 babs/container.py |  7 +++----
 2 files changed, 42 insertions(+), 11 deletions(-)

diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 878f91f5..5cba7472 100644
--- a/babs/bootstrap.py
+++ b/babs/bootstrap.py
@@ -223,10 +223,38 @@ def babs_bootstrap(
         )
         # into `analysis/containers` folder
 
-        # Create initial container for sanity check
-        container = Container(container_ds, container_name, container_config)
+        # Discover container image path from the container dataset:
+        containers_path = op.join(self.analysis_path, 'containers')
+        result = dlapi.containers_list(dataset=containers_path, result_renderer='disabled')
+        container_info = [r for r in result
+                          if r['action'] == 'containers' and r['name'] == container_name]
+        if not container_info:
+            available = [r['name'] for r in result if r['action'] == 'containers']
+            raise ValueError(
+                f"Container '{container_name}' not found in container dataset. "
+                f"Available: {available}"
+            )
+        image_path_in_ds = op.relpath(container_info[0]['path'], containers_path)
+        container_image_path = op.join('containers', image_path_in_ds)
+
+        # Build call_fmt from user's singularity_args:
+        with open(container_config) as f:
+            user_config = yaml.safe_load(f)
+        singularity_args = user_config.get('singularity_args', [])
+        singularity_args_str = ' '.join(singularity_args) if singularity_args else ''
+        call_fmt = f'singularity run -B $PWD --pwd $PWD {singularity_args_str} {{img}} {{cmd}}'
+
+        # Register container at analysis level so datalad containers-run works:
+        print(f'\nRegistering container at analysis level: {container_image_path}')
+        dlapi.containers_add(
+            dataset=self.analysis_path,
+            name=container_name,
+            image=container_image_path,
+            call_fmt=call_fmt,
+        )
 
-        # sanity check of container ds:
+        container = Container(container_ds, container_name, container_config,
+                              container_image_path=container_image_path)
         container.sanity_check(self.analysis_path)
 
         # ==============================================================
@@ -250,9 +278,11 @@ def babs_bootstrap(
             container = containers[0]
         else:
             self._bootstrap_single_app_scripts(
-                container_ds, container_name, container_config, system
+                container_ds, container_name, container_config, system,
+                container_image_path=container_image_path,
             )
-            container = Container(container_ds, container_name, container_config)
+            container = Container(container_ds, container_name, container_config,
+                                  container_image_path=container_image_path)
 
         # Copy in any other files needed:
         self._init_import_files(container.config.get('imported_files', []))
@@ -390,10 +420,12 @@ def babs_bootstrap(
         print('`babs init` was successful!')
 
     def _bootstrap_single_app_scripts(
-        self, container_ds, container_name, container_config, system
+        self, container_ds, container_name, container_config, system,
+        container_image_path=None,
     ):
         """Bootstrap scripts for single BIDS app configuration."""
-        container = Container(container_ds, container_name, container_config)
+        container = Container(container_ds, container_name, container_config,
+                              container_image_path=container_image_path)
 
         # Generate `<containerName>_zip.sh`: ----------------------------------
         # which is a bash script of singularity run + zip
diff --git a/babs/container.py b/babs/container.py
index f3296286..36cad45b 100644
--- a/babs/container.py
+++ b/babs/container.py
@@ -14,7 +14,8 @@
 class Container:
     """This class is for the BIDS App Container"""
 
-    def __init__(self, container_ds, container_name, config_yaml_file):
+    def __init__(self, container_ds, container_name, config_yaml_file,
+                 container_image_path=None):
         """
         This is to initialize Container class.
 
@@ -67,9 +68,7 @@ def __init__(self, container_ds, container_name, config_yaml_file):
         with open(self.config_yaml_file) as f:
             self.config = yaml.safe_load(f)
 
-        self.container_path_relToAnalysis = op.join(
-            'containers', '.datalad', 'environments', self.container_name, 'image'
-        )
+        self.container_path_relToAnalysis = container_image_path
 
     def sanity_check(self, analysis_path):
         """

From dd8b44b982c61522c318b994debc65be6d7e4a6d Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 15:44:24 -0500
Subject: [PATCH 05/12] Replace singularity run with datalad containers-run in
 job template

