printing after the pipeline is initialized, so we have arguments in the log file!

pipelines/cc_mini.py

@@ -50,14 +50,14 @@ def pipeline_parser():
 
 @logged(logging.getLogger("[ PIPELINE %s ]" % os.path.basename(__file__)))
 def main(args):
-    # print arguments
-    for arg in vars(args):
-        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
-
     # initialize Pipeline
     pp = Pipeline(pipeline_path=args.pipeline_dir, keep_jobs=True,
                   config=Config(args.config))
 
+    # print arguments
+    for arg in vars(args):
+        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
+
     fit_order = ['sign0', 'sign1', 'neig1', 'proj1', 'clus1',
                  'sign2', 'neig2', 'proj2', 'clus2',
                  'sign3', 'neig3', 'proj3', 'clus3']

pipelines/cc_update.py

@@ -64,14 +64,14 @@ def pipeline_parser():
 
 @logged(logging.getLogger("[ PIPELINE %s ]" % os.path.basename(__file__)))
 def main(args):
-    # print arguments
-    for arg in vars(args):
-        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
-
     # initialize Pipeline
     pp = Pipeline(pipeline_path=args.pipeline_dir, keep_jobs=True,
                   config=Config(args.config))
 
+    # print arguments
+    for arg in vars(args):
+        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
+
     fit_order = ['sign0', 'sign1', 'clus1', 'proj1', 'neig1',
                  'sign2', 'clus2', 'proj2', 'neig2', 'sign3']
 

pipelines/cc_web.py

@@ -37,7 +37,7 @@ def pipeline_parser():
     parser.add_argument(
         'cc_root', type=str,
         help='Directory of the CC instance the web will refere to '
-        '(e.g. `/aloy/web_checker/package_cc/2020_01`)')
+        '(e.g. `/aloy/web_checker/package_cc/miniCC`)')
     parser.add_argument(
         'pipeline_dir', type=str,
         help='Directory where the pipeline will run '
@@ -71,14 +71,14 @@ def pipeline_parser():
 
 @logged(logging.getLogger("[ PIPELINE %s ]" % os.path.basename(__file__)))
 def main(args):
-    # print arguments
-    for arg in vars(args):
-        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
-
     # initialize Pipeline
     pp = Pipeline(pipeline_path=args.pipeline_dir, keep_jobs=True,
                   config=Config(args.config))
 
+    # print arguments
+    for arg in vars(args):
+        main._log.info('[ ARGS ] {:<25s}: {}'.format(arg, getattr(args, arg)))
+
     libraries = {
         "apd": [
             'Approved drugs',