Update write_pipestat_config doc strings and out put message #459

looper/conductor.py

@@ -85,11 +85,14 @@ def _get_yaml_path(namespaces, template_key, default_name_appendix="", filename=
 
 def write_pipestat_config(looper_pipestat_config_path, pipestat_config_dict):
     """
-    This is run at the project level, not at the sample level.
+    This writes a combined configuration file to be passed to a PipestatManager.
+    :param str looper_pipestat_config_path: path to the created pipestat configuration file
+    :param dict pipestat_config_dict: the dict containing key value pairs to be written to the pipestat configutation
+    return bool
     """
     with open(looper_pipestat_config_path, "w") as f:
         yaml.dump(pipestat_config_dict, f)
-    print(f"Initialized looper config file: {looper_pipestat_config_path}")
+    print(f"Initialized pipestat config file: {looper_pipestat_config_path}")
 
     return True
 

looper_init.py

@@ -2,6 +2,7 @@
 # configuring a .looper.yaml file for a new project. To be used as `looper init`.
 
 import os
+
 cfg = {}
 
 print("This utility will walk you through creating a .looper.yaml file.")
@@ -19,7 +20,7 @@
     "pep_config": "databio/example",
     "output_dir": "results",
     "piface_path": "pipeline_interface.yaml",
-    "project_name": os.path.basename(os.getcwd())
+    "project_name": os.path.basename(os.getcwd()),
 }
 
 
@@ -36,7 +37,8 @@
     print(f"Warning: PEP file does not exist at '{cfg['pep_config']}'")
 
 cfg["output_dir"] = (
-    input(f"Path to output directory: ({DEFAULTS['output_dir']}) ") or DEFAULTS["output_dir"]
+    input(f"Path to output directory: ({DEFAULTS['output_dir']}) ")
+    or DEFAULTS["output_dir"]
 )
 
 # TODO: Right now this assumes you will have one pipeline interface, and a sample pipeline