The job template now uses three steps instead of one:
1. datalad containers-run for the BIDS app
2. datalad run for zipping outputs
3. git rm for raw output cleanup (datalad run --explicit
   doesn't track deletions)

Container args parsed via existing bids_app_args_from_config and
passed through generate_submit_script to the template.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/container.py                        | 25 +++++++++++-
 babs/generate_submit_script.py           | 10 +++++
 babs/templates/participant_job.sh.jinja2 | 49 +++++++++++++++---------
 3 files changed, 64 insertions(+), 20 deletions(-)

diff --git a/babs/container.py b/babs/container.py
index 36cad45b..d5e56664 100644
--- a/babs/container.py
+++ b/babs/container.py
@@ -6,7 +6,10 @@
 import yaml
 from jinja2 import Environment, PackageLoader, StrictUndefined
 
-from babs.generate_bidsapp_runscript import generate_bidsapp_runscript
+from babs.generate_bidsapp_runscript import (
+    bids_app_args_from_config,
+    generate_bidsapp_runscript,
+)
 from babs.generate_submit_script import generate_submit_script, generate_test_submit_script
 from babs.utils import app_output_settings_from_config
 
@@ -164,16 +167,34 @@ def generate_bash_participant_job(
             Shown in the script error message when PROJECT_ROOT is unset.
         """
 
+        input_datasets = input_ds.as_records()
+        _, bids_app_output_dir = app_output_settings_from_config(self.config)
+
+        raw_bids_app_args = self.config.get('bids_app_args', None)
+        if raw_bids_app_args:
+            bids_app_args, subject_selection_flag, _, _, bids_app_input_dir = (
+                bids_app_args_from_config(raw_bids_app_args, input_datasets)
+            )
+        else:
+            bids_app_args = []
+            subject_selection_flag = '--participant-label'
+            bids_app_input_dir = input_datasets[0]['unzipped_path_containing_subject_dirs']
+
         script_content = generate_submit_script(
             queue_system=system.type,
             cluster_resources_config=self.config['cluster_resources'],
             script_preamble=self.config['script_preamble'],
             job_scratch_directory=self.config['job_compute_space'],
-            input_datasets=input_ds.as_records(),
+            input_datasets=input_datasets,
             processing_level=processing_level,
             container_name=self.container_name,
             zip_foldernames=self.config['zip_foldernames'],
             project_root=project_root,
+            container_image_path=self.container_path_relToAnalysis,
+            bids_app_args=bids_app_args,
+            bids_app_input_dir=bids_app_input_dir,
+            bids_app_output_dir=bids_app_output_dir,
+            subject_selection_flag=subject_selection_flag,
         )
 
         with open(bash_path, 'w') as f:
diff --git a/babs/generate_submit_script.py b/babs/generate_submit_script.py
index c586619d..0ed9fd8a 100644
--- a/babs/generate_submit_script.py
+++ b/babs/generate_submit_script.py
@@ -30,6 +30,11 @@ def generate_submit_script(
     container_images=None,
     datalad_run_message=None,
     project_root=None,
+    container_image_path=None,
+    bids_app_args=None,
+    bids_app_input_dir=None,
+    bids_app_output_dir=None,
+    subject_selection_flag=None,
 ):
     """
     Generate a bash script that runs the BIDS App singularity image.
@@ -122,6 +127,11 @@ def generate_submit_script(
         container_images=container_images,
         datalad_run_message=datalad_run_message,
         project_root=project_root,
+        container_image_path=container_image_path,
+        bids_app_args=bids_app_args or [],
+        bids_app_input_dir=bids_app_input_dir or '',
+        bids_app_output_dir=bids_app_output_dir or '',
+        subject_selection_flag=subject_selection_flag or '',
     )
 
 
diff --git a/babs/templates/participant_job.sh.jinja2 b/babs/templates/participant_job.sh.jinja2
index 9b4786b6..8a134d0a 100644
--- a/babs/templates/participant_job.sh.jinja2
+++ b/babs/templates/participant_job.sh.jinja2
@@ -107,9 +107,8 @@ fi
 {{ zip_locator_text }}
 
