correction to replication phase cli parsers

Author: raptor419

.gitignore

@@ -5,19 +5,13 @@
 __pycache__
 .pytest_cache
 demo/
-demo_old/
 catboost_info/
-testlogs/
 dask_logs/
 OUTPUT/
-OSA_OUTPUT/
-OSA/
 docs/build/
-job_old.e
 job.o
 job.e
 logs.log
-Scratchpad.ipynb
 UserData/
 UserRepData/
 UserOutput/
@@ -32,3 +26,6 @@ run_configs/cedars_amd.cfg
 data/AMD_Final/*
 data/PLCO/*
 run_configs/cedars_plco.cfg
+run_configs/cedars_gametes.cfg
+exp_configs/
+exp_data/

streamline/utils/parser.py

@@ -1,7 +1,7 @@
 import argparse
 import configparser
 from streamline.utils.parser_helpers import str2bool, save_config, load_config
-from streamline.utils.parser_helpers import parse_general
+from streamline.utils.parser_helpers import parse_general, parse_replicate
 from streamline.utils.parser_helpers import parse_logistic
 from streamline.utils.parser_helpers import parser_function_all
 from streamline.utils.parser_helpers import PARSER_LIST
@@ -88,6 +88,17 @@ def single_parse(mode_params, argv, config_dict=None):
             else:
                 config_dict = load_config(config_dict['output_path'],
                                           config_dict['experiment_name'], config_dict)
+                if i == 9:
+                    config_dict_copy = parse_replicate(argv, config_dict)
+                    if not config_dict_copy['rep_data_path'] == "":
+                        config_dict['rep_data_path'] = config_dict_copy['rep_data_path']
+                    if not config_dict_copy['dataset_for_rep'] == "":
+                        config_dict['dataset_for_rep'] = config_dict_copy['dataset_for_rep']
+                    if not config_dict_copy['rep_export_feature_correlations']:
+                        config_dict['rep_export_feature_correlations'] \
+                            = config_dict_copy['rep_export_feature_correlations']
+                    if not config_dict_copy['exclude_rep_plots'] == 'None':
+                        config_dict['exclude_rep_plots'] = config_dict_copy['exclude_rep_plots']
             config_dict = parse_logistic(argv, config_dict)
     return config_dict
 
@@ -140,17 +151,26 @@ def parser_function(argv):
         config.read(config_file)
         for s in config.sections():
             config_dict.update({k: eval(v) for k, v in config.items(s)})
+        save_config(config_dict['output_path'],
+                    config_dict['experiment_name'],
+                    config_dict)
     elif mode_params['do_till_report']:
         print("Running till Report Generation Stage")
         config = parser_function_all(argv)
         config_dict.update(config)
         config_dict.update(mode_params)
+        save_config(config_dict['output_path'],
+                    config_dict['experiment_name'],
+                    config_dict)       
 
     for key in mode_params:
         if mode_params[key] and key not in ['config', 'do_till_report']:
             config = single_parse(mode_params, argv, config_dict)
             config_dict.update(config)
             config_dict.update(mode_params)
+            save_config(config_dict['output_path'],
+                        config_dict['experiment_name'],
+                        config_dict)  
 
     config_dict = process_params(config_dict)