add looper init idea. See #466

looper_init.py

@@ -0,0 +1,66 @@
+# A simple utility, to be run in the root of a project, to prompt a user through
+# 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.")
+print("See `looper init --help` for details.")
+print("Use `looper run` afterwards to run the pipeline.")
+print("Press ^C at any time to quit.\n")
+
+looper_cfg_path = ".looper.yaml"  # not changeable
+
+if os.path.exists(looper_cfg_path):
+    print(f"File exists at '{looper_cfg_path}'. Delete it to re-initialize.")
+    raise SystemExit
+
+DEFAULTS = {  # What you get if you just press enter
+    "pep_config": "databio/example",
+    "output_dir": "results",
+    "piface_path": "pipeline_interface.yaml",
+    "project_name": os.path.basename(os.getcwd())
+}
+
+
+cfg["project_name"] = (
+    input(f"Project name: ({DEFAULTS['project_name']}) ") or DEFAULTS["project_name"]
+)
+
+cfg["pep_config"] = (
+    input(f"Registry path or file path to PEP: ({DEFAULTS['pep_config']}) ")
+    or DEFAULTS["pep_config"]
+)
+
+if not os.path.exists(cfg["pep_config"]):
+    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"]
+)
+
+# TODO: Right now this assumes you will have one pipeline interface, and a sample pipeline
+# but this is not the only way you could configure things.
+
+piface_path = (
+    input("Path to sample pipeline interface: (pipeline_interface.yaml) ")
+    or DEFAULTS["piface_path"]
+)
+
+if not os.path.exists(piface_path):
+    print(f"Warning: file does not exist at {piface_path}")
+
+print(f"Writing config file to {looper_cfg_path}")
+print(f"PEP path: {cfg['pep_config']}")
+print(f"Pipeline interface path: {piface_path}")
+
+
+with open(looper_cfg_path, "w") as fp:
+    fp.write(
+        f"""\
+pep_config: {cfg['pep_config']}
+output_dir: {cfg['output_dir']}
+pipeline_interfaces:
+  sample: {piface_path}
+"""
+    )