 # Link to shared container image so each job does not re-clone the same image.
-# If shared path is not available (e.g. Slurm Docker workers), retrieve image in this clone.
-CONTAINER_SHARED="${PROJECT_ROOT}/analysis/containers/.datalad/environments/{{ container_name }}/image"
-CONTAINER_JOB="containers/.datalad/environments/{{ container_name }}/image"
+CONTAINER_SHARED="${PROJECT_ROOT}/analysis/{{ container_image_path }}"
+CONTAINER_JOB="{{ container_image_path }}"
 
 if [ ! -L "${CONTAINER_SHARED}" ]; then
   echo "ERROR: shared container image not found at ${CONTAINER_SHARED}" >&2
@@ -125,35 +124,49 @@ if [ ! -L "${CONTAINER_JOB}" ]; then
   exit 1
 fi
 
-# datalad run:
-datalad run \
-	-i "{{ run_script_relpath if run_script_relpath else 'code/' + container_name + '_zip.sh' }}" \
+# Step 1: Run BIDS app via containers-run
+datalad containers-run \
+	-n {{ container_name }} \
+	--explicit \
 {% for input_dataset in input_datasets %}
 {% if not input_dataset['is_zipped'] %}
-	-i "{{ input_dataset['unzipped_path_containing_subject_dirs'] }}/{% raw %}${subid}{% endraw %}{% if processing_level == 'session' %}/{% raw %}${sesid}{% endraw %}{% endif %}" \
-	-i "{{ input_dataset['path_in_babs'] }}/dataset_description.json" \
+	--input "{{ input_dataset['unzipped_path_containing_subject_dirs'] }}/{% raw %}${subid}{% endraw %}{% if processing_level == 'session' %}/{% raw %}${sesid}{% endraw %}{% endif %}" \
+	--input "{{ input_dataset['path_in_babs'] }}/dataset_description.json" \
 {% else %}
-	-i "${%raw%}{{%endraw%}{{ input_dataset['name'].upper() }}_ZIP{%raw%}}{%endraw%}" \
+	--input "${%raw%}{{%endraw%}{{ input_dataset['name'].upper() }}_ZIP{%raw%}}{%endraw%}" \
 {% endif %}
 {% endfor %}
-{% if container_images %}
-{% for image_path in container_images %}
-	-i "{{ image_path }}" \
-{% endfor %}
-{% else %}
-	-i "containers/.datalad/environments/{{container_name}}/image" \
-{% endif %}
 {% if datalad_expand_inputs %}
 	--expand inputs \
 {% endif %}
+	--output "{{ bids_app_output_dir }}" \
+	-m "{{ container_name }} {% raw %}${subid}{% endraw %}{% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %}" \
+	-- \
+	{{ bids_app_input_dir }} \
+	{{ bids_app_output_dir }} \
+	participant \
+{% for bids_app_arg in bids_app_args %}
+{% if bids_app_arg %}
+	{{ bids_app_arg }} \
+{% endif %}
+{% endfor %}
+	{{ subject_selection_flag }} "{% raw %}${subid}{% endraw %}"
+
+# Step 2: Zip outputs
+datalad run \
 	--explicit \
 {% if zip_foldernames is not none %}
 {% for key, value in zip_foldernames.items() %}
 	-o "{% raw %}${subid}{% endraw %}{% if processing_level == 'session' %}_{% raw %}${sesid}{% endraw %}{% endif %}_{{ key }}-{{ value }}.zip" \
 {% endfor %}
 {% endif %}
-	-m "{{ (datalad_run_message if datalad_run_message is defined and datalad_run_message else container_name) }} {% raw %}${subid}{% endraw %}{% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %}" \
-    "bash ./{{ run_script_relpath if run_script_relpath else 'code/' + container_name + '_zip.sh' }} {% raw %}${subid}{% endraw %} {% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %}{% for input_dataset in input_datasets %}{% if input_dataset['is_zipped'] %} ${%raw%}{{%endraw%}{{ input_dataset['name'].upper() }}_ZIP{%raw%}}{%endraw%}{%endif%}{%endfor%}"
+	-m "Zip {% raw %}${subid}{% endraw %}{% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %}" \
+	-- \
+	bash ./code/{{ container_name }}_zip.sh "{% raw %}${subid}{% endraw %}"{% if processing_level == 'session' %} "{% raw %}${sesid}{% endraw %}"{% endif %}
+
+# Step 3: Remove raw outputs (datalad run --explicit doesn't track deletions)
+git rm -rf {{ bids_app_output_dir }}
+git commit -m "Remove raw outputs for {% raw %}${subid}{% endraw %}{% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %} (zipped)"
 
