Fixed merge script.

- first tool in confi is already used, so removed the warning entry
- fixed bug that merged-repair-directory was not cleaned
- changed output to not report every skipped file due to not matching the pattern
- changed default log level back to info
- removed --create-run-dirs as it was not used, and not feasible to implement

trainbenchmark/trainbenchmark-reporting/do-merge.sh

-python merge_results.py --result-dir ../results/ --create-run-dirs --create-toolwise-dirs $@
+python merge_results.py --result-dir ../results/ --create-toolwise-dirs $@

trainbenchmark/trainbenchmark-reporting/merge_results.json

 {
   "tools": [
-    "WHY IS THE FIRST ONE IGNORED, RENE?",
     "tinkergraph",
     "jastadd-intrinsic",
     "jastadd-intrinsic-incremental",

trainbenchmark/trainbenchmark-reporting/merge_results.py

@@ -43,7 +43,6 @@ def include_file_config(args):
     override_if_defined('max-size', int)
     override_if_defined('dry-run', bool)
     override_if_defined('result-dir')
-    override_if_defined('create-run-dirs', bool)
     override_if_defined('create-toolwise-dirs', bool)
     override_if_defined('no-clean', bool)
     override_if_defined('verbose', bool)
@@ -127,6 +126,7 @@ def main(args):
                 times.csv@          - (only newest measurements of benchmark)
     """
     log_action = logger.info if args.dry_run else logger.debug
+    unmatched_files = []
 
     # Gathering paths, creating top-level directories
     result_dir = os.path.abspath(args.result_dir)
@@ -145,7 +145,7 @@ def main(args):
     # Clean symlinks if requested or max_size is set
     if (args.clean or args.max_size) and not args.dry_run:
         for dir_to_clean in [merged_dir, merged_dir_benchmark, merged_dir_individual,
-                             merged_dir_individual_inject, merged_dir_individual_inject]:
+                             merged_dir_individual_inject, merged_dir_individual_repair]:
             for link in os.listdir(dir_to_clean):
                 linkName = os.path.join(dir_to_clean, link)
                 if os.path.islink(linkName):
@@ -199,7 +199,7 @@ def main(args):
                             tool_name = match.group(2)
                             copy_replace(fileToLink, all_runs_dir, tool_name, run, args.dry_run)
                     else:
-                        logging.warn('file did not match pattern: %s', csvFile)
+                        unmatched_files.append(csvFile)
                 # link file in merged directory
                 if csvFile not in already_merged:
                     if BENCHMARK_PATTERN.match(csvFile):
@@ -216,6 +216,8 @@ def main(args):
                     already_merged.append(csvFile)
                 else:
                     log_action('Skipping %s', csvFile)
+    logging.info('%d files not matching pattern', len(unmatched_files))
+    logging.debug('Files not matching pattern: %s', unmatched_files)
 
 
 if __name__ == '__main__':
@@ -228,9 +230,6 @@ if __name__ == '__main__':
         Its filename is "local-" prepended to the name of the config file.""")
     parser.add_argument(
         "-r", "--result-dir", help="Path to result directory to search in.", type=str)
-    parser.add_argument(
-        "-c", "--create-run-dirs", help="Whether to recreate runs directories.",
-        action="store_true")
     parser.add_argument(
         "-t", "--create-toolwise-dirs", help="Whether to recreate toolwise regression directories.",
         action="store_true")
@@ -239,7 +238,7 @@ if __name__ == '__main__':
         action="store_true")
     parser.add_argument(
         "-n", "--no-clean", help="Don't remove previously existing symlinks in merged dir.",
-        dest='clean', action="store_false")
+        dest='clean', action="store_false", default=True)
     parser.add_argument(
         "-v", "--verbose", help="Print debug messages.", action="store_true")
     parser.add_argument(
@@ -249,5 +248,5 @@ if __name__ == '__main__':
         "-f", "--file-config", default='merge_results.json', help="Config file to use.")
     args = parser.parse_args()
     include_file_config(args)
-    logging.basicConfig(format=FORMAT, level=logging.DEBUG if args.verbose else logging.DEBUG)
+    logging.basicConfig(format=FORMAT, level=logging.DEBUG if args.verbose else logging.INFO)
     main(args)