Merge pull request #451 from dssg/cli-setupfile

Added an argument for a pythonic entrypoint for setting an arbitrary initial configuration

src/triage/cli.py

@@ -19,6 +19,8 @@
 
 logging.basicConfig(level=logging.INFO)
 
+import importlib.util
+
 
 def natural_number(value):
     natural = int(value)
@@ -44,6 +46,20 @@ def __init__(self, parser):
             type=argparse.FileType('r'),
             help="database connection file",
         )
+        parser.add_argument(
+            '-s', '--setup',
+            help="file path to Python module to import before running the Experiment",
+        )
+
+    def setup(self):
+        setup_path = self.args.setup or os.path.abspath('experiment.py')
+        if setup_path is not None:
+            logging.info(f"Loading configurations from {setup_path}")
+            spec = importlib.util.spec_from_file_location("triage_config", setup_path)
+            triage_config = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(triage_config)
+            logging.info(f"Configuration loaded")
+        return None
 
     @cachedproperty
     def db_url(self):
@@ -100,6 +116,7 @@ def __init__(self, parser):
         )
 
     def __call__(self, args):
+        self.root.setup  # Loading configuration (if exists)
         db_engine = create_engine(self.root.db_url)
         feature_config = yaml.load(args.feature_config_file)
 
@@ -166,6 +183,7 @@ def __init__(self, parser):
 
     @cachedproperty
     def experiment(self):
+        self.root.setup  # Loading configuration (if exists)
         db_url = self.root.db_url
         config = yaml.load(self.args.config)
         db_engine = create_engine(db_url)
@@ -213,6 +231,7 @@ def __init__(self, parser):
 
     @cachedproperty
     def runner(self):
+        self.root.setup # Loading configuration (if exists)
         db_url = self.root.db_url
         dir_plot = self.args.directory
         config = yaml.load(self.args.config)
@@ -254,7 +273,7 @@ def upgrade(self, args):
     @cmdmethod('configversion', choices=REVISION_MAPPING.keys(), help='config version of last experiment you ran')
     def stamp(self, args):
         """Instruct the triage results database to mark itself as updated to a known version without doing any upgrading.
-        
+
         Use this if the database was created without an 'alembic_version' table. Uses the config version of your experiment to infer what database version is suitable.
         """
         revision = REVISION_MAPPING[args.configversion]

src/triage/util/db.py

@@ -1,3 +1,5 @@
+# coding: utf-8
+
 import sqlalchemy
 import wrapt