 # Finish up:
 # push result file content to output RIA storage:

From bc6ab49fcbad464638ae62323f0f60013ba627d9 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 16:04:16 -0500
Subject: [PATCH 06/12] Generate zip-only script instead of singularity+zip
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The zip script no longer runs the container or removes outputs —
both are now handled by the job template (containers-run and git rm).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/bootstrap.py                    | 11 +++++------
 babs/container.py                    | 23 +++++++++++++++++++++++
 babs/templates/zip_outputs.sh.jinja2 |  9 +++++++++
 3 files changed, 37 insertions(+), 6 deletions(-)
 create mode 100644 babs/templates/zip_outputs.sh.jinja2

diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 5cba7472..9b116537 100644
--- a/babs/bootstrap.py
+++ b/babs/bootstrap.py
@@ -428,15 +428,14 @@ def _bootstrap_single_app_scripts(
                               container_image_path=container_image_path)
 
         # Generate `<containerName>_zip.sh`: ----------------------------------
-        # which is a bash script of singularity run + zip
-        # in folder: `analysis/code`
-        print('\nGenerating a bash script for running container and zipping the outputs...')
-        print('This bash script will be named as `' + container_name + '_zip.sh`')
+        # Zip-only script (container execution is now handled by containers-run
+        # in participant_job.sh)
+        print('\nGenerating zip script: ' + container_name + '_zip.sh')
         bash_path = op.join(self.analysis_path, 'code', container_name + '_zip.sh')
-        container.generate_bash_run_bidsapp(bash_path, self.input_datasets, self.processing_level)
+        container.generate_bash_zip_outputs(bash_path, self.processing_level)
         self.datalad_save(
             path='code/' + container_name + '_zip.sh',
-            message='Generate script of running container',
+            message='Generate zip script',
         )
 
         # make another folder within `code` for test jobs:
diff --git a/babs/container.py b/babs/container.py
index d5e56664..0c5d6b22 100644
--- a/babs/container.py
+++ b/babs/container.py
@@ -9,6 +9,7 @@
 from babs.generate_bidsapp_runscript import (
     bids_app_args_from_config,
     generate_bidsapp_runscript,
+    get_output_zipping_cmds,
 )
 from babs.generate_submit_script import generate_submit_script, generate_test_submit_script
 from babs.utils import app_output_settings_from_config
@@ -103,6 +104,28 @@ def sanity_check(self, analysis_path):
             + "'."
         )
 
+    def generate_bash_zip_outputs(self, bash_path, processing_level):
+        """Generate a bash script that only zips BIDS App outputs."""
+        dict_zip_foldernames, _ = app_output_settings_from_config(self.config)
+        cmd_zip = get_output_zipping_cmds(dict_zip_foldernames, processing_level)
+
+        env = Environment(
+            loader=PackageLoader('babs', 'templates'),
+            trim_blocks=True,
+            lstrip_blocks=True,
+            autoescape=False,
+            undefined=StrictUndefined,
+        )
+        template = env.get_template('zip_outputs.sh.jinja2')
+        script_content = template.render(
+            processing_level=processing_level,
+            cmd_zip=cmd_zip,
+        )
+
+        with open(bash_path, 'w') as f:
+            f.write(script_content)
+        os.chmod(bash_path, 0o700)
+
     def generate_bash_run_bidsapp(self, bash_path, input_ds, processing_level):
         """
         This is to generate a bash script that runs the BIDS App singularity image.
diff --git a/babs/templates/zip_outputs.sh.jinja2 b/babs/templates/zip_outputs.sh.jinja2
new file mode 100644
index 00000000..b6e59c29
--- /dev/null
+++ b/babs/templates/zip_outputs.sh.jinja2
@@ -0,0 +1,9 @@
+#!/bin/bash
+set -e -u -x
+
+subid="$1"
+{% if processing_level == 'session' %}
+sesid="$2"
+{% endif %}
+
+{{ cmd_zip }}

From e6afd81e7bcb1f1d69c3fa0c7f9136e9804dfbb8 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 16:36:14 -0500
Subject: [PATCH 07/12] Include .datalad in sparse-checkout for containers-run

