Merge pull request #74 from 3dem/pipeline-control

Pipeline control

model_angelo/__init__.py

@@ -5,4 +5,4 @@
 """
 
 
-__version__ = "1.0.3"
+__version__ = "1.0.4"

model_angelo/apps/build.py

@@ -129,7 +129,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 

model_angelo/apps/build_no_seq.py

@@ -105,7 +105,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 

model_angelo/apps/hmm_search.py

@@ -106,7 +106,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 

model_angelo/apps/refine.py

@@ -99,7 +99,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 

model_angelo/utils/misc_utils.py

@@ -71,6 +71,14 @@ def setup_logger(log_path: str):
         enqueue=True,
         diagnose=True,
     )
+    logger.add(
+        sys.stderr,
+        format="{time:YYYY-MM-DD at HH:mm:ss} | {level} | {message}",
+        enqueue=True,
+        level="ERROR",
+        backtrace=False,
+        diagnose=False,
+    )
     return logger
 
 
@@ -129,9 +137,9 @@ def is_relion_abort(directory: str) -> bool:
 
 
 def write_relion_job_exit_status(
-    directory: str, status: str, pipeline_control: bool = False,
+    directory: str, status: str, pipeline_control: str = "",
 ):
-    if pipeline_control:
+    if pipeline_control != "":
         open(os.path.join(directory, f"RELION_JOB_EXIT_{status}"), "a").close()
     elif status == "FAILURE":
         sys.exit(1)