[ENH] implement babs-update-setup

babs/babs.py

@@ -991,6 +991,39 @@ def babs_check_setup(self, input_ds, flag_job_test):
         if flag_warning_output_ria:
             print("\nPlease check out the warning for output RIA!")
 
+    def babs_update_setup(self, input_ds, container_config_yaml_file):
+        """
+        This is to update setup of jobs run in a BABS project.
+
+        Parameters:
+        --------------
+        input_ds: class `Input_ds`
+            information of input dataset(s)
+        container_config_yaml_file: str
+            Path to an updated container's configuration YAML file.
+        """
+
+        babs_proj_config = read_yaml(self.config_path, if_filelock=True)
+
+        # Sanity check: if the user has changed `required_files` section in YAML file:
+        #   if changed, throw out a warning.
+        # TODO^^
+
+        # ==============================================================
+        # Redo: Bootstrap scripts:
+        # ==============================================================
+
+        # Re-generate `<containerName>_zip.sh`: ----------------------------------
+        #   which is a bash script of singularity run + zip
+        #   in folder: `analysis/code`
+        print("\nRe-generating a bash script for running container and zipping the outputs...")
+        print("This bash script will be named as `" + container_name + "_zip.sh`")
+        bash_path = op.join(self.analysis_path, "code", container_name + "_zip.sh")
+        container.generate_bash_run_bidsapp(bash_path, input_ds, self.type_session)
+        self.datalad_save(path="code/" + container_name + "_zip.sh",
+                          message="Generate script of running container")
+
+
     def babs_submit(self, count=1, df_job_specified=None):
         """
         This function submits jobs and prints out job status.

babs/cli.py

@@ -79,7 +79,8 @@ def babs_init_cli():
     parser.add_argument(
         '--container_config_yaml_file', '--container-config-yaml-file',
         help="Path to a YAML file that contains the configurations"
-        " of how to run the BIDS App container")
+        " of how to run the BIDS App container",
+        required=True)
     parser.add_argument(
         "--type_session", "--type-session",
         choices=['single-ses', 'single_ses', 'single-session', 'single_session',
@@ -295,6 +296,51 @@ def babs_check_setup_main():
     # Call method `babs_check_setup()`:
     babs_proj.babs_check_setup(input_ds, args.job_test)
 
+def babs_update_setup_cli():
+    """
+    CLI for: Update setups for job running in a BABS project,
+    e.g., cluster resources request, script preamble.
+    """
+
+    parser = argparse.ArgumentParser(
+        description="Update setups for running jobs.")
+    parser.add_argument(
+        "--project_root", "--project-root",
+        help="Absolute path to the root of BABS project."
+        " For example, '/path/to/my_BABS_project/'.",
+        required=True)
+    parser.add_argument(
+        '--container_config_yaml_file', '--container-config-yaml-file',
+        help="Path to an updated YAML file that contains the configurations"
+        " of how to run the BIDS App container",
+        required=True)
+
+    return parser
+
+def babs_update_setup_main():
+    """
+    Update setups for job running in a BABS project,
+    e.g., cluster resources request, script preamble.
+
+    Parameters:
+    --------------
+    project_root: str
+        Absolute path to the root of BABS project.
+    container_config_yaml_file: str
+        Path to an updated container's configuration YAML file.
+    """
+
+    # Get arguments:
+    args = babs_check_setup_cli().parse_args()
+    project_root = args.project_root
+
+    # Get class `BABS` based on saved `analysis/code/babs_proj_config.yaml`:
+    babs_proj, input_ds = get_existing_babs_proj(project_root)
+
+    # Call `babs_update_setup()`:
+    babs_proj.babs_update_setup(input_ds, args.container_config_yaml_file)
+
+
 def babs_submit_cli():
     """
     Submit jobs.