The job clone uses --no-checkout + sparse-checkout. Cone mode does
not include dotfile directories by default, so .datalad/config (where
containers-add registers the container) was missing. This caused
"No known containers" errors at job runtime.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/templates/participant_job.sh.jinja2 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/babs/templates/participant_job.sh.jinja2 b/babs/templates/participant_job.sh.jinja2
index 8a134d0a..052c7713 100644
--- a/babs/templates/participant_job.sh.jinja2
+++ b/babs/templates/participant_job.sh.jinja2
@@ -70,6 +70,7 @@ if ! git sparse-checkout init --cone; then
 fi
 
 git sparse-checkout set \
+  .datalad \
   code \
   containers \
 {% for input_dataset in input_datasets %}

From 29d63f16fa9ce5a51e0bf51046e009c7d25f4ae3 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 16:55:16 -0500
Subject: [PATCH 08/12] Use git rm --sparse for output cleanup

Output dirs created by containers-run are outside the sparse-checkout
cone, so git rm refuses to touch them without --sparse.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/templates/participant_job.sh.jinja2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/babs/templates/participant_job.sh.jinja2 b/babs/templates/participant_job.sh.jinja2
index 052c7713..3ed23125 100644
--- a/babs/templates/participant_job.sh.jinja2
+++ b/babs/templates/participant_job.sh.jinja2
@@ -166,7 +166,7 @@ datalad run \
 	bash ./code/{{ container_name }}_zip.sh "{% raw %}${subid}{% endraw %}"{% if processing_level == 'session' %} "{% raw %}${sesid}{% endraw %}"{% endif %}
 
 # Step 3: Remove raw outputs (datalad run --explicit doesn't track deletions)
-git rm -rf {{ bids_app_output_dir }}
+git rm -rf --sparse {{ bids_app_output_dir }}
 git commit -m "Remove raw outputs for {% raw %}${subid}{% endraw %}{% if processing_level == 'session' %} {% raw %}${sesid}{% endraw %}{% endif %} (zipped)"
 
 # Finish up:

From 295d4c826f53dacda3a26f252ec41f6037798b33 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 17:34:50 -0500
Subject: [PATCH 09/12] Fix writable check for NFS/ACL filesystems

os.access() is unreliable on NFS and ACL-based filesystems. Use
tempfile.TemporaryFile() to actually test write access.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/bootstrap.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 9b116537..13f1ae8f 100644
--- a/babs/bootstrap.py
+++ b/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."
             )

From 0e50464e389c23bfeae7602e330ac33944a79bef Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 17:45:08 -0500
Subject: [PATCH 10/12] Fetch container image during init for job symlink
 access

The PROJECT_ROOT symlink in job clones points to the analysis
dataset's container image. Without fetching the actual content
during init, it's just an annex pointer and singularity can't
open it.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 babs/bootstrap.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 13f1ae8f..57f2ace6 100644
--- a/babs/bootstrap.py
+++ b/babs/bootstrap.py
@@ -257,6 +257,14 @@ def babs_bootstrap(
             call_fmt=call_fmt,
         )
 
+        # Fetch container image so the PROJECT_ROOT symlink at job time
+        # resolves to actual content, not a dangling annex pointer:
+        print('\nFetching container image...')
+        dlapi.get(
+            dataset=self.analysis_path,
+            path=op.join(self.analysis_path, container_image_path),
+        )
+
         container = Container(container_ds, container_name, container_config,
                               container_image_path=container_image_path)
         container.sanity_check(self.analysis_path)

From 5e34541628e12e05d259ce3c0fb558cdba2a4b2d Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 18:51:35 -0500
Subject: [PATCH 11/12] Add design doc for containers-run support

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 design/containers-run.md | 211 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 211 insertions(+)
 create mode 100644 design/containers-run.md

diff --git a/design/containers-run.md b/design/containers-run.md
new file mode 100644
index 00000000..f3cdc545
--- /dev/null
+++ b/design/containers-run.md
@@ -0,0 +1,211 @@
+# Design: `datalad containers-run` support in BABS
+
+Issue: https://github.com/PennLINC/babs/issues/328
+
+## Goal
+
+Use `datalad containers-run` instead of direct `singularity run` for BIDS app
+execution. This provides:
+
+- **Dynamic container path discovery** — `datalad containers-list` reads the
+  path from the container dataset's `.datalad/config`, so BABS works with any
+  container dataset layout (not just the hardcoded
+  `containers/.datalad/environments/{name}/image`).
+- **Provenance tracking** — datalad records exactly which container ran and how.
+- **Compatibility with repronim/containers** — which uses
+  `images/bids/{name}.sif` instead of the default datalad-containers layout.
+
+## How it works
+
+### During `babs init`
+
+1. Clone container dataset as subdataset of analysis (unchanged)
+2. `datalad containers-list` discovers the image path in the container dataset
+3. `datalad containers-add` registers the container at the analysis level with:
+   - The discovered image path (relative to analysis)
+   - A `call_fmt` built from the user's `singularity_args` config
+4. `datalad get` fetches the container image content so it's available for job
+   symlinks
+
+### During job execution (`participant_job.sh`)
+
+Three-step flow replaces the single `datalad run` that called a combined
+singularity+zip script:
+
+1. **`datalad containers-run`** — runs the BIDS app. Container is accessed via
+   a PROJECT_ROOT symlink to the analysis dataset's fetched image.
+2. **`datalad run`** — calls a zip-only script (no longer contains singularity
+   invocation or output removal).
+3. **`git rm --sparse`** — removes raw outputs. Needed because `datalad run
+   --explicit` doesn't track file deletions. The `--sparse` flag is required
+   because outputs are outside the sparse-checkout cone.
+
+## Prior work
+
+An initial proof-of-concept was developed before upstream's sparse-checkout PR
+(#337) landed: https://github.com/asmacdo/babs/pull/6
+
+That POC was validated end-to-end on a SLURM cluster (Discovery) with both
+handmade container datasets and repronim/containers. Key findings from that
+work:
+
+- **Concurrent `datalad get` failures** — when multiple jobs run simultaneously,
+  they all try to fetch the same container image. Git-annex uses transfer locks,
+  causing all but one job to fail. This is a known git-annex bug:
+  https://git-annex.branchable.com/bugs/concurrent_get_from_separate_clones_fails/
+  The POC solved this with ephemeral clones for the containers subdataset.
+
+- **Ephemeral clones work for containers but not inputs** — container images are
+  resolved on the host before singularity launches, so annex symlinks outside
+  `$PWD` are fine. Input data needs to be accessible inside the container with
+  `--containall -B $PWD`, so symlinks outside `$PWD` break.
+
+- **`datalad run --explicit` doesn't track deletions** — discovered and
+  documented as an upstream issue. The workaround (separate `git rm` step) is
+  carried forward into this implementation.
+
+The current implementation was recreated from scratch on top of the
+sparse-checkout changes, using the POC as reference. The PROJECT_ROOT symlink
+approach (from upstream) combined with `datalad get` of the image during init
+avoids the concurrent get problem entirely — jobs never call `datalad get` for
+the container image, they just follow the symlink to the pre-fetched content.
+Ephemeral clones remain a potential future alternative.
+
+## Problems encountered
+
+### `git sparse-checkout` interaction
+
+The upstream sparse-checkout PR (#337) changed job clones to use
+`--no-checkout` + `git sparse-checkout`. This caused two issues:
+
+- **`.datalad/config` not checked out** — cone mode doesn't include
+  dot-directories by default. Fixed by adding `.datalad` to the sparse-checkout
+  set. Without it, `containers-run` fails with "No known containers."
+
+- **`git rm` blocked by sparse-checkout** — outputs created by `containers-run`
+  are outside the cone, so `git rm` refuses to touch them. Fixed with
+  `git rm --sparse`.
+
+### Container image access in job clones
+
+Job clones don't have the container image content — they clone from input RIA
+with `--no-checkout`. The existing PROJECT_ROOT symlink approach works: symlink
+from the job clone's container path to the analysis dataset's copy. But this
+requires the analysis dataset to have the actual content (not just an annex
+pointer), so `datalad get` during init is necessary.
+
+### `--containall` requires `--pwd $PWD` and `-B $PWD`
+
+When users specify `--containall` in `singularity_args`, singularity disables
+auto-binding of `$PWD` and sets the working directory to `$HOME` inside the
+container. This breaks relative paths to inputs/outputs. The `call_fmt` built
+during init always includes `-B $PWD --pwd $PWD` to handle this.
+
+### datalad `{placeholder}` conflicts with shell `${variables}`
+
+`datalad run` interprets `{name}` as a substitution placeholder, which
+conflicts with shell variable expansion like `${subid}`. The POC initially
+tried inlining zip commands in `datalad run` but this caused placeholder
+conflicts. The solution is a separate zip script called by `datalad run`.
+
+In the jinja2 templates, shell variables use `{%raw%}/${subid}{%endraw%}`
+blocks to prevent jinja2 from interpreting them, and datalad sees the literal
+`${subid}` which it passes through to bash.
+
+### `datalad run --explicit` doesn't track deletions
+
+When outputs are deleted inside a `datalad run --explicit` command, datalad
+doesn't record the deletion — only additions/modifications are tracked. This is
+why raw output removal is a separate `git rm` step outside of datalad run.
+
+This was fixed upstream in https://github.com/datalad/datalad/pull/7823 but
+we keep the `git rm` workaround to avoid requiring the latest datalad version.
+
+## Open questions
+
+### Pipeline support
+
+Pipeline currently uses a separate code path (`_bootstrap_pipeline_scripts`)
+that hardcodes container paths and generates a combined script
+(`pipeline_zip.sh`) with direct `singularity run` calls per step.
+
+Questions:
+- Should pipeline be "a pipeline of 1"? i.e., unify single-app and pipeline
+  into one code path where single-app is just a pipeline with one step.
+- If not unified, pipeline needs the same `containers-list` / `containers-add`
+  treatment per container step.
+- Pipeline currently puts all singularity invocations in one script called by
+  one `datalad run`. With `containers-run`, each step would be a separate
+  `datalad containers-run` call — better provenance but different structure.
+
+### Reusing `call_fmt` / `cmdexec` from container datasets
+
+Currently we build `call_fmt` from the user's `singularity_args` config:
+```
+singularity run -B $PWD --pwd $PWD {user_args} {img} {cmd}
+```
+
+Some container datasets (like repronim/containers) already define `cmdexec` in
+their `.datalad/config`. Should we reuse that instead of building our own?
+
+Related: datalad-container's freeze script approach
+(https://github.com/datalad/datalad-container/issues/287) could provide a
+standardized way to handle this.
+
+### Container image fetch during init
+
+`datalad get` of the container image during `babs init` ensures the symlink
+approach works at job time. But this makes init slow if the image isn't already
+local (e.g., pulling a multi-GB .sif from a remote).
+
+Options:
+- Accept the cost during init (current approach)
+- Advise users to `datalad get` the image in their source container dataset
+  before running `babs init`, so the fetch is a fast local copy
+- Add a separate `babs prepare` step for data orchestration that runs after
+  init but before submit
+
+### Container access mechanism
+
+Currently using PROJECT_ROOT symlink (inherited from upstream). This depends on:
+- `PROJECT_ROOT` environment variable propagating through SLURM
+- Shared filesystem visible from compute nodes
+
+An alternative is ephemeral clones (`datalad get -n --reckless ephemeral
+containers`), which removes these dependencies but requires changing the clone
+source from input RIA to the analysis dataset path. Deferred for now.
+
+### Backwards-incompatible: features from `bidsapp_run.sh.jinja2` not yet ported
+
+The old `bidsapp_run.sh.jinja2` template had several BABS-managed features that
+are not yet in the `containers-run` path. These are **backwards-incompatible**
+for users who depend on them and need to be restored or replaced.
+
+- **TemplateFlow bind mount** — BABS read `TEMPLATEFLOW_HOME` from the
+  environment and added `-B path:path_in_container` + `--env` to the singularity
+  command. Could be restored in BABS, or users could handle this via
+  `singularity_args` in their config.
+
+- **FreeSurfer license bind mount** — BABS intercepted `--fs-license-file` from
+  `bids_app_args` and converted it to a `-B` bind mount. Same options: restore
+  in BABS or let users specify via `singularity_args`.
+
+- **BIDS filter file** — dynamically generated per-job for session-level
+  processing, restricting BIDS layout indexing to the current session. This is
+  BIDS-app-specific (fmriprep gets `bold`, qsiprep gets `dwi`, etc.) and can't
+  be handled by user config alone. Could potentially be supported via a hook or
+  user-provided script mechanism (nothing like this exists in BABS today).
+
+- **`${PWD}/` prefix on paths** — the old script passed absolute paths
+  (`${PWD}/inputs/data/BIDS`). The `containers-run` path passes relative paths,
+  which should work because `call_fmt` includes `--pwd $PWD`. Needs verification
+  with BIDS apps that resolve paths differently.
+
+### `--explicit` flag
+
+We use `--explicit` on both `containers-run` and the zip `datalad run`. The
+POC required `--explicit` because the old subject pruning (`rm -rf` of other
+subjects' directories) dirtied the dataset, and datalad refuses to run on a
+dirty dataset without `--explicit`. Upstream's sparse-checkout PR (#337)
+eliminated subject pruning, so the dataset should stay clean. `--explicit` may
+no longer be strictly necessary — kept for safety, could test removing it.

From 802dae996c21e938c4b84c76b04f1def98592c72 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Mon, 16 Mar 2026 19:22:18 -0500
Subject: [PATCH 12/12] fixup: ruff

---
 babs/bootstrap.py | 42 +++++++++++++++++++++++++++++++-----------
 babs/container.py |  3 +--
 2 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 57f2ace6..5d37749e 100644
--- a/babs/bootstrap.py
+++ b/babs/bootstrap.py
@@ -230,13 +230,14 @@ def babs_bootstrap(
         # Discover container image path from the container dataset:
         containers_path = op.join(self.analysis_path, 'containers')
         result = dlapi.containers_list(dataset=containers_path, result_renderer='disabled')
-        container_info = [r for r in result
-                          if r['action'] == 'containers' and r['name'] == container_name]
+        container_info = [
+            r for r in result if r['action'] == 'containers' and r['name'] == container_name
+        ]
         if not container_info:
             available = [r['name'] for r in result if r['action'] == 'containers']
             raise ValueError(
                 f"Container '{container_name}' not found in container dataset. "
-                f"Available: {available}"
+                f'Available: {available}'
             )
         image_path_in_ds = op.relpath(container_info[0]['path'], containers_path)
         container_image_path = op.join('containers', image_path_in_ds)
@@ -265,8 +266,12 @@ def babs_bootstrap(
             path=op.join(self.analysis_path, container_image_path),
         )
 
-        container = Container(container_ds, container_name, container_config,
-                              container_image_path=container_image_path)
+        container = Container(
+            container_ds,
+            container_name,
+            container_config,
+            container_image_path=container_image_path,
+        )
         container.sanity_check(self.analysis_path)
 
         # ==============================================================
@@ -290,11 +295,18 @@ def babs_bootstrap(
             container = containers[0]
         else:
             self._bootstrap_single_app_scripts(
-                container_ds, container_name, container_config, system,
+                container_ds,
+                container_name,
+                container_config,
+                system,
+                container_image_path=container_image_path,
+            )
+            container = Container(
+                container_ds,
+                container_name,
+                container_config,
                 container_image_path=container_image_path,
             )
-            container = Container(container_ds, container_name, container_config,
-                                  container_image_path=container_image_path)
 
         # Copy in any other files needed:
         self._init_import_files(container.config.get('imported_files', []))
@@ -432,12 +444,20 @@ def babs_bootstrap(
         print('`babs init` was successful!')
 
     def _bootstrap_single_app_scripts(
-        self, container_ds, container_name, container_config, system,
+        self,
+        container_ds,
+        container_name,
+        container_config,
+        system,
         container_image_path=None,
     ):
         """Bootstrap scripts for single BIDS app configuration."""
-        container = Container(container_ds, container_name, container_config,
-                              container_image_path=container_image_path)
+        container = Container(
+            container_ds,
+            container_name,
+            container_config,
+            container_image_path=container_image_path,
+        )
 
         # Generate `<containerName>_zip.sh`: ----------------------------------
         # Zip-only script (container execution is now handled by containers-run
diff --git a/babs/container.py b/babs/container.py
index 0c5d6b22..cc12ac72 100644
--- a/babs/container.py
+++ b/babs/container.py
@@ -18,8 +18,7 @@
 class Container:
     """This class is for the BIDS App Container"""
 
-    def __init__(self, container_ds, container_name, config_yaml_file,
-                 container_image_path=None):
+    def __init__(self, container_ds, container_name, config_yaml_file, container_image_path=None):
         """
         This is to initialize Container class.